Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Synteny: The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Genetic Variation: Genotypic differences observed among individuals in a population.Directed Molecular Evolution: The techniques used to produce molecules exhibiting properties that conform to the demands of the experimenter. These techniques combine methods of generating structural changes with methods of selection. They are also used to examine proposed mechanisms of evolution under in vitro selection conditions.Gene Transfer, Horizontal: The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Genome Size: The amount of DNA (or RNA) in one copy of a genome.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Retroelements: Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.Genome, Insect: The genetic complement of an insect (INSECTS) as represented in its DNA.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Gene Order: The sequential location of genes on a chromosome.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Genome, Protozoan: The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Polyploidy: The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Genome, Plastid: The genetic complement of PLASTIDS as represented in their DNA.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.Pseudogenes: Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.PrimatesSymbiosis: The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.Adaptation, Biological: Changes in biological features that help an organism cope with its ENVIRONMENT. These changes include physiological (ADAPTATION, PHYSIOLOGICAL), phenotypic and genetic changes.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Genome, Helminth: The genetic complement of a helminth (HELMINTHS) as represented in its DNA.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Mutation Rate: The number of mutations that occur in a specific sequence, GENE, or GENOME over a specified period of time such as years, CELL DIVISIONS, or generations.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Pan troglodytes: The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.Genes, Plant: The functional hereditary units of PLANTS.Sorghum: A plant genus of the family POACEAE. The grain is used for FOOD and for ANIMAL FEED. This should not be confused with KAFFIR LIME or with KEFIR milk product.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Cultural Evolution: The continuous developmental process of a culture from simple to complex forms and from homogeneous to heterogeneous qualities.Buchnera: A genus of gram-negative bacteria which are obligately intracellular endosymbionts of APHIDS. The bacteria are found within specialized cells in the aphid body cavity.Genetic Speciation: The splitting of an ancestral species into daughter species that coexist in time (King, Dictionary of Genetics, 6th ed). Causal factors may include geographic isolation, HABITAT geometry, migration, REPRODUCTIVE ISOLATION, random GENETIC DRIFT and MUTATION.Angiosperms: Members of the group of vascular plants which bear flowers. They are differentiated from GYMNOSPERMS by their production of seeds within a closed chamber (OVARY, PLANT). The Angiosperms division is composed of two classes, the monocotyledons (Liliopsida) and dicotyledons (Magnoliopsida). Angiosperms represent approximately 80% of all known living plants.Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Mammals: Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Tetraodontiformes: A small order of primarily marine fish containing 340 species. Most have a rotund or box-like shape. TETRODOTOXIN is found in their liver and ovaries.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Oryza sativa: Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.Genes, Duplicate: Two identical genes showing the same phenotypic action but localized in different regions of a chromosome or on different chromosomes. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Terminal Repeat Sequences: Nucleotide sequences repeated on both the 5' and 3' ends of a sequence under consideration. For example, the hallmarks of a transposon are that it is flanked by inverted repeats on each end and the inverted repeats are flanked by direct repeats. The Delta element of Ty retrotransposons and LTRs (long terminal repeats) are examples of this concept.Plastids: Self-replicating cytoplasmic organelles of plant and algal cells that contain pigments and may synthesize and accumulate various substances. PLASTID GENOMES are used in phylogenetic studies.Likelihood Functions: Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.Eukaryota: One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.Eukaryotic Cells: Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Clonal Evolution: The process of accumulation of genetic and epigenetic changes over time in individual cells and the effect of the changes on CELL PROLIFERATION.Brassica rapa: A plant species cultivated for the seed used as animal feed and as a source of canola cooking oil.Cuscuta: A plant genus of the family Cuscutaceae. It is a threadlike climbing parasitic plant that is used in DRUGS, CHINESE HERBAL.Microsporidia: A phylum of fungi comprising minute intracellular PARASITES with FUNGAL SPORES of unicellular origin. It has two classes: Rudimicrosporea and MICROSPOREA.Isochores: Large regions of the GENOME that contain local similarities in BASE COMPOSITION.Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.INDEL Mutation: A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.Diplomonadida: A group of flagellated, mostly symbiotic EUKARYOTES characterized by twofold symmetry associated with the presence of a pair of karyomastigont organellar systems. Two nuclei are attached by fibers to the flagella and there are no MITOCHONDRIA. Diplomonadida were formerly members of the class Zoomastigophora in the old five kingdom paradigm.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.Adaptation, Physiological: The non-genetic biological changes of an organism in response to challenges in its ENVIRONMENT.Convolvulaceae: The morning glory family of flowering plants, of the order Solanales, which includes about 50 genera and at least 1,400 species. Leaves are alternate and flowers are funnel-shaped. Most are twining and erect herbs, with a few woody vines, trees, and shrubs.Interspersed Repetitive Sequences: Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.Chromosome Inversion: An aberration in which a chromosomal segment is deleted and reinserted in the same place but turned 180 degrees from its original orientation, so that the gene sequence for the segment is reversed with respect to that of the rest of the chromosome.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Physical Chromosome Mapping: Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Chromosomes: In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Chromosomes, Insect: Structures within the CELL NUCLEUS of insect cells containing DNA.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Genes, Mitochondrial: Genes that are located on the MITOCHONDRIAL DNA. Mitochondrial inheritance is often referred to as maternal inheritance but should be differentiated from maternal inheritance that is transmitted chromosomally.Genes, Bacterial: The functional hereditary units of BACTERIA.Fossils: Remains, impressions, or traces of animals or plants of past geological times which have been preserved in the earth's crust.Fishes: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Gene Dosage: The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.Solanaceae: A plant family of the order Solanales, subclass Asteridae. Among the most important are POTATOES; TOMATOES; CAPSICUM (green and red peppers); TOBACCO; and BELLADONNA.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.Drosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.DNA, Algal: Deoxyribonucleic acid that makes up the genetic material of algae.Genetics, Population: The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Ferns: Seedless nonflowering plants of the class Filicinae. They reproduce by spores that appear as dots on the underside of feathery fronds. In earlier classifications the Pteridophyta included the club mosses, horsetails, ferns, and various fossil groups. In more recent classifications, pteridophytes and spermatophytes (seed-bearing plants) are classified in the Subkingdom Tracheobionta (also known as Tracheophyta).Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Genomic Instability: An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.Long Interspersed Nucleotide Elements: Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.Bacterial Proteins: Proteins found in any species of bacterium.Chlorophyta: A phylum of photosynthetic EUKARYOTA bearing double membrane-bound plastids containing chlorophyll a and b. They comprise the classical green algae, and represent over 7000 species that live in a variety of primarily aquatic habitats. Only about ten percent are marine species, most live in freshwater.Comparative Genomic Hybridization: A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Tragopogon: A plant genus of the family ASTERACEAE. The root and shoots have been used for food.Nematoda: A class of unsegmented helminths with fundamental bilateral symmetry and secondary triradiate symmetry of the oral and esophageal structures. Many species are parasites.Bayes Theorem: A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.Archaea: One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).Inverted Repeat Sequences: Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.Hominidae: Family of the suborder HAPLORHINI (Anthropoidea) comprising bipedal primate MAMMALS. It includes modern man (HOMO SAPIENS) and the great apes: gorillas (GORILLA GORILLA), chimpanzees (PAN PANISCUS and PAN TROGLODYTES), and orangutans (PONGO PYGMAEUS).Nested Genes: Genes whose entire sequences are contained within other genes.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Vertebrates: Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.Poaceae: A large family of narrow-leaved herbaceous grasses of the order Cyperales, subclass Commelinidae, class Liliopsida (monocotyledons). Food grains (EDIBLE GRAIN) come from members of this family. RHINITIS, ALLERGIC, SEASONAL can be induced by POLLEN of many of the grasses.Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.Gene Conversion: The asymmetrical segregation of genes during replication which leads to the production of non-reciprocal recombinant strands and the apparent conversion of one allele into another. Thus, e.g., the meiotic products of an Aa individual may be AAAa or aaaA instead of AAaa, i.e., the A allele has been converted into the a allele or vice versa.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Typhaceae: A plant family of the order Typhales, subclass Commelinidae, class Liliopsida (monocotyledons) that contains a single genus, Typha, that grows worldwide.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Evolution, Chemical: Chemical and physical transformation of the biogenic elements from their nucleosynthesis in stars to their incorporation and subsequent modification in planetary bodies and terrestrial biochemistry. It includes the mechanism of incorporation of biogenic elements into complex molecules and molecular systems, leading up to the origin of life.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Caenorhabditis: A genus of small free-living nematodes. Two species, CAENORHABDITIS ELEGANS and C. briggsae are much used in studies of genetics, development, aging, muscle chemistry, and neuroanatomy.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Karyotype: The full set of CHROMOSOMES presented as a systematized array of METAPHASE chromosomes from a photomicrograph of a single CELL NUCLEUS arranged in pairs in descending order of size and according to the position of the CENTROMERE. (From Stedman, 25th ed)Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Brachypodium: A plant genus in the family POACEAE. Brachypodium distachyon is a model species for functional genomics studies.Classification: The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.Zea mays: A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.Sex Chromosomes: The homologous chromosomes that are dissimilar in the heterogametic sex. There are the X CHROMOSOME, the Y CHROMOSOME, and the W, Z chromosomes (in animals in which the female is the heterogametic sex (the silkworm moth Bombyx mori, for example)). In such cases the W chromosome is the female-determining and the male is ZZ. (From King & Stansfield, A Dictionary of Genetics, 4th ed)Invertebrates: Animals that have no spinal column.Aphids: A family (Aphididae) of small insects, in the suborder Sternorrhyncha, that suck the juices of plants. Important genera include Schizaphis and Myzus. The latter is known to carry more than 100 virus diseases between plants.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.Triticum: A plant genus of the family POACEAE that is the source of EDIBLE GRAIN. A hybrid with rye (SECALE CEREALE) is called TRITICALE. The seed is ground into FLOUR and used to make BREAD, and is the source of WHEAT GERM AGGLUTININS.Virulence: The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.Human Genome Project: A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.DNA Copy Number Variations: Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Centromere: The clear constricted portion of the chromosome at which the chromatids are joined and by which the chromosome is attached to the spindle during cell division.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.Genetic Drift: The fluctuation of the ALLELE FREQUENCY from one generation to the next.Reproduction: The total process by which organisms produce offspring. (Stedman, 25th ed)Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Chordata, Nonvertebrate: A portion of the animal phylum Chordata comprised of the subphyla CEPHALOCHORDATA; UROCHORDATA, and HYPEROTRETI, but not including the Vertebrata (VERTEBRATES). It includes nonvertebrate animals having a NOTOCHORD during some developmental stage.Genes, Viral: The functional hereditary units of VIRUSES.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.X Chromosome: The female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in human and other male-heterogametic species.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Genes, Insect: The functional hereditary units of INSECTS.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Genetic Fitness: The capability of an organism to survive and reproduce. The phenotypic expression of the genotype in a particular environment determines how genetically fit an organism will be.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Proteome: The protein complement of an organism coded for by its genome.Xanthomonadaceae: A family of gram-negative bacteria, in the order Xanthomonadales, pathogenic to plants.Hybridization, Genetic: The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Viral Proteins: Proteins found in any species of virus.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Karyotyping: Mapping of the KARYOTYPE of a cell.Arthropods: Members of the phylum Arthropoda, composed of organisms having a hard, jointed exoskeleton and paired jointed legs. It includes the class INSECTS and the subclass ARACHNIDA, many species of which are important medically as parasites or as vectors of organisms capable of causing disease in man.Evolution, Planetary: Creation and development of bodies within solar systems, includes study of early planetary geology.
He is coauthor along with Wen-Hsiung Li of Fundamentals of Molecular Evolution. His Molecular and Genome Evolution was ... in the Human Genome According to the Evolution-Free Gospel of ENCODE". Genome Biology and Evolution. 5 (3): 578-590. doi: ... Dan Graur (2016). Molecular and Genome Evolution. Sinauer Associates, Inc. ISBN 0878932666. Graur, D.; Zheng, Y.; Price, N.; ... Dan Graur \ˈɡra.ur\ is an American scientist working in the field of molecular evolution. He is the John and Rebecca Moores ...
Helitrons seem to have a major role in the evolution of host genomes. They frequently capture diverse host genes, some of which ... Journal of Molecular Evolution. 48 (6): 684-691. doi:10.1007/pl00006512. Kapitonov, Vladimir; Jurka, Jerzy (2001). "Rolling- ... 2014). "Rolling-Circle Transposons Catalyze Genomic Innovation in a Mammalian Lineage". Genome Biology and Evolution. 6 (10): ... Helitrons, as most of other mobile elements in the A. thaliana and C. elegans genomes are present in the genomes in multiple ...
Plains viscacha rat
Genome Biology and Evolution. doi:10.1093/gbe/evx113. Svartman, Marta; Stone, Gary; Stanyon, Roscoe (2005). "Molecular ... Evans, Ben J.; Upham, Nathan S.; Golding, Brian G.; Ojeda, Ricardo A.; Ojeda, Agustina A. "Evolution of the largest mammalian ... Gallardo, M.H.; González, CA; Cebrián, I (2006), "Molecular cytogenetics and allotetraploidy in the red vizcacha rat, ... "New analysis of rare Argentinian rat unlocks origin of the largest mammalian genome". PhysOrg. 2017-07-12. Retrieved 2017-07-17 ...
Amino acid replacement
Graur, Dan (2015-01-01). Molecular and Genome Evolution. Sinauer. ISBN 9781605354699. Sneath, P. H. (1966-11-01). "Relations ... Xia, Xuhua (2000-03-31). Data Analysis in Molecular Biology and Evolution. Springer Science & Business Media. ISBN ... Journal of Molecular Evolution. 12 (3): 219-236. Bibcode:1979JMolE..12..219M. doi:10.1007/BF01732340. ISSN 0022-2844. PMID ... Journal of Molecular Evolution. 22 (1): 53-62. Bibcode:1985JMolE..22...53G. doi:10.1007/BF02105805. ISSN 0022-2844. PMID ...
Wendel, Jonathan F. (January 2000). "Genome evolution in polyploids". Plant Molecular Biology. Kluwer Academic Publishers. 42 ( ... Evolution. Hoboken, NJ: John Wiley & Sons for the Society for the Study of Evolution. 60 (1): 87-96. doi:10.1554/05-374.1. ISSN ... Evolution. Hoboken, NJ: John Wiley & Sons for the Society for the Study of Evolution. 47 (6): 1637-1653. doi:10.2307/2410209. ... Evolution. Hoboken, NJ: John Wiley & Sons for the Society for the Study of Evolution. 43 (6): 1308-1311. doi:10.2307/2409365. ...
Polyploidy and genome evolution. Berlin, Heidelberg: Springer. pp. 147-180. doi:10.1007/978-3-642-31442-1_9. ISBN 978-3-642- ... Molecular Phylogenetics and Evolution. 65 (1): 149-162. doi:10.1016/j.ympev.2012.05.035. Cardoso D, Pennington RT, de Queiroz ... Several molecular phylogenies in the early 2000s showed that the other two subfamilies of Fabaceae (Faboideae and Mimosoideae) ... doi:10.1111/j.1558-5646.2012.01720.x. Doyle JJ (2011). "Phylogenetic perspectives on the origins of nodulation". Molecular ...
"Genetic aspects of mitochondrial genome evolution". Molecular Phylogenetics and Evolution. 69 (2): 328-338. doi:10.1016/j.ympev ... Understanding viral genomes is very important for understanding the evolution and mutation of the virus. Some viruses, such as ... Viral genomes can be made up of single stranded DNA (ssDNA), double stranded DNA (dsDNA) and can be found in both linear and ... Lodish, Harvey (2013). Molecular Cell Biology, 7th edition. New York: W.H. Freeman and Company. pp. 245-251. ISBN 978-1-4641- ...
Molecular Biology and Evolution 23: 1741-1750. Asher D. Cutter, Scott E. Baird and Deborah Charlesworth. 2006 Patterns of ... 2001) Breeding systems and genome evolution. Current Opinion in Genetics & Development 11, 685-690. Jesper S. Bechsgaard, ... She is best known for her work on the evolution of genetic self-incompatibility in plants and is recognised as a leader in that ... Evolution 66: 505-516. DOI: 10.1111/j.1558-5646.2011.01448.x Mable, Barbara; Hill Bill (February 2008). "Deborah Charlesworth ...
"Plastid genome evolution in mycoheterotrophic Ericaceae" (PDF). Plant Molecular Biology. 79 (1-2): 5-20. doi:10.1007/s11103-012 ... 1994). "Molecular phylogeny of the Monotropoideae (Ericaceae) with a note on the placement of the Pyroloideae". Journal of ... Contemporary molecular phylogenetics has clearly established the Monotropoideae as a group within the larger Ericaceae, though ... Molecular Ecology. 10 (9): 2285-2295. doi:10.1046/j.1365-294X.2001.01358.x. Bidartondo MI. (2005). "The evolutionary ecology of ...
Beatty, volume editor, J. Thomas (2013). Genome Evolution of Photosynthetic Bacteria (1st ed.). San Diego: Elsevier Science. ... ISBN 0-12-398479-3. editors, Larry L. Barton, Martin Mandl, Alexander Loy, (2010). Geomicrobiology molecular and environmental ... Koblízek, M; Janouskovec, J; Oborník, M; Johnson, JH; Ferriera, S; Falkowski, PG (October 2011). "Genome sequence of the marine ...
Horizontal gene transfer
Gogarten, J. P.; Townsend, J. P. (2005). "Horizontal gene transfer, genome innovation and evolution". Nature Reviews ... Molecular Biology and Evolution. 30 (8): 1843-1852. doi:10.1093/molbev/mst084. PMID 23645554. Ivics Z.; Hackett P.B.; Plasterk ... Genome Biology and Evolution. 4 (8): 801-811. doi:10.1093/gbe/evs055. La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, ... to mitochondrial genome of Phaseolus". Plant Molecular Biology. 56 (5): 811-20. doi:10.1007/s11103-004-5183-y. PMID 15803417. ...
Natural genetic engineering
Wilkins, Adam S. (January 2012). "(Review) Evolution: A View from the 21st Century". Genome Biology and Evolution. 4: 423-426. ... Buratti, Emanuele (2012). "Evolutionary Lessons for 21st Century Molecular Biotechnologists". Molecular Biotechnology. 52 (1): ... From these, Shapiro concludes: [I]t can be argued that much of genome change in evolution results from a genetic engineering ... Shapiro, James A. (2002). "Genome Organization and Reorganization in Evolution: Formatting for Computation and Function" (PDF ...
American Genetic Association
Lynda Delph 2015: Chromosome evolution: molecular mechanisms & evolutionary consequences. Catherine Peichel 2014: Evolution and ... Trudy Mackay 2007: Mechanisms of Genome Evolution. Michael Lynch The keynote speaker at the annual symposium gives the Key ... Proposals addressing genome-scale questions, or ecological, evolutionary and conservation genetics questions best addressed ... Kerry Shaw 2012: Recombination: Molecular Mechanisms & Evolutionary Consequences. Mohamed Noor 2011: 2011: Genomics and ...
March 2015). "Building the avian tree of life using a large-scale, sparse supermatrix". Molecular Phylogenetics and Evolution. ... Genome Biology and Evolution, 7 (12):3180-3189. doi:10.1093/gbe/evv213 PDF fulltext. Burleigh, J.G.; et al. ( ... Based on a whole-genome analysis of the bird orders, the kagu and sunbittern (Eurypygiformes) and the three species of ... 12 December 2014). "Whole-genome analyses resolve early branches in the tree of life of modern birds". Science. 346 (6215): ...
Genome Biology And Evolution 17(2004)985-993. doi: 10.1111/j.1420-9101.2004.00748.x Pilar F. & Al (2006). Phylogenetic ... Molecular Microbiology (2007) 64(2), 260-268. doi: 10.1111/j.1365-2958.2007.05671.x Sicard M. & Al (2004). When mutualists are ... Genome Biology and Evolution. 6 (6): 1495-1513. doi:10.1093/gbe/evu119. PMC 4079199 . PMID 24904010. Retrieved 2014-05-30. Wolf ... Convergent Lifestyles from Divergent Genomes", which is licensed in a way that permits reuse under the Creative Commons ...
J Mol Evol 39:306-314 Yang Z, Lauder IJ, Lin HJ (1995). "Molecular evolution of the hepatitis B virus genome". J. Mol. Evol. 41 ... Professor Ziheng Yang's page at UCL Computational Molecular Evolution, Oxford University Press Molecular Evolution: A ... Computational molecular evolution. Oxford University Press. 2006. ISBN 978-0-19-856702-8. Molecular Evolution: A Statistical ... Molecular Biology and Evolution. 24 (8): 1639-1655. doi:10.1093/molbev/msm081. ISSN 0737-4038. Ziheng,, Yang,. Molecular ...
Mycobacterium virus D29
... implications for phage evolution". Journal of Molecular Biology. 279: 143-164. doi:10.1006/jmbi.1997.1610. Retrieved 2 November ... With a genome length over 49000 bp long, D29 is considered to have a large genome size. Large genome sizes generally point to a ... Five tRNA genes are also present in D29's genome (genes 6-9.2). The G+C content of the D29 genome is 63.6%, which is similar to ... The attachment site for D29 is at a very similar location on its genome to that of L5. The attachment site divides the genome ...
Candidatus Carsonella ruddii
"Genome Reduction and Co-evolution between the Primary and Secondary Bacterial Symbionts of Psyllids". Molecular Biology and ... Spaulding, A. W.; von Dohlen, C. D. (1998). "Phylogenetic Characterization and Molecular Evolution of Bacterial Endosymbionts ... Genome Biology and Evolution. 5 (9): 1675-1688. doi:10.1093/gbe/evt118. PMC 3787670 . PMID 23918810. Sloan, D. B.; Moran, N. A ... Molecular Biology and Evolution. 15 (11): 1506-1513. doi:10.1093/oxfordjournals.molbev.a025878. Nakabachi A, Yamashita A, Toh H ...
"Evolution of Rosaceae fruit types based on nuclear phylogeny in the context of geological times and genome duplication". Mol ... CS1 maint: Uses authors parameter (link) Potter D. (2003). "Molecular phylogenetic studies in Rosaceae". In Sharma AK, Sharma A ... Plant Genome: Biodiversity and Evolution. 1, Part A: Phanerogams. Enfield, NH: Scientific Publications. pp. 319-351. ISBN 978-1 ... More recently (1971), Chrysobalanoideae was placed in Malpighiales in molecular analyses and Neuradoideae has been assigned to ...
Russek SJ (February 1999). "Evolution of GABA(A) receptor diversity in the human genome". Gene. 227 (2): 213-22. doi:10.1016/ ... Allison, Lizabeth A. (2012). Fundamental Molecular Biology. New Jersey: John Wiley & Sons, Inc. p. 363. ISBN 978-1-118-05981-4 ... The GABRB3 gene is located on the long arm of chromosome 15, within the q12 region in the human genome. It is located in a gene ... In mice the Gabrb3 gene is located on chromosome 7 of its genome in a similar gene cluster style with some of the other ...
Infinite sites model
One way to think of the ISM is in how it applies to genome evolution. To understand the ISM as it applies to genome evolution, ... The Infinite sites model (ISM) is a mathematical model of molecular evolution first proposed by Motoo Kimura in 1969. Like ... Multiple assumptions are applied to understanding the ISM in terms of genome evolution: k breaks are made in these chromosomes ... 2008). "The infinite sites model of genome evolution". Proceedings of the National Academy of Sciences. 105 (38): 14254-14261. ...
"The Mycobacterium phlei Genome: Expectations and Surprises". Genome Biology and Evolution. 8 (4): evw049. doi:10.1093/gbe/ ... doi:10.1007/s40588-015-0023-1. "Molecular & Biochemical Parasitology". Molecular and Biochemical Parasitology. 201 (2). August ... These studies are known to have widened the understanding of the pathogenesis of the protozoan at the molecular level. For ... His studies elucidated the molecular mechanisms during the opsonization process of the pathogen and identified new proteins ...
Teichmann, Sarah Amalia (1999). Genome evolution : analysing proteomes with new methods (PhD thesis). University of Cambridge. ... After his PhD Chothia worked in the Laboratory of Molecular Biology (LMB) for three years. He then worked with Michael Levitt ... Gough, Julian John Thurstan (2002). Hidden Markov models and their application to genome analysis in the context of protein ... Two types of hinges produce one motion in lactate dehydrogenase". Journal of Molecular Biology. 220 (1): 133-149. doi:10.1016/ ...
Origin of the domestic dog
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Gene conversion and linkage: Effects on genome evolution and speciation. Molecular Ecology, 26: 351-364. doi:10.1111/mec.13736 ... He has served as president of the American Genetic Association (2012) and Society for the Study of Evolution (2014) and as a ... He is editor-in-chief of the international journal Evolution (2016-2019), is or was associate editor for several other journals ... His team's research approaches have included both classical genetic mapping, as well as analyses of whole genome sequences. ...
"Systematics and Mitochondrial Genome Evolution of Australian rosellas (Aves: Platycercidae)" (PDF). Molecular Biology and ... Molecular Phylogenetics and Evolution. 91: 150-159. doi:10.1016/j.ympev.2015.05.012. PMID 26021439. Parks & Wildlife Service ( ... In 2015, Ashlee Shipham and colleagues published a molecular study based on nuclear DNA finding that the North Queensland ... Evolution. 4 (5): 526-543. Shipham A, Schmidt D, Joseph L, Hughes J (2015). "Phylogenetic analysis of the Australian rosella ...
Gogarten, J. Peter; Doolittle, W. Ford (1 December 2002). "Prokaryotic Evolution in Light of Gene Transfer". Molecular Biology ... Lamichhaney, Sangeed; Berglund, Jonas (19 February 2015). "Evolution of Darwin's finches and their beaks revealed by genome ... The most notable example of niche adaptation comes from the original subject of the topic of evolution, the finches of the ... al (2007). "Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche ...
Methods - Molecular Cytogenetics and Genome Evolution: Pat Heslop-Harrison and Trude Schwarzacher
Molecular Cytogenetics and Genome Evolution: Pat Heslop-Harrison and Trude Schwarzacher, Leicester UK
Genomics & genetics for crop improvement, food security, biodiversity, and genome evolution research. Lab of Pat Heslop- ... We research crop plants and farm animals, studying their evolution and organization at the DNA to genome levels: large-scale ... Another 2017 publication considers the role of polyploidy or whole genome duplication in ecology and evolution. Publications ... Molecular cytogenetics homepage. The MolCyt.com site has this homepage linking to topics, molcyt.org blogs, our Department at ...
Molecular Anatomy of Chilo Iridescent Virus Genome and the Evolution of Viral Genes | SpringerLink
Molecular Anatomy of Chilo Iridescent Virus Genome and the Evolution of Viral Genes. ... Schnitzler P., Rösen-Wolff A., and Darai G. (eds.), Molecular Biology of Fish Lymphocystis Disease Virus. Molecular Biology of ... Darai G. (ed.) Molecular Biology of Iridoviruses. Developments in Molecular Virology. Kluwer, Boston, Dordrecht, London, 1990. ... Odell M., Skrskanda V., Shuman S., and Nikolov D.B., Molecular Cell 6, 1183-1193, 2000.PubMedGoogle Scholar ...
Compositional heterogeneity and patterns of molecular evolution in the Drosophila genome. | Genetics
Compositional heterogeneity and patterns of molecular evolution in the Drosophila genome.. J P Carulli, D E Krane, D L Hartl ... Compositional heterogeneity and patterns of molecular evolution in the Drosophila genome.. J P Carulli, D E Krane, D L Hartl ... Compositional heterogeneity and patterns of molecular evolution in the Drosophila genome.. J P Carulli, D E Krane, D L Hartl ... Compositional heterogeneity and patterns of molecular evolution in the Drosophila genome. Message Subject (Your Name) has ...
Recent Articles | Genome, Evolution And Cell & Molecular Biology | The Scientist Magazine®| Page 126
Single-cell genome analyses reveal the amount of mutations a human brain cell will collect from its fetal beginnings until ... From single-cell analysis to whole-genome sequencing, this years best new products shine on many levels. ... tags: genome x evolution x cell & molecular biology x The Scientist. » genome, evolution and cell & molecular biology ...
Profile Articles - cell & molecular biology, Human Genome Project and evolution | The Scientist Magazine®
tags: cell & molecular biology x Human Genome Project x evolution x Profile. » cell & molecular biology, Human Genome Project ... Single-cell genome analyses reveal the amount of mutations a human brain cell will collect from its fetal beginnings until ... Ron Vale has spent a career studying how molecular motors transport cargo within cells. Hes also developed tools to help ... From single-cell analysis to whole-genome sequencing, this years best new products shine on many levels. ...
Molecular-evolution] EMBO practical course on Bioinformatics and Comparative Genome Analyses (Institut Pasteur Paris)
Molecular-evolution] EMBO practical course on Bioinformatics and Comparative Genome Analyses (Institut Pasteur Paris). Fredj ... Next message: [Molecular-evolution] Bioinformatics for gene expression analysis * Messages sorted by: [ date ] [ thread ] [ ... Next message: [Molecular-evolution] Bioinformatics for gene expression analysis * Messages sorted by: [ date ] [ thread ] [ ... genome alignments, Methods for repeats detection in genomes sequences, orthologs prediction and classification, Genome data ...
Molecular and Genome Evolution - Dan Graur - Oxford University Press
This book describes the driving forces behind the evolutionary process at the molecular and genome levels, the effects of the ... and genomes, the methodology and the analytical tools involved in dealing with molecular data from an evolutionary perspective ... various molecular mechanisms on the structure of genes, proteins, ... 8:Evolution by Molecular Tinkering. 9:Mobile Elements in Evolution. 10:Prokaryotic Genome Evolution. 11:Eukaryotic Genome ...
Molecular Evolution of Viruses of the Family Filoviridae Based on 97 Whole-Genome Sequences | Journal of Virology
Genetic Diversity and Evolution. Molecular Evolution of Viruses of the Family Filoviridae Based on 97 Whole-Genome Sequences. ... Molecular Evolution of Viruses of the Family Filoviridae Based on 97 Whole-Genome Sequences ... Molecular Evolution of Viruses of the Family Filoviridae Based on 97 Whole-Genome Sequences ... Molecular Evolution of Viruses of the Family Filoviridae Based on 97 Whole-Genome Sequences ...
Complete Nucleotide Sequence, Molecular Analysis and Genome Structure of Bacteriophage A118 of Listeria Monocytogenes:...
Electron microscopic and enzymatic analyses revealed that the A118 genome is a linear, circularly permuted, terminally ... Molecular Analysis and Genome Structure of Bacteriophage A118 of Listeria Monocytogenes: Implications for Phage Evolution Mol ... Seventy-two open reading frames (ORFs) were identified on the A118 genome, which are apparently organized in a life cycle- ... Electron microscopic and enzymatic analyses revealed that the A118 genome is a linear, circularly permuted, terminally ...
Life: The Science of Biology 11th Edition Chapter 23 - Evolution of Genes and Genomes - 23.4 - Molecular Evolution Has Many...
Molecular Evolution Has Many Practical Applications - 23.4 Recap - Learning Outcomes - Page 504 3 including work step by step ... Chapter 23 - Evolution of Genes and Genomes - 23.4 - Molecular Evolution Has Many Practical Applications - 23.4 Recap - ... Chapter 23 - Evolution of Genes and Genomes - 23.4 - Molecular Evolution Has Many Practical Applications - 23.4 Recap - ... Previous Answer Chapter 23 - Evolution of Genes and Genomes - 23.4 - Molecular Evolution Has Many Practical Applications - 23.4 ...
Targeted Sequencing of Venom Genes from Cone Snail Genomes Improves Understanding of Conotoxin Molecular Evolution
... ... To expand our capacity to discover venom sequences from the genomes of venomous organisms, we applied targeted sequencing ... with comparisons to transcriptome data showing that cone snails only express a fraction of the genes available in their genome ... and used these data to provide new insights into conotoxin evolution. First, we found that conotoxin gene superfamilies are ...
Data from: Domestication and the mitochondrial genome: comparing patterns and rates of molecular evolution in domesticated...
Data from: Domestication and the mitochondrial genome: comparing patterns and rates of molecular evolution in domesticated ... Data from: Domestication and the mitochondrial genome: comparing patterns and rates of molecular evolution in domesticated ... comparing patterns and rates of molecular evolution in domesticated mammals and birds and their wild relatives. Genome Biology ... In this study, our aim is to test whether the impact on mitochondrial genome evolution is a general feature of domestication, ...
The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms | BMC...
... rate in angiosperms and its effects on genome architecture and selection at the molecular level using genetic maps and genome ... suggesting that global recombination rates affect variation in rates of molecular evolution across distantly related angiosperm ... Recombination can reduce genome size by enabling the removal of LTR retrotransposons, alter codon usage by GC biased gene ... rate across species may explain some of the variation in genomic architecture as well as rates of molecular evolution. We used ...
Stress‐response balance drives the evolution of a network module and its host genome | Molecular Systems Biology
Stress‐response balance drives the evolution of a network module and its host genome. Caleb González, Joe Christian J Ray, ... A synthetic gene circuit is integrated into the yeast genome to model the evolution of drug resistance networks with inherent ... Yet, the evolution of stress resistance networks is not well understood. Here, we use a two‐component synthetic gene circuit ... The evolution of a synthetic gene circuit that trades off costly gene expression for drug resistance is analyzed ...
Molecular evolution of the MAGUK family in metazoan genomes | BMC Evolutionary Biology | Full Text
In summary, we have characterized here the molecular and structural evolution of the large MAGUK family. Using the MAGUKs as an ... It further suggests that larger superfamilies encoded in the different genomes can be analyzed in a similar manner. ... and the SH3-domains all suggested a matching evolutionary model which was further supported by molecular modeling of the 3D ... Journal of Molecular Evolution. 2004, 59 (1): 41-50. 10.1007/s00239-004-2602-2.View ArticlePubMedGoogle Scholar. ...
Current topics in genome evolution: Molecular mechanisms of new gene formation<...
Current topics in genome evolution: Molecular mechanisms of new gene formation. Cellular and Molecular Life Sciences. 2007 Mar ... Current topics in genome evolution: Molecular mechanisms of new gene formation. Cellular and Molecular Life Sciences, 64(5), ... Current topics in genome evolution: Molecular mechanisms of new gene formation, Cellular and Molecular Life Sciences, vol. 64 ... Current topics in genome evolution : Molecular mechanisms of new gene formation. In: Cellular and Molecular Life Sciences. 2007 ...
Insights into hominid evolution from the gorilla genome sequence. - MRC Weatherall Institute of Molecular Medicine
Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes ... In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding ... use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution. ... A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, ...
Society for Molecular Biology and Evolution (SMBE) Council and Business Meetings, 2009, Iowa City, IA : Genome Biology and...
The amphioxus genome and the evolution of the chordate karyotype. - MRC Weatherall Institute of Molecular Medicine
These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during ... and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the ... Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida ... as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. ...
CpG Mutation Rates in the Human Genome Are Highly Dependent on Local GC Content : Molecular Biology and Evolution - oi
Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution. -...
Structure (Molecular Modeling Database). *Vector Alignment Search Tool (VAST). *All Domains & Structures Resources... ... Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution.. ... Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution ... Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution ...
Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution. - PubMed - NCBI
Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For ... Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution.. Moyers BA1, Zhang J2. ... Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution ... Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution ...
Press | Molecular cytogenetics and genome evolution
Media and public understanding from the Molecular Cytogenetics group, University of Leicester. This category includes ... Molecular cytogenetics, plant nuclear genome organization, in situ hybridization, genomics and evolution of crops and other ... Using genome diversity for the environment, livelihoods and tropical grasslands blog.ciat.cgiar.org/using-genome-d… via @CIAT_ ... Postdoctoral PDA RA positions in South China Botanical Gardens Plant Genome Evolution Research Group ...
Contacts/Directions | Molecular cytogenetics and genome evolution
The Molecular Cytogenetics Group is in the University of Leicester, UK. Our telephone is +44/0 116 252 3397. Pat Heslop- ... Pingback: Opportunities in the molecular cytogenetics group , Molecular cytogenetics and genome evolution ... Molecular cytogenetics, plant nuclear genome organization, in situ hybridization, genomics and evolution of crops and other ... Postdoctoral PDA RA positions in South China Botanical Gardens Plant Genome Evolution Research Group ...
Stress‐response balance drives the evolution of a network module and its host genome | Molecular Systems Biology
Stress‐response balance drives the evolution of a network module and its host genome. Caleb González, Joe Christian J Ray, ... A synthetic gene circuit is integrated into the yeast genome to model the evolution of drug resistance networks with inherent ... For example, Appendix Fig S4B shows just the whole‐genome inferred allele frequencies for all whole‐genome‐sequenced time ... genome sequencing (Appendix Fig S4D and E). We repeated the evolution experiment with 24‐h resuspensions and observed similar ...
Molecular Anthropology Lab - The Mobile Genome in Human Evolution
Centre for Genome Biology. website. Department of Biological, Geological and Environmental Sciences (BiGeA). website. ... The aim of our researches is to explore and understand the role of transposable elements in the recent evolution of Homo, as ... In order to evaluate the impact of transposable elements in the recent evolution of our species, we compare our insertion ... Large part of the human genome (~66-69%) is made by repetitive elements, most of which are trasposons (~46%). Trasposons are ...
Phylogenetics and molecular evolution of Alismatales based on whole plastid genomes - UBC Library Open Collections
Down the slippery slope: plastid genome evolution in Convolvulaceae. Journal of Molecular Evolution, 61: 292-305. Stevens, P.F ... for understanding genome evolution in Poaceae. Journal of Molecular Evolution, 70: 149-66. Haynes, R.R., Les, D.H. and Holm- ... Phylogenetics and molecular evolution of Alismatales based on whole plastid genomes Ross, Thomas Gregory 2014 pdf ... PHYLOGENETICS AND MOLECULAR EVOLUTION OF ALISMATALES BASED ON WHOLE PLASTID GENOMES by Thomas Gregory Ross B.Sc. The University ...
Evolution and molecular characteristics of SARS-CoV-2 genome | bioRxiv
Evolution and molecular characteristics of SARS-CoV-2 genome. View ORCID ProfileYunmeng Bai, Dawei Jiang, View ORCID Profile ... Evolution and molecular characteristics of SARS-CoV-2 genome Message Subject (Your Name) has forwarded a page to you from ... In the evolution analysis of 622 complete human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes with high ... The evolution and molecular characteristics of more than 3500 genomic sequences provided a new perspective for revealing the ...
Evolution and molecular characteristics of SARS-CoV-2 genome | bioRxiv
Evolution and molecular characteristics of SARS-CoV-2 genome. View ORCID ProfileYunmeng Bai, Dawei Jiang, View ORCID Profile ... Evolution and molecular characteristics of SARS-CoV-2 genome Message Subject (Your Name) has forwarded a page to you from ... while H1 haplotype subgroup was going through a neutral evolution and globally increased with time. The evolution and molecular ... In the evolution analysis of 622 or 3624 complete SARS-CoV-2 genomes, the estimated Ka/Ks ratio is 1.008 or 1.094, which is ...
GenesSequencesApplied GeneticsBiology and EvolutionEvolutionaryMechanismsSpeciationGenomicsGeneticSpeciesPhylogenyAnalysesGenomicRecombinationHuman genomePhylogeneticPlant genomesPhylogeneticsOrganizationTransposable ElementsEukaryotesDynamicsSequencingChromosomesCompletely sequenced genomesDrosophilaReference genomeVariationDiversityBacterialBioinformaticsLineagesNuclear genomesDuplicationCytogeneticsProteinsMicrobialProcessesDivergenceOrganelle genomesUniversity of LeicesCellularChromosomalMitochondrial genomesRegions of the genomePatternsNucleotide sequenceHumansAllowed genome-wideApproachesComparisonsAnalysisEcologyOrganismsInsightsContentFungalPopulationsTranscriptomeBacteriaVertebrates
- We have examined the Drosophila genome to explore relationships between the nucleotide content of large chromosomal segments and the base composition and rate of evolution of genes within those segments. (genetics.org)
- This book describes the driving forces behind the evolutionary process at the molecular and genome levels, the effects of the various molecular mechanisms on the structure of genes, proteins, and genomes, the methodology and the analytical tools involved in dealing with molecular data from an evolutionary perspective, and the logic of evolutionary hypothesis testing. (oup.com)
- Comparative analysis of the A118 genome structure with other bacteriophages revealed local, but sometimes extensive, similarities to a number of phages spanning a broader phylogenetic range of various low G+C host bacteria, which implies relatively recent exchange of genes or genetic modules. (nih.gov)
- Recombination can reduce genome size by enabling the removal of LTR retrotransposons, alter codon usage by GC biased gene conversion, contribute to complex histories of gene duplication and loss through tandem duplication, and enhance purifying selection on genes. (biomedcentral.com)
- An analysis of the correlation between the ratio of nonsynonymous to synonymous substitution rates ( dN/dS ) and recombination rate in 3748 genes indicates that higher recombination rates are associated with an increased efficacy of purifying selection, suggesting that global recombination rates affect variation in rates of molecular evolution across distantly related angiosperm species, not just between populations. (biomedcentral.com)
- Comparative genome analyses reveal that most functional domains of human genes have homologs in widely divergent species. (elsevier.com)
- Although the domain-shuffling hypothesis is generally accepted, determining the molecular mechanisms that lead to domain shuffling and novel gene creation has been challenging, as sequence features accompanying the formation of known genes have been obscured by accumulated mutations. (elsevier.com)
- The growing availability of genome sequences and EST databases allows us to study the characteristics of newly emerged genes. (elsevier.com)
- Here we review recent genome-wide DNA and EST analyses, and discuss the three major molecular mechanisms of gene formation: (1) atypical spicing, both within and between genes, followed by adaptation, (2) tandem and interspersed segmental duplications, and (3) retrotransposition events. (elsevier.com)
- this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. (ox.ac.uk)
- A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. (ox.ac.uk)
- However, the landscape of PT and TPS genes in plant genomes is unclear. (nih.gov)
- Here, using a customized algorithm for systematically searching plant genomes, we reveal a suite of physically colocalized pairs of PT and TPS genes for the biosynthesis of a large sesterterpene repertoire in the wider Brassicaceae. (nih.gov)
- Identification of candidate STS genes from plant genomes. (nih.gov)
- Although gene duplication is conventionally thought to dominate the production of new genes, this view was recently challenged by a proposal of widespread de novo gene origination in eukaryotic evolution. (nih.gov)
- Together, these findings are consistent with the prevailing view that de novo gene birth is a relatively minor contributor to new genes in genome evolution. (nih.gov)
- I recovered whole plastid genomes (plastid gene sets representing up to 83 genes per taxa) and analyzed them using maximum likelihood and parsimony approaches. (ubc.ca)
- The discovery of premature termination codons in 38% of expressed genes was consistent with ongoing pseudogenization of the wheat genome. (plantphysiol.org)
- Enhancers play an important role in morphological evolution and speciation by controlling the spatiotemporal expression of genes. (biomedcentral.com)
- We found that 46.6% of P. damicornis genes had orthologs in all other scleractinians, defining a coral 'core' genome enriched in basic housekeeping functions. (nature.com)
- Of these core genes, 3.7% were unique to scleractinians and were enriched in immune functionality, suggesting an important role of the immune system in coral evolution. (nature.com)
- Genes occurring only in P. damicornis were enriched in cellular signaling and stress response pathways, and we found similar immune-related gene family expansions in each coral species, indicating that immune system diversification may be a prominent feature of scleractinian coral evolution at multiple taxonomic levels. (nature.com)
- Scientists believe that the study of genes that encode the proteins for molecular motors will help solve the mysteries of evolution. (icr.org)
- The authors stated, 'The number of myosin genes varies markedly between lineages [types of eukaryotes],' and 'holozoan genomes, as well as some amoebozoans and heterokonts, have the highest numbers of myosins of all eukaryotes. (icr.org)
- Specifically, the ideas of convergent evolution and lineage-specific expansions are nothing more than fancy terms for the fact that these different types of myosin genes appeared suddenly in unrelated creatures at the same time. (icr.org)
- it can also obfuscate correlations between teleost disease models and their human counterparts because of the difficulty of ortholog assignment after lineage-specific loss of duplicated genes and the asymmetric evolution of gene duplicates. (genetics.org)
- The Ehrlichia genome contains many different variants of genes that encode outer membrane proteins. (wikipedia.org)
- When sequencing their genomes, there were many active genomic modifications such as high substitution rates, truncated genes, and the presence of pseudogenes and tandem repeats. (wikipedia.org)
- These Rf -like genes show a number of characteristic features compared with other PPR genes, including chromosomal clustering and unique patterns of evolution, notably high rates of nonsynonymous to synonymous substitutions, suggesting diversifying selection. (pnas.org)
- We suggest that the selection patterns on Rf -like genes reveal a molecular "arms-race" between the nuclear and mitochondrial genomes that has persisted throughout most of the evolutionary history of angiosperms. (pnas.org)
- In plants, the rapid evolution of leucine-rich repeat (LRR) R genes provides the best examples of such coevolutionary "arms races" ( 5 , 6 ). (pnas.org)
- The CMS trait is carried by the mitochondrial genome and many different CMS genes have been identified in a range of disparate plant species ( 7 , 8 , 10 - 13 ). (pnas.org)
- Gynodioecy is fairly common in flowering plants (observed in about 7% of the species), although modeling has shown that under most plausible conditions, the female state provides little or no advantage for nuclear genes ( 20 ), leading to the proposition that the mitochondrial and nuclear genomes are in conflict ( 3 , 21 ). (pnas.org)
- G3: Genes, Genomes, Genetics. (umass.edu)
- This book explores the forces that have shaped the evolution of organelle genomes and the expression of the genes encoded by them. (springer.com)
- We compared approximately 10 000 protein-coding genes culled from the bottlenose dolphin genome with nine other genomes to reveal molecular correlates of the remarkable phenotypic features of these aquatic mammals. (royalsocietypublishing.org)
- In addition, genes expressed in the mitochondrion have a significantly higher mean d N/ d S ratio in the dolphin lineage than others examined, indicating evolution in energy metabolism. (royalsocietypublishing.org)
- Adaptive evolution of genes involved in aerobic metabolism (i.e. the mitochondrial electron transport chain) has been documented within the relatively large-brained anthropoid primates and along the lineage leading to humans [ 10 ]. (royalsocietypublishing.org)
- Recent phylogenomic studies of molecular evolution have also discovered parallels in the evolution of aerobic metabolism genes between the large-brained African elephant and primates [ 11 ]. (royalsocietypublishing.org)
- This association suggests that the evolution of metabolic genes underlies the evolution of a large brain in other groups with a significant shift in relative brain size and/or cognitive complexity. (royalsocietypublishing.org)
- One study has recovered signatures of molecular adaptation in the cytochrome b gene of cetaceans [ 12 ], but other genes expressed in mitochondria have not been evaluated. (royalsocietypublishing.org)
- In this context, "genome size" was being used in the sense of genotype to mean the number of genes. (wikipedia.org)
- In eukaryotes, but not prokaryotes, variation in genome size is not proportional to the number of genes, an observation that was deemed wholly counterintuitive before the discovery of non-coding DNA and which became known as the C-value paradox as a result. (wikipedia.org)
- Many mitochondria have less than 20 genes in their entire genome, whereas a free-living bacterium generally has at least 1000 genes. (wikipedia.org)
- We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI), conserved marker genes (31 and 400), pan genome and tetranucleotide frequency. (frontiersin.org)
- The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. (frontiersin.org)
- Two overlapping bacterial artificial chromosome (BAC) clones from the B genome of the tetraploid wheat Triticum turgidum were identified, each of which contains one of the two high-molecular-weight (HMW) glutenin genes, comprising the complex Glu-B1 locus. (unboundmedicine.com)
- The two paralogous x-type ( Glu-1-1 ) and y-type ( Glu-1-2 ) HMW-glutenin genes of the complex Glu-B1 locus were found to be separated by ca. 168 000 bp instead of the 51 000 bp separation previously reported for the orthologous Glu-D1 locus of Aegilops tauschii, the D-genome donor of hexaploid wheat. (unboundmedicine.com)
- Otherwise, the orientation and order of the HMW glutenins and adjacent genes were identical in the two genomes. (unboundmedicine.com)
- Since the discovery of CIV in 1966, many attempts were made to elucidate the viral genome structure and the amino acid sequences of different viral gene products. (springer.com)
- The course topics will include theoretical and practical aspects in: large-scale genome comparisons, evolutionary analyses, sequence and genome alignments, Methods for repeats detection in genomes sequences, orthologs prediction and classification, Genome data visualization and statistical methods needed in Genome Wide Association Studies. (bio.net)
- To expand our capacity to discover venom sequences from the genomes of venomous organisms, we applied targeted sequencing techniques to selectively recover venom gene superfamilies and nontoxin loci from the genomes of 32 cone snail species (family, Conidae), a diverse group of marine gastropods that capture their prey using a cocktail of neurotoxic peptides (conotoxins). (ovid.com)
- In particular, analyses of mitochondrial genome sequences from domestic dogs and yaks have yielded higher ratios of non-synonymous to synonymous substitutions in the domesticated lineages than in their wild relatives. (datadryad.org)
- We test whether domesticated mammals and birds have consistently different patterns of molecular evolution than their wild relatives for 16 phylogenetically independent comparisons of mitochondrial genome sequences. (datadryad.org)
- We used phylogenetic comparative methods to investigate the evolution of global meiotic recombination rate in angiosperms and its effects on genome architecture and selection at the molecular level using genetic maps and genome sequences from thirty angiosperm species. (biomedcentral.com)
- Furthermore, since NGS sequences are typically aligned on the reference genome, structural variants cannot be observed. (bioanthropologybologna.eu)
- The evolution and molecular characteristics of more than 3500 genomic sequences provided a new perspective for revealing the epidemiology mechanism of SARS-CoV-2 and coping with SARS-CoV-2 effectively. (cdc.gov)
- Furthermore, they can be classified into two families, i.e., glycoside hydrolase 18 and 19, differing in their amino acid sequences, three-dimensional structures and molecular mechanisms of catalysis. (thewinnower.com)
- The evolution of protein-coding sequences, gene exon-intron structure, and alternative splicing ( AS ) define the diversity of proteome structure and function ( Koonin and Wolf, 2010 ). (plantphysiol.org)
- Mass sequencing technologies that enable the acquisition of complete pathogen genome sequences provide a new approach to address questions related to the roles played by host specialization and speciation. (prolekare.cz)
- Non-coding cis-regulatory sequences act as the 'eyes' of the genome and their role is to perceive, organise and relay cellular communication information to RNA polymerase II at gene promoters. (cambridge.org)
- The evolution of these sequences, that include enhancers, silencers, insulators and promoters, has progressed in multicellular organisms to the extent that cis-regulatory sequences make up as much as 10% of the human genome. (cambridge.org)
- To better understand the evolutionary history and genetic make-up of this aggressive tree-infecting bacterium, draft genome sequences were generated for seven isolates of P. syringae pv. (forestry.gov.uk)
- Genomic resources for hundreds of species of evolutionary, agricultural, economic, and medical importance are unavailable due to the expense of well-assembled genome sequences and difficulties with multigenerational studies. (genetics.org)
- The significant phylogenetic signal in genome size data suggests that distribution of genome size is in accordance with phylogenetic clades identified by the analysis of nuclear ITS sequences. (bioone.org)
- Even after these genomes are sequenced, it will still be a tremendous challenge to understand the evolution of plant nuclear genomes, like the maize genome, for which entire DNA sequences will not be readily available. (pnas.org)
- Apart from these importin-4-like sequences, the other Y repetitive sequences are not shared with the X chromosome, suggesting molecular differentiation of these two chromosomes. (biomedsearch.com)
- CONCLUSIONS/SIGNIFICANCE: The identification of Y-linked sequences may tell us much about the repetitive nature, the origin and the evolution of Y chromosomes. (biomedsearch.com)
- Here, we compared approximately 10 000 protein-coding sequences (CDS) from the genome of the common bottlenose dolphin ( Tursiops truncatus ) with nine other amniote genomes, including the closest relative with a sequenced genome, the domestic cow ( Bos taurus ). (royalsocietypublishing.org)
- Studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. (mdpi.com)
Biology and Evolution6
- Genome Biology and Evolution 6(1): 161-169. (datadryad.org)
- The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution. (ox.ac.uk)
- However, the result of a study published in the journal Genome Biology and Evolution has only served to support the predictions of special creation-that unique variants of cellular complexity and innovation exist at all levels of life. (icr.org)
- Genome Biology and Evolution, 11 (3), 748-758. (mpg.de)
- Molecular Biology and Evolution, 36 (7): msz083, pp. 1490-1506. (mpg.de)
- Molecular Biology and Evolution, 35 (11), 2719-2735. (mpg.de)
- Significant negative correlations between codon-usage bias and rates of synonymous site divergence, however, provide strong support for an argument that selection among alternative codons may be a major contributor to variability in evolutionary rates within Drosophila genomes. (genetics.org)
- Describes the driving forces behind the evolutionary process at the molecular and genome levels. (oup.com)
- Evolutionary phenomena at the molecular level are detailed in a way that can be understood without much prerequisite knowledge of molecular biology, evolution, or mathematics. (oup.com)
- Meiotic recombination has been a topic of interest in evolutionary biology since Fisher first addressed the effects of linkage on substitutions in a population [ 1 ], yet the macroevolutionary consequences of recombination on plant genomes are still poorly understood. (biomedcentral.com)
- Recombination affects both genome architecture and evolutionary rates. (biomedcentral.com)
- Notably, the phylogenetic trees for the guanylate kinase (GK)-, the PDZ- and the SH3-domains all suggested a matching evolutionary model which was further supported by molecular modeling of the 3D structures of different GK domains. (biomedcentral.com)
- Whereas these processes mostly contribute to the degeneration of a duplicated genome and its diploidization, they have the potential to facilitate the origin of new functional variations, which, upon selection in the evolutionary lineage, may play an important role in the origin of novel traits. (plantphysiol.org)
- Among plant species, wheat ( Triticum aestivum ) provides a unique opportunity to study early phases of duplicated gene evolution after WGD , the impact of increased genome size on the evolutionary dynamic of gene space, and understand how these processes shaped the coding potential of the wheat genome. (plantphysiol.org)
- Therefore, additional complete coral genomes and more comprehensive comparative analysis may be transformative in our understanding of the genomic content and evolutionary history of reef-building corals, as well as the importance of specific gene repertoires and diversification within coral lineages. (nature.com)
- We are now using a novel "molecular palaeontology" approach to trace the evolutionary process and identify functionally significant loci under selection. (blogspot.com)
- Research interests in the Edwards lab stem from a fascination with the molecular basis of evolutionary change and how we can harness the g. (blogspot.com)
- Describing and understanding the evolution of this diversity of body plans - from vertebrates such as humans and fish to the numerous invertebrate groups including sponges, insects, molluscs, and the many groups of worms - is a major goal of evolutionary biology. (oxfordscholarship.com)
- The last decade has seen growing interest in evolutionary biology fuelled by a wealth of data from molecular biology. (oxfordscholarship.com)
- A newly discovered genome for the unicellular chromosome-morphing ciliate Stylonychia lemnae has been published, and it's breaking all the evolutionary rules. (icr.org)
- Three strains have arisen from this species due to evolutionary change in their genomes. (wikipedia.org)
- The challenges are to infer the mechanisms of evolution and to construct a comprehensive picture of evolutionary change. (pnas.org)
- Patterns of genetic diversity provide insight into the population genetic processes that act on different regions of the genome and thus uncover the evolutionary forces that act on genomes. (pnas.org)
- This volume is organized into four sections encompassing 22 chapters and begins with an overview of discoveries concerning parapatric differentiation of weed populations, including adaptive evolution in herbicide resistant biotypes and complex evolutionary patterns in weed-crop complexes of various groups. (elsevier.com)
- It is widely accepted that eukaryotes obtained mitochondria via an ancient symbiosis with a bacterium ( 1 ) and generally assumed that the nuclear and mitochondrial genomes now share a common evolutionary path. (pnas.org)
- The most evolutionary significant cases of genome reduction may be the eukaryotic organelles that are derived from bacteria: the mitochondrion and plastid. (wikipedia.org)
- Gross imperfection at the molecular level presents a conundrum for the traditional paradigms of natural theology as well as for recent assertions of ID, but it is consistent with the notion of nonsentient contrivance by evolutionary forces. (nap.edu)
- I n Darwin's Black Box, biochemist Michael Behe (1996) issued a challenge to evolutionary biology by claiming that various molecular apparatuses within cells are "irreducibly complex" and therefore could only have been designed purposefully by a higher intelligence. (nap.edu)
- There is no dispute that molecular systems can be astonishingly complex, but most geneticists attribute such biological complexity to the cumulative effects of evolutionary tinkering by natural forces (including a mindless directive agent, natural selection) rather than to conscious engineering by a supernatural entity. (nap.edu)
- However, morphological corroboration of these trees is an essential part of understanding evolutionary history, and sometimes, as in the case of the asteroids (Echinodermata) morphology provides a very different story to the molecular phylogeny. (port.ac.uk)
- In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods. (mdpi.com)
- Our members work to advance knowledge in the basic mechanisms of inheritance, from the molecular to the population level. (genetics.org)
- These data will be valuable for understanding the evolution of filoviruses in the context of natural history as new reservoir hosts are identified and, further, for determining mechanisms of emergence, pathogenicity, and the ongoing threat to public health. (asm.org)
- Although our analyses only reveal correlations, not mechanisms, and do not include potential covariates of recombination rate, like effective population size, they suggest that global recombination rates may play an important role in shaping the macroevolutionary patterns of gene and genome evolution in plants. (biomedcentral.com)
- Overall, these findings reveal how the timing and mechanisms of stress response network evolution depend on the environment. (embopress.org)
- The focus of this volume is at the level of major animal groups, the morphological innovations that define them, and the mechanisms of change to their embryology that have resulted in their evolution. (oxfordscholarship.com)
- Objective:The objective of this study was to determine molecular alterations and mediating resistant mechanisms and to suggest additional treatment options.Design, Setting, and Participants:Four patients were enrolled into the MORE (Molecular Renal Cancer Evolution) trial. (ega-archive.org)
- Recently developed techniques in molecular biology, including genomics and other omics, can reveal the complex molecular mechanisms involved in the control of agronomic traits. (mdpi.com)
- Genomic information representing a fish lineage that diverged before the teleost genome duplication (TGD) would provide an outgroup for exploring the mechanisms of evolution after whole-genome duplication. (genetics.org)
- 2013. Pyrenophora tritici-repentis genome reveals mechanisms that contribute to high genetic variations. (umass.edu)
- Cellular and Molecular Mechanisms of Mammalian. (hhmi.org)
- Michael Behe's purported biochemical challenge to evolution rests on the assertion that Darwinian mechanisms are simply not adequate to explain the existence of complex biochemical machines. (nap.edu)
- We discuss the possible molecular mechanisms underlying electrical rectification, as well as the potential contribution of intracellular soluble factors to this phenomenon. (frontiersin.org)
- Therefore, studies on bacterial evolution are of increasing interest to understand the basic mechanisms of evolution. (mdpi.com)
- They aim to understand the biological chemistry and molecular mechanisms of redox-based cellular regulation and signal transduction, with emphasis on the role of cysteine oxidation. (rsc.org)
- Research in my lab is focused on understanding molecular mechanisms through which chromatin dynamics and nuclear organization contribute to gene regulation. (lsu.edu)
- Cycles of whole-genome duplication ( WGD ) and diploidization are hallmarks of eukaryotic genome evolution and speciation. (plantphysiol.org)
- Individual chapters provide concise overviews of the many flavors of plant transposons and of their roles in gene creation, gene regulation, development, genome evolution, and organismal speciation, as well as of their epigenetic regulation. (wiley.com)
- Thus, genome size variation reflects incipient speciation or diversification in Allium subgenus Melanocrommyum . (bioone.org)
- Due to its large genome size (1 C ~ 4.45 gigabases, Gb 9 ), pea genomics has lagged behind that of legumes with smaller genomes, such as Medicago truncatula Gaertn. (nature.com)
- We use a comparative genomics approach to assess how the process of host specialization affected the genome structure of M. graminicola since divergence from the closest known progenitor species named M. graminicola S1. (prolekare.cz)
- Application of our F 1 dense mapping strategy to species with no prior genome information promises to facilitate comparative genomics and provide a scaffold for ordering the numerous contigs arising from next generation genome sequencing. (genetics.org)
- That approach has made its way to Drosophila genomics with the publication of a paper describing polymorphism across the entire genome of D. simulans , a sibling species to D. melanogaster . (scienceblogs.com)
- Jonathan explains how this is a model for population genomics - studying genome wide patterns of variation. (scienceblogs.com)
- 2007. Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans . (scienceblogs.com)
- Dr. DeSalle works in molecular systematics, microbial evolution, and genomics. (amnh.org)
- Dr. DeSalle has worked closely with colleagues from Cold Spring Harbor Labs, New York University, and the New York Botanical Garden on seed plant genomics and development of tools to establish gene family membership on a genome- wide scale. (amnh.org)
- Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. (frontiersin.org)
- We study chromatin domain insulators and insulator binding proteins in Drosophila melanogaster, using a combination of genetics, molecular cell biology, biochemistry and genomics. (lsu.edu)
- Recent genome sequencing and genetic mapping efforts, which provide physical measurements of genome size and map length, make studies of global recombination rate possible in plants. (biomedcentral.com)
- These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution. (ox.ac.uk)
- The online free retroviruses and primate genome evolution molecular, and the importance on the library, is the democracy of the request of the Indian Plate with the executive Plate through genetic request between 20 and 50 million notions not. (aminswessi.com)
- We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. (nature.com)
- 4 The problem for evolution is that incredible and amazing genetic complexity exists at all levels of life, from one-celled creatures to the pinnacle of God's creation: mankind. (icr.org)
- Hardie and Hebert 2004 ) have virtually no genome resources and have life history traits inconvenient for the construction of large-scale genetic maps. (genetics.org)
- The scope of Chromosoma encompasses genetic, biophysical, molecular and cell biological studies. (springer.com)
- Population genetic processes also affect the evolution of genomes. (pnas.org)
- Did genetic drift drive increases in genome complexity? (wiley.com)
- Molecular genetic methods. (mpi.nl)
- The Biodiversity and Evolution group explores the diversity of life at levels ranging from the molecular and genetic, to organismal and ecosystem. (port.ac.uk)
- Therefore, variation in recombination rate across species may explain some of the variation in genomic architecture as well as rates of molecular evolution. (biomedcentral.com)
- Lynch [ 5 ] showed that generation scaled global recombination rate (centimorgans/basepairs/generation) decreases as species genome size increases in unicellular eukaryotes, invertebrates, vertebrates, and land plants. (biomedcentral.com)
- In order to evaluate the impact of transposable elements in the recent evolution of our species, we compare our insertion patterns with those of extinct hominins (Denisova, Neanderthal) and of our closest relatives (bonobo, chimp), thus identifying and characterizing species-specific insertions. (bioanthropologybologna.eu)
- The hexaploid wheat genome (comprised of about 16,000 Mb) resulted from the union of three diploid grass species. (plantphysiol.org)
- This resource was generated using a common deep RNA sequencing protocol to obtain the most exhaustive gene repertoire possible in each species that allows between-species comparisons to study the evolution of gene expression in different lineages. (nih.gov)
- The purpose of this Special Issue is to explore the molecular basis of agronomically important traits in rice, which is a monocot model crop species. (mdpi.com)
- Ehrlichia and their closely related species Anaplasma show extreme diversity in the structure and content of their genomes. (wikipedia.org)
- The observed 2C genome size variation in 160 accessions of 70 species of the subgenus was high, varying from 26.26-78.73 pg. (bioone.org)
- In species where intraspecific genome size differences were in a range of 6-9%, we suggest the existence of cryptic species, as previously inferred by molecular markers. (bioone.org)
- The 2000s witnessed an explosion of genome sequencing and mapping in evolutionarily diverse species. (wikipedia.org)
- While full genome sequencing of mammals is rapidly progressing, the ability to assemble and align orthologous whole chromosomal regions from more than a few species is not yet possible. (wikipedia.org)
- It was found that in most orders, there are species with rates of chromosome evolution that can be considered as 'default' rates. (wikipedia.org)
- Other grass species exhibit far larger genomes. (pnas.org)
- Numerical values next to species names represent the 2C genome content of the species, measured in picograms. (pnas.org)
- Interactions in host-parasite systems are important forces driving genome diversity within species, and may even contribute to the formation of new species. (pnas.org)
- According to our measurements, such heterochromatin represents about 35% of the genome of the species, probably originated through amplification processes after the splitting off of the species from the common trunk. (nii.ac.jp)
- It was initially about sequencing the genome a single representative individual from a particular species. (scienceblogs.com)
- Around the same time as that white paper, another proposal was submitted to bring the total number of sequenced Drosophila genomes to twelve (making it the eukaryotic genus with the most species with completely sequenced genomes, although the diversity in this genus is equivalent to that of all eutherian mammals ). (scienceblogs.com)
- Nuclear genome sizes are well known to vary enormously among eukaryotic species. (wikipedia.org)
- Furthermore, such dysfunctional traits abound not only in the phenotypes but inside the genomes of eukaryotic species. (nap.edu)
- Current research themes and future prospects are highlighted including phylogeny reconstruction, comparative developmental biology, the value of different sources of data and the importance of fossils, homology assessment, character evolution, phylogeny of major groups of animals, and genome evolution. (oxfordscholarship.com)
- These topics are integrated in the light of a 'new animal phylogeny', to provide fresh insights into the patterns and processes of animal evolution. (oxfordscholarship.com)
- Phylogenetic analysis using these "comparative-genome markers" (CGMs) produced a highly unusual phylogeny with a complete absence of secondary branches. (asm.org)
- The phylogeny and genome content information is taken from figure 1 of ref. 51 . (pnas.org)
- We are currently working on barnacle (Cirripedia, Crustacea) phylogeny in collaboration with molecular studies currently underway in the USA and Europe. (port.ac.uk)
- Single-cell genome analyses reveal the amount of mutations a human brain cell will collect from its fetal beginnings until death. (the-scientist.com)
- The main objective of this intensive course is to strengthen capacities of Phd students and young scientists, in Bioinformatics and large-scale genome data analyses skills. (bio.net)
- Electron microscopic and enzymatic analyses revealed that the A118 genome is a linear, circularly permuted, terminally redundant collection of double-stranded DNA molecules. (nih.gov)
- 2012. Life-style transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. (umass.edu)
- Comparative analyses of 31 fungal genomes (12 generated for this study). (usda.gov)
- More recently (1971), Chrysobalanoideae was placed in Malpighiales in molecular analyses and Neuradoideae has been assigned to Malvales. (eol.org)
- These results suggest that nucleotide sequence evolution in Drosophila differs from that of many vertebrates and does not reflect distinct mutational biases, as a function of base composition, in different genomic regions. (genetics.org)
- Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. (ox.ac.uk)
- Although comparative genomic studies reveal large-scale turnover of enhancers, a specific understanding of the molecular steps by which mammalian or primate enhancers evolve remains elusive. (biomedcentral.com)
- Comparative analysis of the expanding genomic resources for scleractinian corals may provide insights into the evolution of these organisms, with implications for their continued persistence under global climate change. (nature.com)
- Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. (nature.com)
- Genomic resources from a ray-fin (Actinopterygian) fish that diverged from teleosts before the TGD ( Figure 1 ) would facilitate the connectivity of teleost and mammalian genomes. (genetics.org)
- The comparative-genomic sequencing of two Mycobacterium tuberculosis strains enabled us to identify single nucleotide polymorphism (SNP) markers for studies of evolution, pathogenesis, and epidemiology in clinical M . tuberculosis . (asm.org)
- Genomic technologies have produced a wealth of data on the organization and structure of genomes. (pnas.org)
- 2009. Genomic analysis of a basal fungus Rhizopus oryzae reveals whole genome duplication. (umass.edu)
- There's also a Plos Genetics paper from the same group that looks at evolution of gene expression in simulans, yakuba and melanogaster, compared to genomic evolution. (scienceblogs.com)
- Although homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown. (biomedcentral.com)
- Recombination rate is negatively correlated with genome size, which is likely caused by the removal of LTR retrotransposons. (biomedcentral.com)
- Interspecific recombination rate variation is tightly correlated with genome size as well as variation in overall LTR retrotransposon abundances. (biomedcentral.com)
- In this study, we take advantage of these new data to explore the relationship between recombination rate, genome structure, and patterns of molecular evolution throughout angiosperms in order to better characterize the broad macroevolutionary patterns of recombination rate variation and its possible consequences for genome evolution. (biomedcentral.com)
- Similarly, in plants, Cavalier-Smith [ 6 ] proposed that the recombination rate is higher in smaller angiosperm genomes than in larger genomes. (biomedcentral.com)
- Both of these studies estimated nuclear genome size in picograms per haploid genome (C-values) and recombination rates based on observable chiasma from pachytene chromosomes. (biomedcentral.com)
- Differences in molecular evolution can be related to different transmission and recombination patterns, as well as to differences in effective population sizes of essential and dispensable chromosomes. (prolekare.cz)
- Recombination in this genome appears to underlie a number of important phenomena. (springer.com)
- The first step of the Human Genome Project took place when Tjio and Levan, in 1956, reported the accurate diploid number of human chromosomes as 2n = 46. (wikipedia.org)
- Here, I highlight several outlandish features of the human genome that defy notions of ID by a caring cognitive agent. (nap.edu)
- These range from de novo mutational glitches that collectively kill or maim countless individuals (including embryos and fetuses) to pervasive architectural flaws (including pseudogenes, parasitic mobile elements, and needlessly baroque regulatory pathways) that are endogenous in every human genome. (nap.edu)
- Finally, using comparative phylogenetic methods, we found that while diet specificity did not predict patterns of conotoxin evolution, dietary breadth was positively correlated with total conotoxin gene diversity. (ovid.com)
- B ) Phylogenetic tree constructed using TPSs from 55 plant genomes together with fungal and bacterial TPSs. (nih.gov)
- In addition, no-root phylogenetic tree of the 622 SARS-CoV-2 genomes were constructed by maximum likelihood (ML) with the bootstrap value of 100. (cdc.gov)
- According to the phylogenetic trees, all genomes were divided into Cluster 1 to 3, in which genomes were mainly from North America, global and Europe respectively. (cdc.gov)
- We measured DNA content in subgenus Melanocrommyum using flow cytometry based on propidium iodide staining and analyzed the evolution of genome size in a phylogenetic context. (bioone.org)
- These comparative-genome marker (CGM) SNPs represent a distinct class of phylogenetic markers that has unique advantages. (asm.org)
- In some respects, it is premature to discuss the evolution of plant genomes, because the pending completion of the Arabidopsis ( Arabidopsis thaliana ) genome, with rice ( Oryza sativa ) following, is sure to unlock many mysteries about plant genome evolution. (pnas.org)
- A diploid with 12 chromosomes (2 n = 24), rice has one of the smallest plant genomes, with only 0.9 pg of DNA per 2C nucleus (Fig. 1 ). (pnas.org)
- We research crop plants and farm animals, studying their evolution and organization at the DNA to genome levels: large-scale processes with chromosomes, polyploidy and DNA sequence. (le.ac.uk)
- Expanding understanding of gene and genome organization has revealed the profound extent of their impact on both. (wiley.com)
- The organization of the mitochondrial genome of yeast and these recombinational events are discussed in relationship with the organization and evolution of the nuclear genome of eukaryotes. (springer.com)
- The Challenge of the New Cytochemistry : Highlighting the Obscure Meaning of Genome Composition-Organization. (nii.ac.jp)
- His research group aims to gain a detailed understanding of how regulation is achieved at distinct levels of organization in cellular systems with the ultimate objective of deriving general principles of living systems at a molecular level. (rsc.org)
- Specifically, his group investigates regulation at three levels of organization: molecules, processes and genomes. (rsc.org)
- The aim of our researches is to explore and understand the role of transposable elements in the recent evolution of Homo, as well as their functional and biomedical implications. (bioanthropologybologna.eu)
- Plant Transposons and Genome Dynamics in Evolution captures and distills the voluminous research literature on plant transposable elements and seeks to assemble the big picture of how transposons shape gene structure and regulation, as well as how they sculpt genomes in evolution. (wiley.com)
- Combined with duplication and adaptive evolution, domain shuffling is responsible for the great phenotypic complexity of higher eukaryotes. (elsevier.com)
- One group of molecular motors is called the myosins, which have recently been studied in everything from one-celled eukaryotes to humans. (icr.org)
- The main problem with this idea is that, not only does no such creature exist, but eukaryotes also contain molecular similarities to both bacteria and archaea-prokaryotes that are found in completely separate domains of cellular life. (icr.org)
- Another major problem is that many complex molecular and cellular features unique among eukaryotes are not found in any prokaryotes. (icr.org)
- The genome sizes of thousands of eukaryotes have been analyzed over the past 50 years, and these data are available in online databases for animals, plants, and fungi (see external links). (wikipedia.org)
- Nuclear genome size is typically measured in eukaryotes using either densitometric measurements of Feulgen-stained nuclei (previously using specialized densitometers, now more commonly using computerized image analysis) or flow cytometry. (wikipedia.org)
- The nonlinear correlation for eukaryotes, although claim of its existence contrasts the previous view that no correlation exists for this group of organisms, reflects disproportionately fast increasing noncoding DNA in increasingly large eukaryotic genomes. (wikipedia.org)
- How these processes may impact the dynamics of gene evolution was studied by comparing the patterns of gene structure changes, alternative splicing ( AS ), and codon substitution rates among wheat and model grass genomes. (plantphysiol.org)
- Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. (nature.com)
- From single-cell analysis to whole-genome sequencing, this year's best new products shine on many levels. (the-scientist.com)
- Recent work emphasizes new ways to quantitatively map the inputs and outputs of gene networks in a genome-wide manner using "next generation" ultra-high throughput DNA sequencing, and applying these methods to muscle and brain networks. (hudsonalpha.org)
- We are using PacBio whole-genome sequencing and deep population resequencing to explore the evolution of a novel biochemical pathway in yeast over several thousand generations. (blogspot.com)
- Populations at seven key time points during their evolution have been sequenced using Illumina short-read sequencing. (blogspot.com)
- In addition, all the parental strains from the founding population have been subject to PacBio de novo whole-genome sequencing and assembly. (blogspot.com)
- Technological innovation now enables the sequencing and assembly of large genomes, bridging the gap between models and crops for quantitative trait analysis and genome-wide breeding approaches. (nature.com)
- The genome of S1 was obtained by Illumina sequencing resulting in a 35 Mb draft genome sequence of 32X. (prolekare.cz)
- We investigated the mutational spectra of metastatic clear cell renal cell carcinoma (ccRCC) at baseline and compared them to those upon clonal evolution at progression on systemic therapy with tyrosine kinase inhibitors.Outcome Measurements:DNA was isolated from tumor tissues after surgery, metastasis biopsies after progression on sunitinib or axitinib, and subjected to whole-exome sequencing (WES). (ega-archive.org)
- Comparative full-genome sequencing of bacteria is a powerful method to detect sequence diversity. (asm.org)
- Comparative full-genome sequencing has uncovered large numbers of synonymous SNPs and other sequence polymorphisms ( 6 , 24 ). (asm.org)
- 2011. Genome Sequencing and Assembly. (umass.edu)
- In prokaryotes, pulsed field gel electrophoresis and complete genome sequencing are the predominant methods of genome size determination. (wikipedia.org)
- Although sequenced genome data are practically biased toward small genomes, which may compromise the accuracy of the empirically derived correlation, and the ultimate proof of the correlation remains to be obtained by sequencing some of the largest eukaryotic genomes, current data do not seem to rule out a correlation. (wikipedia.org)
- The MBL provides access to state-of-the-art instrumentation, innovative imaging technology, genome sequencing, model marine and freshwater organisms, and modern laboratory facilities. (mbl.edu)
- Most DNA in an individual genome is found in chromosomes but DNA found outside the nucleus also serves important biological functions. (wikipedia.org)
- As a diploid with 10 chromosomes (2 n = 20) and a 2C genome content roughly 6-fold larger than rice, maize lies somewhere in the middle of grass genome size and structural complexity (Fig. 1 ). (pnas.org)
Completely sequenced genomes1
- Compositional heterogeneity and patterns of molecular evolution in the Drosophila genome. (genetics.org)
- The D. simulans and D. yakuba genomes mark the third and fourth sequenced Drosophila genomes - the second being the more distantly related D. pseudoobscura . (scienceblogs.com)
- If you're curious as to how long it takes to go from the initial proposal to the published sequence of a genome, check out the white papers proposing various Drosophila genome projects . (scienceblogs.com)
- 2000. The Genome Sequence of Drosophila melanogaster . (scienceblogs.com)
- Dr. Nickerson is a Professor of Genome Sciences at the University of Washington (UW), who, for two decades, has pioneered the development of new methods and tools that have been widely adopted for the identification and genotyping of human sequence variation, including single nucleotide variations (SNVs), insertion-deletions (indels) and copy number variations (CNVs). (hudsonalpha.org)
- Thus, the cytological, ecological, and physiological factors often correlated with genome size should have negligible effect on genome size variation in Melanocrommyum . (bioone.org)
- For reasons of conceptual clarification, the various puzzles that remain with regard to genome size variation instead have been suggested by one author to more accurately comprise a puzzle or an enigma (the C-value enigma). (wikipedia.org)
- The linear plasmids with a covalently attached protein may assist with bacterial conjugation and integration of the plasmids into the genome. (wikipedia.org)
- Mitochondria and chloroplasts are eukaryotic organelles that evolved from bacterial ancestors and harbor their own genomes. (springer.com)
- In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. (mdpi.com)
- Particularly relevant in this respect are the studies on the evolution of bacterial pathogens that produce long-lasting chronic infections. (mdpi.com)
- Microscopy, image processing, bioinformatics, in situ hybridization, molecular (epi)genetics and systems biology lets us explore and exploit fundamental processes. (le.ac.uk)
- Announcement and Call for Application to the EMBO practical Course on 'Bioinformatics and Comparative Genome Analysis' ( http://cwp.embo.org/pc11-09/index.html ) that will take place in the Institut Pasteur Paris, France, June 27 July 9, 2011. (bio.net)
- The course will focus on reviews on advanced fundamental algorithms and methods used in Bioinformatics and their applications in genome studies. (bio.net)
- The topics that will be included in the course programme are similar to those included in previously organized courses: http:// www.pasteur.fr/~tekaia/BGA_courses.html The course is aimed at motivated Ph.D students and Post-Doctoral Researchers in Academic Institutions, with background in Mathematics, Statistics, Biology or Computer Science and who are involved in Bioinformatics and Genomes studies. (bio.net)
- Our results suggest that, while some domesticated lineages may have undergone changes to selective regime or effective population size that could have affected mitochondrial evolution, it is not possible to generalise these patterns over all domesticated mammals and birds. (datadryad.org)
- During Pisum evolution, translocation and transposition differentially occurred across lineages. (nature.com)
- Estimation of ancestral genome sizes using generalized least squares revealed lineages with increasing as well as decreasing DNA content. (bioone.org)
- Some striking examples of trends in organelle evolution explored here are the reduction in genome size and gene coding content observed in most lineages, the complete loss of organelle DNA in certain lineages, and the unusual modes of gene expression that have emerged, such as the extensive and essential mRNA editing that occurs in plant mitochondria and chloroplasts. (springer.com)
- Another 2017 publication considers the role of polyploidy or whole genome duplication in ecology and evolution . (le.ac.uk)
- The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root of the teleost lineage about 350 million years ago (Mya) and more recent WGD events in salmonids, carps, suckers and others. (nih.gov)
- There are still unanswered questions about repetitive DNA, including the distribution of repetitive DNA throughout the genome, the relative impacts of retrotransposons and chromosomal duplication in plant genome evolution, and the hypothesized correlation of duplication events with transposition. (pnas.org)
- This paper focuses on the impact of chromosomal duplication, transposition, and nucleotide substitution on the evolution of the maize genome. (pnas.org)
- By the early 1970s, "genome size" was in common usage with its present definition, probably as a result of its inclusion in Susumu Ohno's influential book Evolution by Gene Duplication, published in 1970. (wikipedia.org)
- Our key methods for in situ hybridization are given at this website with more information about methods for molecular cytogenetics and in situ hybridization as well as some other methods used in our laboratory. (le.ac.uk)
- Media and public understanding from the Molecular Cytogenetics group, University of Leicester. (molcyt.org)
- The Molecular Cytogenetics Group is in the University of Leicester, UK. (molcyt.org)
- Computational Genome Analysis of Proteins and. (hhmi.org)
- They investigate wood-consuming marine organisms to determine which proteins are produced during the digestive process (with Matt Guille of the Epigenetics and Development Group), to define enzyme characteristics (with John McGeehan of Molecular Biophysics Group) and to build up a whole-genome from one of the borers. (port.ac.uk)
- At the molecular level, they aim to discover novel features of regulatory and signalling proteins such as G protein-coupled receptors. (rsc.org)
- In particular, they approach tree-of-life questions concerning microbial life using whole genome information. (amnh.org)
- In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation. (mdpi.com)
- From environmental microbiology to microbial evolution, find out how biotechnology is fundamental to solving disease-related problems and providing food, fuel and medicines. (york.ac.uk)
- Our Biotechnology and Microbiology course examines how microorganisms can be used to produce improved therapeutic drugs, and why an understanding of microbial evolution is important for controlling pathogens. (york.ac.uk)
- We use these data to quantify the relationship between sequence and functional divergence, and to identify CpG deamination as a potentially important force in driving changes in enhancer activity during primate evolution. (biomedcentral.com)
- The authors compared polymorphism in D. simulans with divergence from D. melanogaster ( already sequenced ), and used the D. yakuba genome sequence to polarize the differences along either the D. simulans lineage or the D. melanogaster lineage. (scienceblogs.com)
- A comparison of these orthologous regions indicates modes and patterns of sequence divergence, with implications for the overall Triticeae genome structure and evolution. (unboundmedicine.com)
- The intergenic regions of the two loci are composed of different patterns and classes of retrotransposons, indicating that insertion times of these retroelements were after the divergence of the two wheat genomes. (unboundmedicine.com)
University of Leices2
- Cellular and Molecular Life Sciences , 64 (5), 542-554. (elsevier.com)
- We argue that the importance of the cis-regulatory genome for the interpretation of cellular communication pathways cannot be overstated and understanding its role in health and disease will be critical for the future development of personalised medicine. (cambridge.org)
- Clearly, the only scientific model that predicts this type of molecular and cellular complexity and innovation across all forms of life is one associated with special creation. (icr.org)
- We conclude that asymmetries in molecular composition and sensitivity to cellular factors of each contributing hemichannel can profoundly influence the transmission of electrical signals, endowing electrical synapses with more complex functional properties. (frontiersin.org)
Regions of the genome1
- The rates and patterns of molecular evolution in many eukaryotic organisms have been shown to be influenced by the compartmentalization of their genomes into fractions of distinct base composition and mutational properties. (genetics.org)
- Studies of domesticated animals have led to the suggestion that domestication could have significant effects on patterns of molecular evolution. (datadryad.org)
- These results are important because they imply that changes to selection or population size operating over a short timescale can cause significant changes to the patterns of mitochondrial molecular evolution. (datadryad.org)
- The development trends in chronological order and Ka/Ks ratio of each major haplotype subgroup showed the four major haplotype subgroups were going through different evolution patterns, the H3 haplotype subgroup was going through a purifying evolution and almost disappeared after detection, while H1 haplotype subgroup was going through a neutral evolution and globally increased with time. (cdc.gov)
- Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. (ox.ac.uk)
- A wide range of genomes are considered including those of bacteria, yeast, insects and humans. (le.ac.uk)
- Results showed that the gar lineage diverged from teleosts before the TGD and its genome is organized more similarly to that of humans than teleosts. (genetics.org)
- That's well under way in humans, with HapMap and various other projects designed to generate DNA polymorphism data on a genome-wide scale. (scienceblogs.com)
- The approach introduced here appears to be a better approximation to actual biological evolution than models based upon the application of mutation from uniform probability distributions, and because evolution by algorithmic probability converges faster to regular structures (both artificial and natural, as tested on a small biological network), it also approaches a formal version of open-ended evolution based on previous results. (scoop.it)
- Comparative chromosome painting and related techniques are very powerful approaches in comparative genome studies. (wikipedia.org)
- We employ molecular, biochemical and physiological approaches to address these issues in crustaceans, insects, fish and mammals. (lsu.edu)
- The analysis of the coding capacity of the CIV genome revealed that 50% (234 ORFs) of all identified ORFs (468 ORFs) were non-overlapping. (springer.com)
- By explaining the fundamental concepts of population genetics, which is essential to understanding molecular evolution, Graur gives his readers the necessary tools for a critical analysis of the different topics covered by his volume. (oup.com)
- Data and analysis files for Domestication and the Mitochondrial Genome, Moray et al. (datadryad.org)
- Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. (ox.ac.uk)
- In the evolution analysis of 622 or 3624 complete SARS-CoV-2 genomes, the estimated Ka/Ks ratio is 1.008 or 1.094, which is higher than that of SARS-CoV and MERS-CoV, and the time to the most recent common ancestor (tMRCA) is inferred in late September 2019, indicating that SARS-CoV-2 may have completed positive selection pressure of the cross-host evolution in the early stage. (cdc.gov)
- Researchers have studied the role of enhancers in evolution through two main methods: high-resolution, systematic analysis of single enhancers, or low-resolution, genome-wide analysis of many enhancers. (biomedcentral.com)
- Comparative genome analysis provides insights into the evolution and adaptation of Pseudomonas syringae pv. (forestry.gov.uk)
- Comparative analysis of a fish genome occupying a lineage that diverged from teleosts shortly before the TGD would test whether chromosome rearrangements detected in teleosts arose before or after the TGD. (genetics.org)
- These maps also provide an unprecedented opportunity to use multispecies analysis as a tool to infer karyotype evolution. (wikipedia.org)
- Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness. (frontiersin.org)
- Along with the studies on experimental evolution, the analysis on the in vivo evolution of microorganisms provides relevant information for understanding general aspects of the theory of evolution. (mdpi.com)
- Foundationally, EGS research involves an understanding of how evolution shapes organisms and generates biodiversity, and has a strong emphasis on examination of specimens. (auburn.edu)
- In diploid organisms, genome size is used interchangeably with the term C-value. (wikipedia.org)
- The classical theory of evolution is mainly based on the study of multicellular organisms. (mdpi.com)
- On the other hand, whereas experimental evolution studies are not easily achievable for multicellular organisms [ 1 ], due to the extensive time lapse required, these studies can be performed on microorganisms, which can present very large population sizes and extremely short generation times. (mdpi.com)
- 100× coverage) and used these data to provide new insights into conotoxin evolution. (ovid.com)
- Insights into hominid evolution from the gorilla genome sequence. (ox.ac.uk)
- In contrast, high-resolution studies can provide clear insights into the evolution of individual enhancers, but the findings may not be broadly generalizable. (biomedcentral.com)
- insights into genome evolution and inter- and intra-specific diversification. (umass.edu)
- Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. (ox.ac.uk)
- Once the amount of heterochomatin is subtracted from total genome content, all mammals have very similar genome sizes. (wikipedia.org)