Genome Size: The amount of DNA (or RNA) in one copy of a genome.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Cell Nucleus Size: The quantity of volume or surface area of a CELL NUCLEUS.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Ischemic Preconditioning, Myocardial: Exposure of myocardial tissue to brief, repeated periods of vascular occlusion in order to render the myocardium resistant to the deleterious effects of ISCHEMIA or REPERFUSION. The period of pre-exposure and the number of times the tissue is exposed to ischemia and reperfusion vary, the average being 3 to 5 minutes.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.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Polyploidy: The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.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.Particle Size: Relating to the size of solids.Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.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.Body Size: The physical measurements of a body.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Cell Size: The quantity of volume or surface area of CELLS.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Myocardial Reperfusion Injury: Damage to the MYOCARDIUM resulting from MYOCARDIAL REPERFUSION (restoration of blood flow to ischemic areas of the HEART.) Reperfusion takes place when there is spontaneous thrombolysis, THROMBOLYTIC THERAPY, collateral flow from other coronary vascular beds, or reversal of vasospasm.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Genetic Variation: Genotypic differences observed among individuals in a population.Genome, Insect: The genetic complement of an insect (INSECTS) as represented in its DNA.Myocardial Infarction: NECROSIS of the MYOCARDIUM caused by an obstruction of the blood supply to the heart (CORONARY CIRCULATION).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.Festuca: A plant genus of the family POACEAE. The common name of fescue is also used with some other grasses.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.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Cardiotonic Agents: Agents that have a strengthening effect on the heart or that can increase cardiac output. They may be CARDIAC GLYCOSIDES; SYMPATHOMIMETICS; or other drugs. They are used after MYOCARDIAL INFARCT; CARDIAC SURGICAL PROCEDURES; in SHOCK; or in congestive heart failure (HEART FAILURE).Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.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.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.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.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.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.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.Phalaris: A plant genus of the family POACEAE.Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.Portulacaceae: A plant family of the order Caryophyllales, subclass Caryophyllidae, class Magnoliopsida. There are no true petals; each flower has two to six sepals. They produce betacyanin and betaxanthin pigments and lack anthocyanins.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.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).Genome, Protozoan: The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Carex Plant: A plant genus of the family CYPERACEAE. The seed contains oligostilbenes (STILBENES).Gene Order: The sequential location of genes on a chromosome.Propidium: Quaternary ammonium analog of ethidium; an intercalating dye with a specific affinity to certain forms of DNA and, used as diiodide, to separate them in density gradients; also forms fluorescent complexes with cholinesterase which it inhibits.Genome, Helminth: The genetic complement of a helminth (HELMINTHS) as represented in its DNA.Drosophilidae: A family of the order DIPTERA. These flies are generally found around decaying vegetation and fruit. Several species, because of their short life span, giant salivary gland chromosomes, and ease of culturing, have been used extensively in studies of heredity.Myocardium: The muscle tissue of the HEART. It is composed of striated, involuntary muscle cells (MYOCYTES, CARDIAC) connected to form the contractile pump to generate blood flow.Ploidies: The degree of replication of the chromosome set in the karyotype.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).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.Time Factors: Elements of limited time intervals, contributing to particular results or situations.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.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.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.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).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)Asteraceae: A large plant family of the order Asterales, subclass Asteridae, class Magnoliopsida. The family is also known as Compositae. Flower petals are joined near the base and stamens alternate with the corolla lobes. The common name of "daisy" refers to several genera of this family including Aster; CHRYSANTHEMUM; RUDBECKIA; TANACETUM.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.Treatment Outcome: Evaluation undertaken to assess the results or consequences of management and procedures used in combating disease in order to determine the efficacy, effectiveness, safety, and practicability of these interventions in individual cases or series.Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.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.Hemodynamics: The movement and the forces involved in the movement of the blood through the CARDIOVASCULAR SYSTEM.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)Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.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.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.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.Nucleic Acid Renaturation: The reformation of all, or part of, the native conformation of a nucleic acid molecule after the molecule has undergone denaturation.Eleocharis: A plant genus of the family CYPERACEAE.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.Orchidaceae: A plant family of the order Orchidales, subclass Liliidae, class Liliopsida (monocotyledons). All orchids have the same bilaterally symmetrical flower structure, with three sepals, but the flowers vary greatly in color and shape.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Anthocerotophyta: A plant division that includes hornworts, named for the horn-like appearance of the spore-producing plant (sporophyte).Allium: A genus of the plant family Liliaceae (sometimes classified as Alliaceae) in the order Liliales. Many produce pungent, often bacteriostatic and physiologically active compounds and are used as VEGETABLES; CONDIMENTS; and medicament, the latter in traditional medicine.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.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.Coffea: A plant genus of the family RUBIACEAE. It is best known for the COFFEE beverage prepared from the beans (SEEDS).Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Brassicaceae: A plant family of the order Capparales, subclass Dilleniidae, class Magnoliopsida. They are mostly herbaceous plants with peppery-flavored leaves, due to gluconapin (GLUCOSINOLATES) and its hydrolysis product butenylisotrhiocyanate. The family includes many plants of economic importance that have been extensively altered and domesticated by humans. Flowers have 4 petals. Podlike fruits contain a number of seeds. Cress is a general term used for many in the Brassicacea family. Rockcress is usually ARABIS; Bittercress is usually CARDAMINE; Yellowcress is usually RORIPPA; Pennycress is usually THLASPI; Watercress refers to NASTURTIUM; or RORIPPA or TROPAEOLUM; Gardencress refers to LEPIDIUM; Indiancress refers to TROPAEOLUM.Nymphaea: A plant genus of the family NYMPHAEACEAE. The common name of lotus is also used for LOTUS and NELUMBO.Reptiles: Cold-blooded, air-breathing VERTEBRATES belonging to the class Reptilia, usually covered with external scales or bony plates.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.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.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.Genes, Plant: The functional hereditary units of PLANTS.Genes, Bacterial: The functional hereditary units of BACTERIA.Spiroplasma: A genus of gram-negative, helical bacteria, in the family SPIROPLASMATACEAE, order Entomoplasmatales, causing disease in PLANTS. It has been isolated from TICKS; INSECTS; and PLANTS.Symbiosis: 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.Diploidy: The chromosomal constitution of cells, in which each type of CHROMOSOME is represented twice. Symbol: 2N or 2X.Genome, Plastid: The genetic complement of PLASTIDS as represented in their DNA.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.Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.Anethum graveolens: Anethum graveolens L. is a plant species of the family APIACEAE. The leaves are considered as a spice (SPICES).Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)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.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.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)Eukaryotic Cells: Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.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)Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.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.Human Genome Project: A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.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).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).Haploidy: The chromosomal constitution of cells, in which each type of CHROMOSOME is represented once. Symbol: N.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.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.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.Hybridization, Genetic: The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.DNA, Algal: Deoxyribonucleic acid that makes up the genetic material of algae.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.Vertebrates: Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.Mice, Inbred C57BLMutation 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.Genes, Viral: The functional hereditary units of VIRUSES.Adaptation, Biological: Changes in biological features that help an organism cope with its ENVIRONMENT. These changes include physiological (ADAPTATION, PHYSIOLOGICAL), phenotypic and genetic changes.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Takifugu: A genus of pufferfish commonly used for research.Geography: The science dealing with the earth and its life, especially the description of land, sea, and air and the distribution of plant and animal life, including humanity and human industries with reference to the mutual relations of these elements. (From Webster, 3d ed)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.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.Rats, Sprague-Dawley: A strain of albino rat used widely for experimental purposes because of its calmness and ease of handling. It was developed by the Sprague-Dawley Animal Company.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.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Viral Proteins: Proteins found in any species of virus.Acholeplasma: A genus of gram-negative organisms including saprophytic and parasitic or pathogenic species.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.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.Bryophyta: A division of the plant kingdom. Bryophyta contains the subdivision, Musci, which contains the classes: Andreaeopsida, BRYOPSIDA, and SPHAGNOPSIDA.Software: Sequential operating programs and data which instruct the functioning of a digital computer.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.Bacteriophages: Viruses whose hosts are bacterial cells.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.Flow Cytometry: Technique using an instrument system for making, processing, and displaying one or more measurements on individual cells obtained from a cell suspension. Cells are usually stained with one or more fluorescent dyes specific to cell components of interest, e.g., DNA, and fluorescence of each cell is measured as it rapidly transverses the excitation beam (laser or mercury arc lamp). Fluorescence provides a quantitative measure of various biochemical and biophysical properties of the cell, as well as a basis for cell sorting. Other measurable optical parameters include light absorption and light scattering, the latter being applicable to the measurement of cell size, shape, density, granularity, and stain uptake.Veronica: A plant genus of the family Plantaginaceae. Members contain bis-sesquiterpene and iridoid glucosides.Mammals: Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.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.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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Electrophoresis, Gel, Pulsed-Field: Gel electrophoresis in which the direction of the electric field is changed periodically. This technique is similar to other electrophoretic methods normally used to separate double-stranded DNA molecules ranging in size up to tens of thousands of base-pairs. However, by alternating the electric field direction one is able to separate DNA molecules up to several million base-pairs in length.Embryophyta: Higher plants that live primarily in terrestrial habitats, although some are secondarily aquatic. Most obtain their energy from PHOTOSYNTHESIS. They comprise the vascular and non-vascular plants.Gymnosperms: Gymnosperms are a group of vascular plants whose seeds are not enclosed by a ripened ovary (fruit), in contrast to ANGIOSPERMS whose seeds are surrounded by an ovary wall. The seeds of many gymnosperms (literally, "naked seed") are borne in cones and are not visible. Taxonomists now recognize four distinct divisions of extant gymnospermous plants (CONIFEROPHYTA; CYCADOPHYTA; GINKGOPHYTA; and GNETOPHYTA).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.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Bacterial Proteins: Proteins found in any species of bacterium.Myoviridae: A family of BACTERIOPHAGES and ARCHAEAL VIRUSES which are characterized by complex contractile tails.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.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.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.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).Genetic Drift: The fluctuation of the ALLELE FREQUENCY from one generation to the next.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.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.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.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.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.Fossils: Remains, impressions, or traces of animals or plants of past geological times which have been preserved in the earth's crust.Pinus: A plant genus in the family PINACEAE, order Pinales, class Pinopsida, division Coniferophyta. They are evergreen trees mainly in temperate climates.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.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Mycoplasma: A genus of gram-negative, mostly facultatively anaerobic bacteria in the family MYCOPLASMATACEAE. The cells are bounded by a PLASMA MEMBRANE and lack a true CELL WALL. Its organisms are pathogens found on the MUCOUS MEMBRANES of humans, ANIMALS, and BIRDS.Cirsium: A plant genus of the family ASTERACEAE. Members contain pectolinarin (a flavonoid glycoside).Dianthus: A plant genus of the family CARYOPHYLLACEAE. Members contain dianthins, which are ribosome inactivating proteins.Seeds: The encapsulated embryos of flowering plants. They are used as is or for animal feed because of the high content of concentrated nutrients like starches, proteins, and fats. Rapeseed, cottonseed, and sunflower seed are also produced for the oils (fats) they yield.Gossypium: A plant genus of the family MALVACEAE. It is the source of COTTON FIBER; COTTONSEED OIL, which is used for cooking, and GOSSYPOL. The economically important cotton crop is a major user of agricultural PESTICIDES.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).Deoxyribonucleases, Type II Site-Specific: Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 126.96.36.199.Siphoviridae: A family of BACTERIOPHAGES and ARCHAEAL VIRUSES which are characterized by long, non-contractile tails.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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Metagenomics: The genomic analysis of assemblages of organisms.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.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.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.Alligators and Crocodiles: Large, long-tailed reptiles, including caimans, of the order Loricata.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.RNA, Transfer: The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.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).Rotifera: A class of minute animals of the phylum Aschelminthes.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.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.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.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.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.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.Virus Replication: The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.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.Electrophoresis, Agar Gel: Electrophoresis in which agar or agarose gel is used as the diffusion medium.DNA Replication: The process by which a DNA molecule is duplicated.Chromosome Painting: A technique for visualizing CHROMOSOME ABERRATIONS using fluorescently labeled DNA probes which are hybridized to chromosomal DNA. Multiple fluorochromes may be attached to the probes. Upon hybridization, this produces a multicolored, or painted, effect with a unique color at each site of hybridization. This technique may also be used to identify cross-species homology by labeling probes from one species for hybridization with chromosomes from another species.RNA Viruses: Viruses whose genetic material is RNA.Karyotyping: Mapping of the KARYOTYPE of a cell.
Those researchers think that "the prolonged pressure of genome and particle size reduction eventually reduced virocells into ... In 2016, a set of 355 genes likely present in the Last Universal Common Ancestor (LUCA) of all organisms living on Earth was ... Coughlan, Andy (2016) "Smallest ever genome comes to life: Humans built it but we don't know what a third of its genes actually ... The data suggest that viruses originated from ancient cells that co-existed with the ancestors of modern cells. These ancient ...
Genome reduction, also known as Genome degradation, is the process by which a genome shrinks relative to its ancestor. Genomes ... which has allowed for an increase in genome size. Comparison of different genome sizes Animal Genome Size Database Cell nucleus ... genome size reduction is most significant in bacteria. The most evolutionary significant cases of genome reduction may be the ... Animal Genome Size Database Plant DNA C-values Database Fungal Genome Size Database Fungal Database - by CBS. ...
... it was shown that bacterial genome size reduction increased in rate by as much as 50 times. These results indicate that genome ... Molecular phylogenetics has revealed that every clade of bacteria with genome sizes under 2 Mb was derived from ancestors with ... there is relatively little variation in genome size when compared with the genome sizes of other major groups of life. Genome ... the strong correlation between the number of genes and the genome size makes the size of bacterial genomes an interesting topic ...
Genomes fluctuate in size regularly, and genome size reduction is most significant in bacteria. ... also known as genome degradation, is the process by which an organism's genome shrinks relative to that of its ancestors. ... Genome reductionEdit. Genome size compared to number of genes. Log-log plot of the total number of annotated proteins in ... reflect genome size". In this context, "genome size" was being used in the sense of genotype to mean the number of genes. ...
... of conserving energy or conserving phosphorus have been suggested to be operative in the reduction of the nuclear genome size ... Utricularia gibba and the tomato split from a common ancestor approximately 87 million years ago. Since that time, both plants ... Despite its size, the genome accommodates 28,500 genes - more than plants with much larger genomes. The main difference between ... T. Ryan Gregory who studies the evolution of genome sizes said "The study further challenges simplistic accounts of genome ...
Genomic evolution of birds
It is known that similar reductions have also taken place in bats. This fact suggests that genome-size reduction could give ... It is thought that the common ancestor of birds already lacked mineralized teeth, and that later genome changes pushed the ... Another example of genome reduction in birds is that of short interspersed nuclear elements (SINEs). Their total size has been ... Whereas mammal and reptilian genomes range between 1.0 and 8.2 giga base pairs (Gb), bird genomes have sizes between 0.91 Gb ( ...
... has undergone a dramatic reduction in genome size with the loss of many genes. This genome reduction is ... There is evidence that many of the genes that were present in the genome of the common ancestor of M. leprae and M. ... The first genome sequence of a strain of M. leprae, was completed in 1998. The genome sequence of a strain originally isolated ... Downsizing from a genome of 4.42 Mbp, such as that of M. tuberculosis, to one of 3.27 Mbp would account for the loss of some ...
Reduction in genome size, %GC and coding density and genes are generally attributed to genetic drift and Muller's ratchet. ... 2011). "Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade". Sci Rep. 1: 13. doi:10.1038/srep00013 ... Genetic drift is enhanced in Rickettsiales genomes due to low population sizes (given their endosymbiotic nature) and frequent ... Viklund J, Ettema TJ, Andersson SG (2012). "Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 ...
Hologenome theory of evolution
"Extreme genome reduction in Buchnera spp.: Toward the minimal genome needed for symbiotic life". Proc. Natl. Acad. Sci. USA. 99 ... it has been discovered that genome size in various Buchnera species has become extremely reduced, in some cases down to 450 kb ... Inheritance of acquired traits - individuals inherit the traits of their ancestors. Although Lamarckian theory was rejected by ... the genome of the host can act in consortium with the genomes of the associated symbiotic microorganisms to create a hologenome ...
... last universal cellular ancestor' that gave rise to modern cells. Evolutionary pressure to reduce genome and particle size may ... Reduction hypothesis: This idea states that viruses may have once been small cells that parasitized larger cells. This is also ... However, the genomes of many organisms contain endogenous viral elements (EVEs). These DNA sequences are the remnants of ... This is supported by the idea that all viral genomes encode for proteins that do not have cellular homologs. The virus-first ...
Bacteriophage experimental evolution
... and because of their small genome sizes, sequencing the full genomes of evolved strains is trivial. Therefore, comparisons can ... Bacteriophages, and microbial organisms, can be frozen in stasis, facilitating comparison of evolved strains to ancestors. ... virulence results either in reduction of bacterial division rates or, more typically, in the death (via lysis) of individual ... large population sizes, and small sizes increase the feasibility of experimental studies in a laboratory context. For these ...
The population size of genotype 1 increased noticeably in the last 30-35 years. Genotypes 3 and 4 population sizes began to ... The virus itself is a small nonenveloped particle.The genome is about 7200 bases in length, is a polyadenylated, single-strand ... The most recent common ancestor of hepatitis E evolved between 536 and 1344 years ago. It diverged into two clades - an ... In individuals with solid-organ transplantation, viral clearance can be achieved by temporal reduction of the level of ...
Human respiratory syncytial virus
The genome of HRSV was completely sequenced in 1997. Bayesian estimates of the mutation rates in the subtype A genomes give a ... The population size has remained constant over the last 70 years and the G protein appears to be the main site of diversifying ... The most recent common ancestor of the currently circulating subgroup B strains was estimated to date back to around the year ... reduction in length of stay: 2.6 ± 1.9 days, compared with 3.5 ± 2.9 days in the normal-saline treated group (p=0.05). ...
... genome encoding thousands of proteins. Plastids and mitochondria exhibit a dramatic reduction in genome size when compared ... "Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor". Molecular Biology and ... having a genome size 3 Mb, with 3300 genes) revealed that chromatophores underwent a drastic genome shrinkage. Chromatophores ... Organellar genomes. Plastomes and mitogenomes. The human mitochondrial genome has retained genes encoding 2 rRNAs, ...
... namely that the number of genes that make up the genome does not correlate with genome size. In other words, the genome size is ... Many species exhibit genome reduction when subsets of their genes are not needed anymore. This typically happens when organisms ... By comparing genomes of both close relatives and distant ancestors the stark differences and similarities between species began ... Genome evolution is the process by which a genome changes in structure (sequence) or size over time. The study of genome ...
Genomics of domestication
In seed or grain crops, these hallmark traits include increases in seed size, a reduction in natural seed dispersal, reduced ... genomes. One of the most prominent publicly funded genome projects was the Human Genome Project which helped to refine existing ... These domesticated species and in some cases, their wild ancestors, have received focus due to their agricultural and economic ... The Potato Genome Sequencing Consortium (July 2011). "Genome sequence and analysis of the tuber crop potato". Nature. 475 (7355 ...
... genome encoding thousands of proteins. Plastids and mitochondria exhibit a dramatic reduction in genome size when compared ... 2008). "Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor". Mol. Biol. ... having a genome size 3 Mb, with 3300 genes) revealed that chromatophores underwent a drastic genome shrinkage. Chromatophores ... Organellar genomes. Plastomes and mitogenomes. The human mitochondrial genome has retained genes encoding 2 rRNAs, ...
It was previously believed that lateral gene transfer was responsible for the severe gene reduction in the Buchnera genome but ... It has been reduced to one-seventh of the size of its closest free-living relative, E. coli. Buchnera has lost genes that would ... Therefore, there was likely one original Buchnera infection of the common ancestor of aphids and co-speciation of the ... The aphid genome is 464MB with aphid-specific orphan genes making up 20% of the genome and gene duplication present in more ...
Evolution of olfaction
Once cetaceans evolved from their terrestrial ancestors, the reduction in their olfactory apparatus was primarily clade- ... The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome research, 18(7), 1100-1111. Mezler, M ... The olfactory genetics of mammals are divergent from the vertebrate lineage when looking at the size of the OR gene family. ... Genome research, 17(2), 166-174. Rowe, T. B., Macrini, T. E., & Luo, Z. X. (2011). Fossil evidence on origin of the mammalian ...
... so this can only be explained by a reduction in the effective population size Ne of species B, which is inferred as an act of ... Kimura noted that there was much too high of a rate of mutation within the genome (i.e. high polymorphism) to be strictly under ... if we know the time since the two species diverged from the common ancestor. A test that suggests neutral evolution: Suppose ... Kimura then postulated that most of the modifications to the genome are neutral or nearly neutral, and evolve by random genetic ...
Human genetic variation
In contrast, populations that have undergone dramatic size reductions or rapid expansions in the past and populations formed by ... tested the hypothesis that contemporary African genomes have signatures of gene flow with archaic human ancestors and found ... Human genome projects are scientific endeavors that determine or study the structure of the human genome. The Human Genome ... Ke, X; Taylor, M. S.; Cardon, L. R. (2008). "Singleton SNPs in the human genome and implications for genome-wide association ...
This reduction creates products toxic to the anaerobic cell, and allows for selective accumulation of the drug in anaerobes. ... However, a hydrogenosomal genome has been detected in the cockroach ciliate Nyctotherus ovalis, and the stramenopile ... The matrix of N. ovalis hydrogenosomes contains ribosome-like particles of the same size as a numerous type of ribosome (70s) ... For example: Which came first: mitochondria, or hydrogenosomes, or some common ancestor? Mitochondria Chloroplast Müller M, ...
Pig cells have been engineered to inactivate all 62 PERVs in the genome using CRISPR Cas9 genome editing technology, and ... First, the sow digs a depression about the size of her body. She then collects twigs, grasses and leaves, and carries these in ... 2005); from google (Çayönü pig ancestor) result 2; 'Çayönü Tepesi' in wiki (Cattle)". Mol Biol Evol. 30: 824-32. doi:10.1093/ ... As part of animal conservation (The Three Rs (animals)), these animals contribute to the reduction methods for animal research ...
Reductions in the size of host populations may cause a long-lasting reduction of louse taxonomic richness, for example, birds ... share a common ancestor with chimpanzee lice, while pubic lice (genus Pthirus) share a common ancestor with gorilla lice. Using ... The body louse has the smallest genome of any known insect; it has been used as a model organism and has been the subject of ... The mitochondrial genome of the human species of body lice (Pediculus humanus humanus), the head louse (Pediculus humanus ...
... will include various viruses likely to share a common ancestor with Mimivirus and Megavirus, although their present genome size ... "Mimivirus shows dramatic genome reduction after intraamoebal culture". Proceedings of the National Academy of Sciences. 108 (25 ... Genome. The Megavirus chilensis genome is a linear, double-stranded molecule of DNA with 1,259,197 base pairs in length. ... First, it indicates that the limit of viral genome sizes has not been found and that even more complex viruses may remain to be ...
Outline of evolution
Biological genomes are structured in ways that make beneficial changes less unlikely than they would otherwise be. Evolution ... Such an event is identified by a sharp reduction in the diversity and abundance of macroscopic life. Also known as a mass ... Molecular phylogenetics Most recent common ancestor - most recent individual from which all organisms in a group are directly ... Natural selection Sexual selection Artificial selection Ecological selection Gene flow Genetic drift Small population size ...
"Codon size reduction as the origin of the triplet genetic code". PLOS ONE. 4 (5): e5708. Bibcode:2009PLoSO...4.5708B. doi: ... The following codon usage table is for the human genome. A The codon AUG both codes for methionine and serves as an initiation ... Yarus, Michael (2010). Life from an RNA World: The Ancestor Within. Harvard University Press. ISBN 978-0-674-05075-4. " ... NCN yields amino acid residues that are small in size and moderate in hydropathy; NAN encodes average size hydrophilic residues ...
The genome was found to contain one 16S-23S-5S rRNA operon and 44 tRNA coding genes. The GC content of the genome is 44%, which ... The size is about .3-.5 microns in width and 2-3 microns in length. Gram staining was done using a Hucker Modification and the ... H. thermophilus also contains the necessary genes for nitrate reduction and assimilation. Hydrogenobacter thermophilus has ... it indicates that the characteristics of the last common ancestor of life were possibly thermophilic and fixed carbon ...
Race and genetics
In The Ancestor's Tale Richard Dawkins devotes a chapter to the subject of race and genetics. Dawkins agreed with Lewontin on ... It is estimated that approximately 0.4 percent of the genomes of unrelated people differ, apart from copy number. When copy- ... Selecting for informative genetic markers allowed a reduction to less than 650, while retaining near-total accuracy. ... and head size and shape. (Measurements of the latter through craniometry were repeatedly discredited in the late 19th and mid- ...
Genome size - Wikipedia
Genome reduction, also known as Genome degradation, is the process by which a genome shrinks relative to its ancestor. Genomes ... which has allowed for an increase in genome size. Comparison of different genome sizes Animal Genome Size Database Cell nucleus ... genome size reduction is most significant in bacteria. The most evolutionary significant cases of genome reduction may be the ... Animal Genome Size Database Plant DNA C-values Database Fungal Genome Size Database Fungal Database - by CBS. ...
Graduate student positions (MS and PhD) in environmental microbiology and molecular biology at Bowling Green State University ...
Mitochondrial genomes of vertebrates are generally thought to evolve under strong selection for size reduction and gene order ... Our results imply that a previously undescribed V1R gene inherited from an ancient Silurian ancestor may have played an ... Moreover, the species can be differentiated on the basis of genome size (GS), genome content, and immune system composition. ... Nonetheless, all the Thermosipho genomes, like other Thermotogae genomes, show evidence of genome streamlining. GS differences ...
Genome size in turtle and crocodile | Biology Letters
These data suggest that a common ancestor of birds, turtles and crocodiles had a small genome size and a chromosomal size- ... It is suggested that the formation of microchromosomes leads to a reduction of genome size . We find that TSC and CNI ... TSC and CNI genome sizes based on the sum of chromosome sizes are close to GGA, but these sizes are smaller than those in the ... 2011 Paleogenomic data suggest mammal-like genome size in the ancestral amniote and derived large genome size in amphibians. J ...
Animal with the Most Genes? A Tiny Crustacean
The genome is made compact by the reduction in size of spaces (introns) between the gene parts that code for proteins. • First ... Only 4.5 percent of genes are shared exclusively between Daphnia and insects, arthropods which shared a common ancestor some ... Daphnias genome is no ordinary genome. "More than one-third of Daphnias genes are undocumented in any other organism -- in ... The genome project signals the coming-of-age of Daphnia as a research tool for investigating the molecular underpinnings of key ...
Robert Davis : USDA ARS
... cell wall-less bacteria that underwent massive reductions in genome size during their evolution from walled bacterial ancestors ... Thus, these unusual microbes possess genomes that are among the smallest known in bacteria, approaching the minimal sets of ... Gene degradation and the loss of biosynthetic pathways that resulted in small genomes and obligate intracellular life styles * ...
Earth Times: show/197430,eu-us-summit-to-take-place-in-slovenia-in-june.html
Flying and genome size: it s true about the reduction!. Posted Tue, 28 Jan 2014 20:03:42 GMT by JW. Dowey ... Xmas comes very early for us this year, with a tremendous guide to all our ancestors and their evolution into modern forms. You ... Salamander polyploid amazes with its genome (s). Posted Fri, 23 Jun 2017 10:56:47 GMT by Dave Armstrong. The polyploids among ... Ancestor of Tyrannosaurus found. Posted Thu, 07 Nov 2013 08:58:59 GMT by Dave Armstrong ...
Genome size - Wikipedia
Genomes fluctuate in size regularly, and genome size reduction is most significant in bacteria. ... also known as genome degradation, is the process by which an organisms genome shrinks relative to that of its ancestors. ... Genome reductionEdit. Genome size compared to number of genes. Log-log plot of the total number of annotated proteins in ... reflect genome size". In this context, "genome size" was being used in the sense of genotype to mean the number of genes. ...
Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of Mollicutes
This is true for bacteria belonging to the class Mollicutes that are characterized by reduced genomes and hence considered as ... is a class of parasitic bacteria that have evolved from a common Firmicutes ancestor mostly by massive genome reduction. With ... compare Figure 2 with genome sizes indicated in Table S1). Indeed, the hemoplasma M. haemofelis genome (1.1 Mbp) is larger than ... The progressive reduction of the size of precursor RNAs (mainly mRNAs and tRNAs) by reducing their 3′ and/or 5′-tails is ...
Abiogenesis - Wikipedia
Those researchers think that "the prolonged pressure of genome and particle size reduction eventually reduced virocells into ... In 2016, a set of 355 genes likely present in the Last Universal Common Ancestor (LUCA) of all organisms living on Earth was ... Coughlan, Andy (2016) "Smallest ever genome comes to life: Humans built it but we dont know what a third of its genes actually ... The data suggest that viruses originated from ancient cells that co-existed with the ancestors of modern cells. These ancient ...
Frontiers | Chromatin organization and cytological features of carnivorous Genlisea species with large genome size differences ...
Genlisea nigrocaulis, with 86 Mbp one of the smallest plant genomes, and the 18-fold larger genome of G. hispidula (1,550 Mbp) ... G. nigrocaulis, with 86 Mbp one of the smallest plant genomes, and the 18-fold larger genome of G. hispidula (1550 Mbp) possess ... Interphase nuclei of G. nigrocaulis and of related species with small genomes, G. aurea (133 Mbp, 2n=104) and G. pygmaea (179 ... Interphase nuclei of G. nigrocaulis and of related species with small genomes, G. aurea (133 Mbp, 2n ≈ 104) and G. pygmaea (179 ...
Animal with the most genes? A tiny crustacean: IU News Room: Indiana University
Daphnia is the first crustacean to have its genome sequenced. Those superlatives are two of many in a Science report this week ... The genome is made compact by the reduction in size of spaces (introns) between the gene parts that code for proteins. ... Only 4.5 percent of genes are shared exclusively between Daphnia and insects, arthropods which shared a common ancestor some ... Daphnias genome is no ordinary genome. "More than one-third of Daphnias genes are undocumented in any other organism -- in ...
Genetic structure and domestication history of the grape | PNAS
Although the reduction of diversity attributable to domestication and breeding appears to be weak on a genome-wide scale [i.e ... haplotype diversity was measured in nonoverlapping sliding windows of varying sizes across the grape genome. Although we ... S2). Moreover, the decay of LD is very rapid in vinifera and appears unchanged between the wild ancestor and the domesticated ... genome-wide association. The grape is the most valuable horticultural crop in the world. The fruit from the worlds ∼8 million ...
Genome Sequencing Highlights the Dynamic Early History of Dogs
To investigate dog origins, we sequence three wolf genomes from the putative centers of origin, two basal dog breeds (Basenji ... largely because no studies thus far have leveraged deeply sequenced whole genomes from wolves and dogs to simultaneously ... interpreted to reflect a relatively weak two-fold reduction in effective population size of dogs relative to their ancestors, ... Ancestral population sizes of dogs and wolves. Genome-wide patterns of heterozygosity provide useful information on long-term ...
Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits
An ancestral character reconstruction suggests that the most recent common ancestor of cyanobacteria had a genome size of ... while a single event of reduction is evident in a clade dominated by unicellular cyanobacteria. Genome sizes and gene family ... The different rates of genome-size evolution and multi-copy gene abundance suggest two routes of genome development in the ... Sequencing efforts have shown that genomes within this phylum are equally diverse in terms of size and protein-coding capacity ...
Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida | BMC Genomics | Full Text
This suggests that there was a genome reduction event in the common ancestor of more recently evolving Wolbachia strains. ... The genome size and gene repertoire of the wFol genome thus represents an exception to the general trend that a strong ... we show that wFol has the largest genome size of all Wolbachia genomes analyzed so far. ... Moreover, size, AT percentage and gene content were highly comparable to C. antarcticus as well as to the mt genome of O. ...
Organelle Genetics - Evolution of Organelle Genomes and | Charles E. Bullerwell | Springer
Mitochondria and chloroplasts are eukaryotic organelles that evolved from bacterial ancestors and harbor their own genomes. The ... Some striking examples of trends in organelle evolution explored here are the reduction in genome size and gene coding content ... Mitochondria and chloroplasts are eukaryotic organelles that evolved from bacterial ancestors and harbor their own genomes. The ... Evolution of Organelle Genomes and Gene Expression. Editors. * Charles E. Bullerwell Copyright. 2012. Publisher. Springer- ...
Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus | G3: Genes | Genomes | Genetics
Further, it is possible that transposon proliferation and genome size increase occurred in the common ancestor of both ... followed by a chromosome fusion or reduction; and another possibility is that repetitive DNA has proliferated to drive the ... The genome sizes of A. aphyllus, A. stipularis, and A. falcatus were estimated by flow cytometry using the known genome size of ... Flow cytometry genome size estimation. The genome sizes of A. officinalis, A. virgatus, and A. asparagoides were estimated by ...
The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss | mBio
Bacterial genome size reduction by experimental evolution. Proc. Natl. Acad. Sci. U. S. A. 102:12112-12116. ... in competition with the ancestor (12). In nature, some free-living bacteria also have reduced genomes, and in these cases large ... Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol. 6:10. ... Economy, speed and size matter: evolutionary forces driving nuclear genome miniaturization and expansion. Ann. Bot. 95:147-175 ...
... in several bacterial lineages that have independently undergone changes in genome size. As genomes degrade, virtually all multi ... the dynamics of gene loss and genome reduction, Genome Res. 2007 Aug;17(8):1178-85. ... Figure 4- Characteristics of Gammaproteobacterial genomes and of the reconstructed ancestor of these species (from Ochman, JEZ ... Bacterial genomes suffer frequent reductions and expansions concomitant with changes in lifestyle. The most thoroughly studied ...
Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of...
Birds have smaller genomes relative to mammals, and the genome-wide frequency and distribution of Numts is still unknown. The ... Because fewer Numts were detected in the chicken nuclear genome, they do not represent all regions of the mitochondrial genome ... genome by the Genome Sequencing Center at Washington University, St. Louis provided an opportunity to search this first avian ... Human and plant genomes harbor a large number of Numts, some of which have high similarity to mitochondrial fragments and thus ...
Giant pandoraviruses create their own genes. | Nature Research Ecology & Evolution Community
Our comparative analysis of 6 strains of the spectacular Pandoraviridae family now suggests that their giant genomes may be ... Giant viruses overlapping in size and genome complexity with unicellular organisms are among the most unexpected discoveries of ... what evolutionary incentives could lead to such gigantic genome sizes, when many viruses are doing extremely well with 100 ... why are these viruses escaping the ubiquitous trends toward genome reduction exhibited by all obligate intracellular parasitic ...
The Plant Genome Abstract - Original Research SNP Discovery via Genomic Reduction, Barcoding, and 454-Pyrosequencing in...
Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of ... Home » Publications » The Plant Genome. The Plant Genome Abstract - Original Research. SNP Discovery via Genomic Reduction, ... Developing molecular tools and insights into the Penstemon genome using genomic reduction and next-generation sequencing BMC ... Single nucleotide polymorphism discovery in cutthroat trout subspecies using genome reduction, barcoding, and 454 pyro- ...
Metabolic flexibility revealed in the genome of the cyst-forming α-1 proteobacterium Rhodospirillum centenum | BMC Genomics |...
R. centenum contains a singular circular chromosome of 4,355,548 base pairs in size harboring 4,105 genes. It has an intact ... Here, we present an analysis of the genome of this bacterium. ... Yet, the nitrate reduction by periplasmic nitrate reductase ( ... Lateral and polar flagellar systems have diverged twice in α-proteobacteria as well as in the common ancestor of β/γ- ... using size fractions of 2-3 kb and 6-8 kb, respectively), and a large insert fosmid library in pEpiFOS-5 (insert sizes ranging ...
"It's Complicated": Untangling the Knots in Dog Domestication - American Kennel...
Freedman and his colleagues discovered that dogs suffered a 16-fold reduction in their population size as they diverged from ... The dog genomes all were more similar to each other than to any of the three wolf genomes. Novembre and his colleagues had to ... "Whats interesting is that it doesnt appear to be an ancestor of modern dogs." Not an ancestor of modern dogs?!? One of my ... After comparing the genomes of modern dogs to these modern wolves, the modern dogs were not more closely related to any of the ...
For First Nations people, effects of European contact are recorded in the genome - Popular Archeology
Further analyses pointed to a steep population decline among the ancestors of modern Coast Tsimshian, a "reduction in effective ... population size of 57 percent," the researchers reported. This dramatic die-off occurred roughly 175 years ago, about the time ... For First Nations people, effects of European contact are recorded in the genome. Tue, Nov 15, 2016 SHARE ON: TwitterFacebook ... The genomes of a majority of the ancient individuals contained alleles, or variants, of the HLA-DQ gene that differed from the ...
Sandwalk: The last molecular evolution exam: Question #3
Endosymbiosis evolved after the original fusion when one of the genomes underwent a reduction in size. The fact that you give ... I expect student to understand that even if Eukaryotic ancestors acquired the bulk of their genome from Eubacteria - the ... which became the nuclear genome. In the beginning, you couldnt tell which genome was going to become the biggest (see b ... With many of the mentioned theories there is reduction of complexity. In my theory the only reduction is when the eukaryote ...
Unraveling the Tree of Life
A third comprehensive tree of life is based on completely sequenced genomes with genome sizes arrayed around the boundary. ... euarchontoglires ancestor; EUT, eutherian ancestor; GAP, great apes ancestor; HUC, human-chimp ancestor; SIM, simian ancestor. ... 2017) A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction Current Biology 27 doi:10.1016/j.cub.2017.10 ... It as been suggested the the even larger klosneuviruses, with genome sizes up to 3 Mb (Schultz et al. 2017) shows they have ...
Viruses are living things that share common ancestry with cells | WIRED UK
They write that the prolonged pressure of genome and particle size reduction eventually reduced virocells into modern viruses ... harboured segmented RNA genomes and coexisted with the ancestors of modern cells. ... and have put forward a case for viruses sharing a common ancestor with all other cells. ...
Quick Glimpse of Viral History | May 25, 2020
... origin from primordial cells and coexistence with cellular ancestors, and (2) prolonged pressure of genome reduction and ... In a recent genome-wide structural phylogenomic analysis, it was shown that large-to-medium-sized viruses coevolved with ... The NCLDVs also possess large genomes. Again, poxvirus genomes often approach 200,000 base pairs, and Mimivirus has a genome of ... These mobile genetic elements make up an astonishing 42% of the human genome and can move within the genome via an RNA ...
Tempo and mode of early gene loss in endosymbiotic bacteria from insects | BMC Evolutionary Biology | Full Text
... size and types of deletions) of gene losses. In this study, we analysed five endosymbiotic genome sequences of the gamma- ... We used a parsimony method to reconstruct a minimal ancestral genome of insect endosymbionts and quantified gene loss along the ... Understanding evolutionary processes that drive genome reduction requires determining the tempo (rate) and the mode ( ... genome reduction in this group has been extreme, yielding a ten fold range of genome sizes; second, free-living relatives of ...
GenomicLarger genomesEukaryotic genomesBacterial genomesMitochondrialHigh-quality genomeBacteriaChromosomesArabidopsisChromosomeSmaller genomesIntracellularAncestralArchaealTerms of genome sizePhylogenyAnalysesHaploid genome sizeAllowed us to reconstructEukaryoteVariationSymbiontsGenetic diversityBiologyTransposablePopulationsPlastid GenomesComparativeDiversityLarge genomesRepetitiveGenes in a genomeDifferencesWhole genome studiesSlow evolviSmallest genome
- Thus, genome-wide association (GWA) ( 6 ) and genomic selection (GS) ( 7 ) are attractive alternatives to traditional linkage mapping in the grape and other long-lived perennial fruit crops. (pnas.org)
- To increase our understanding of genomic changes in the lineage, the genomes of 58 contemporary cyanobacteria were analysed for shared and unique orthologs. (uio.no)
- We report the development of a novel genomic reduction protocol based on restriction-site conservation and multiplex identifiers (MID) barcodes to discover single nucleotide polymorphisms (SNPs) from a pooled amaranth library of four mapping parents. (sciencesocieties.org)
- The reduction of genome size within the Chlamydiae does not correlate with a decrease in genomic G + C content, an effect observed in other bacterial groups, for example, the Gammaproteobacteria (light gray circles). (nih.gov)
- Three genomic islands were identiﬁed in the E. antarcticum B7 genome. (deepdyve.com)
- A reduction in the genomic content of E. antarc- ticum B7 was observed. (deepdyve.com)
- Comparative genomic analysis clearly shows that the last eukaryotic common ancestor (LECA) possessed most of the signature complex features of modern eukaryotic cells, in particular the mitochondria, the endomembrane system including the nucleus, an advanced cytoskeleton and the ubiquitin network. (royalsocietypublishing.org)
- Using genomic data from eight red algal lineages, we identified 155 spliceosomal machinery (SM)-associated genes that were putatively present in the red algal common ancestor. (springer.com)
- The markedly slow evolution of the elephant shark genome and its similarity to the human genome, further underscores its importance as a reference genome for comparative genomic studies aimed at better understanding of the human genome. (technologynetworks.com)
- Not only has our research team sequenced the first shark-family member genome, they have also uncovered many insights significant to the field of genomic and medical research through the genome analysis. (technologynetworks.com)
- The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. (biomedcentral.com)
- Genomic approaches are expected to improve our understanding of how the interaction between genetic drift, mutation, recombination, and natural selection shapes the genome of endangered populations and to contribute to a more effective conservation by facilitating the identification and subsequent management of deleterious variants. (biomedcentral.com)
- This wealth of new genomic data allows us to revisit previous work on archaeal comparative genomics and to better characterise the features and processes of archaeal genome evolution. (emergtoplifesci.org)
- Genomic reconstructions suggest that the last common ancestor of archaea might have been (nearly) as advanced as the modern archaeal hyperthermophiles. (beds.ac.uk)
- Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se. (nih.gov)
- A comparison of turtle genomes with those of chicken, selected nonavian reptiles, and human revealed shared and novel genomic features, such as numerous chromosomal rearrangements. (harvard.edu)
- Reconstructions of the gene set of the shared ancestor of the γ- Proteobacteria provide strong evidence that B. aphidicola genomes are derived from larger genomes through loss of most genes ( 12 , 19 ). (asm.org)
- In other words, all these microbes certainly evolved from ancestors with larger genomes. (biomedcentral.com)
- 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 number of Numts in chicken is low compared to those in human and plant genomes, and is within the range found for most sequenced eukaryotic genomes. (biomedcentral.com)
- Reproductive proteins are often observed to be the most rapidly evolving elements within eukaryotic genomes. (g3journal.org)
- Microsporidian parasites are also model organisms for the study of genome reduction since they possess some of the smallest eukaryotic genomes known to date. (ubc.ca)
- The recent sequencing of a large number of eukaryotic genomes has provides a more accurate understanding of their DNA content and type. (evostudies.org)
- We demonstrated that a simple time lag model provides a general, parsimonious explanation of the extensive variation in the dN / dS ratio seen when comparing closely related bacterial genomes. (pasteur.fr)
- These results provide a common explanatory framework for the data showing that among very closely related bacterial genomes the rate of non-synonymous changes is close to the one of synonymous (Figure 1). (pasteur.fr)
- Reduced bacterial genomes are particularly lacking in genes regulating transcription. (asm.org)
- Mitochondrial genomes of vertebrates are generally thought to evolve under strong selection for size reduction and gene order conservation. (smbe.org)
- Human and plant genomes harbor a large number of Numts , some of which have high similarity to mitochondrial fragments and thus may have been inadvertently included in population genetic and phylogenetic studies using mitochondrial DNA. (biomedcentral.com)
- Because fewer Numts were detected in the chicken nuclear genome, they do not represent all regions of the mitochondrial genome and are not widespread in all chromosomes. (biomedcentral.com)
- One of the reasons why mitochondrial genes would benefit from being located in the nuclear genome is reduction in the accumulation of deleterious mutations. (biomedcentral.com)
- Non-functional nuclear copies or pseudogenes have been termed Numts (pronounced 'new-mights', for NUclear MiTochondrial DNA segments) by Lopez and collaborators [ 5 ], who found tandem-duplicated mitochondrial copies of a 7.9 kilobases (kb) fragment in the nuclear genome of cats. (biomedcentral.com)
- The discovery that mutations in the mitochondrial genome can cause a variety of human diseases has increased our interest in this 'other' human genome. (jrank.org)
- As an aftermath, a quintessential animal mitochondrial genome harbors only 13 genes encoding essential energy pathway proteins, 2 ribosomal RNA genes and 22 transfer RNA genes. (biomedcentral.com)
- 28 Genetics of human origin The greatest contribution of mitochondrial DNA studies to the understanding of Native American prehistory has been in the area of reconstruction of population size history. (yumpu.com)
- The evidence for this is that all Native American mitochondrial DNA lineages to day descend from just five founding maternal lines [11-that each had a common ancestor around 18,000 to 15,000 years ago, implying a population size bottleneck around this time [14- (yumpu.com)
- It is now clear that so many founder events and fluctuations in population size have occurred before, during, and after the peopling of the Americas that the evidence from one position in the genome - mitochondrial DNA, the Y chromosome, or any other location - is too subject to random changes in frequency (genetic drift) to provide a complete picture by itself. (yumpu.com)
- In addition to the nuclear DNA, the mitochondrial genome of a cell contains its own haploid genome of approximately 16,000 base pairs of DNA (mtDNA), which are usually passed on from mother to offspring. (nap.edu)
- Genomes fluctuate in size regularly, however, genome size reduction is most significant in bacteria. (wikipedia.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)
- Thus, these unusual microbes possess genomes that are among the smallest known in bacteria, approaching the minimal sets of genes required for cellular life and parasitism in plants and insects. (usda.gov)
- Mollicutes is a class of parasitic bacteria that have evolved from a common Firmicutes ancestor mostly by massive genome reduction. (plos.org)
- This is true for bacteria belonging to the class Mollicutes that are characterized by reduced genomes and hence considered as models for minimal cells. (plos.org)
- Mollicutes constitute a monophyletic class that share a common ancestor with Gram-positive bacteria of low G+C content or Firmicutes but have adopted a parasitic life style ( Figure S1 ) . (plos.org)
- In nature, some free-living bacteria also have reduced genomes, and in these cases large population sizes and the apparent absence of transmission bottlenecks suggest that selection, not drift, must be responsible. (asm.org)
- Genomes of B. aphidicola are only 500 to 640 kb in length and contain 450 to 580 protein-coding genes, essentially all of which have orthologs in related bacteria, including Escherichia coli ( 12 , 28 - 30 , 33 ). (asm.org)
- The mutualistic role of these pathways is highlighted by the observations that genes underlying synthesis of the nonessential amino acids have been eliminated from B. aphidicola genomes and that all amino acid biosynthetic pathways are typically missing from similarly small genomes of pathogenic bacteria, which obtain the needed nutrients from hosts. (asm.org)
- The trend toward large scale gene loss could reflect the inefficiency of natural selection at maintaining genes in the genomes of these cytoplasmically inherited bacteria. (biomedcentral.com)
- These organelle genomes are evolutionary relics of free-living bacteria that entered into a symbiotic relationship with a host cell. (jrank.org)
- This indicates that the ancestors of modern viruses were independently replicating virocells that co-evolved with the bacteria and archaea, and all three of them - virocells, bacteria and archaea - had a last universal common ancestor (LUCA). (quillette.com)
- in the Heterokonta, which may be up to 30 m in length), but also many bacteria-sized (1-5 μm) coccoid taxa (e.g. (plantphysiol.org)
- Although Bacteria and Archaea share a common prokaryotic genome architecture, the extant diversity of Bacteria appears to be much higher than that of Archaea. (emergtoplifesci.org)
- Compared with Archaea, Bacteria also show much greater genome-level specialisation to specific ecological niches, including parasitism and endosymbiosis. (emergtoplifesci.org)
- Until recently, few archaeal genomes were available, and it has been difficult to determine whether Bacteria and Archaea share a common prokaryotic evolutionary regime, or if instead there are conserved differences in the evolutionary processes and macroevolutionary trajectories of the two prokaryotic groups. (emergtoplifesci.org)
- This ancestor formed from a merger between some protozoan-like host and cyanobacterium, a kind of bacteria that use photosynthesis to make energy, that "moved in" and became the chloroplast of this first alga. (abovetopsecret.com)
- Now that phylogenetic relationships and genome sizes are determined for a broader array of organisms, it is clear that the mycoplasmas are just one example of genome shrinkage that has occurred in a variety of obligately host-associated bacteria. (wikiquote.org)
- In this study, size and GC content of all chromosomes are measured from the flow karyotypes of GGA, TSC and CNI. (royalsocietypublishing.org)
- genomes provide evidence of significant variation in the density of SNPs along chromosomes. (genetics.org)
- Nevertheless, the main chromosomes show considerable conservation of genome colinearity with the exception of a single ∼19-kb inversion (Fig. 1 ). (asm.org)
- An organism or cell with two sets of chromosomes (2N) or two genomes. (apsnet.org)
- An organism or cell having only one complete set (N) of chromosomes or one genome. (apsnet.org)
- Various studies have found evidence for such effects, primarily in nonrecombining genomes or chromosomes. (biomedcentral.com)
- The panels c-e show orthologous genes on chromosomes X, II, and IV, with chromosome size scaled to linkage group size in C. remanei (X 18.5Mb, II 12.5Mb, IV 14.5 Mb). (nih.gov)
- Genome sizes estimated from the total chromosome size demonstrate that TSC and CNI are 1.21 Gb and 1.29 Gb, respectively. (royalsocietypublishing.org)
- This contrasts with mammals and squamates in which GC content does not correlate with chromosome size. (royalsocietypublishing.org)
- Alternatively, genome size can be calculated from the sum of chromosome sizes determined by flow-karyotypic analysis using a flow cytometer [ 3 - 7 ]. (royalsocietypublishing.org)
- For example, the sum of chromosome sizes in human (HSA) [ 4 ] and dog [ 5 ] by this method gives a value of 3.15 Gb and 2.75 Gb, respectively. (royalsocietypublishing.org)
- Genlisea nigrocaulis , with 86 Mbp one of the smallest plant genomes, and the 18-fold larger genome of G. hispidula (1,550 Mbp) possess identical chromosome numbers (2 n = 40) but differ considerably in chromatin organization, nuclear and cell size. (frontiersin.org)
- R. centenum contains a singular circular chromosome of 4,355,548 base pairs in size harboring 4,105 genes. (biomedcentral.com)
- However, this effect cannot entirely explain the observed three- to fourfold reduction in Z chromosome diversity. (genetics.org)
- Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. (nih.gov)
- Birds have smaller genomes relative to mammals, and the genome-wide frequency and distribution of Numts is still unknown. (biomedcentral.com)
- Likewise, it has recently been reported that pterosaurs had smaller genomes than their non-flying relatives ( Organ & Shedlock 2008 ). (royalsocietypublishing.org)
- One of the best-studied cases of genome reduction is that of the intracellular bacterial symbiont Buchnera aphidicola , which shows a long evolutionary history of strict maternal transmission in its aphid hosts (Insecta: Homoptera: Aphidoidea) ( 18 ). (asm.org)
- Genome reduction in intracellular pathogens and endosymbionts is usually compensated by reliance on the host for energy and nutrients. (springer.com)
- An ancestral character reconstruction suggests that the most recent common ancestor of cyanobacteria had a genome size of approx. (uio.no)
- The establishment of the mitochondrion as a cellular organelle by endosymbiosis [ 1 ] changed the fate of the ancestral genome that free-living eubacterial ancestors possessed. (biomedcentral.com)
- Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of ∼1.4-fold around ∼970 kya and a recent ∼5.6-fold contraction in population size ∼23 kya. (meta.org)
- By looking at genome-wide data from several hundred individuals from a population, scientists can learn not only the current effective population size, but also the sizes of the ancestral populations that once contributed their genes. (eurekalert.org)
- We found that around 100 generations ago, which is approximately several thousand years ago, the effective sizes of the ancestral European, African and indigenous American populations contributing to current-day American populations were around several tens of thousands of individuals each. (eurekalert.org)
- 23 ] applied this idea to the first comprehensive genome-wide data from Native American populations (52 populations, but none from the continental United States), and concluded that at least three ancestral populations were required to explain the similarities between Native Americans and East Asians. (yumpu.com)
- The authors of the current paper estimate a 13,601 ancestral and 22,915 current size for Yoruba , with an expansion beginning at 20.15ky . (blogspot.com)
- For Europeans , a more complex model provides a better fit, with an ancestral size of 10,065 going through a bottleneck to 3,300 at 39.5ky and recovering at 32.5ky to a current size of 18,300. (blogspot.com)
- Plastids, like mitochondria, possess remnants of their ancestral genomes, which vary considerably in size and gene content in spite of a probable single primary endosymbiosis (reviewed by Douglas, 1998 ). (plantcell.org)
- 2000. Horizontal gene transfer in bacterial and archaeal complete genomes. (springer.com)
- 1997. Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. (springer.com)
- New Archaeal Clusters of Orthologous Genes (arCOGs) were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon) using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. (beds.ac.uk)
- The archaeal gene core (protein-coding genes found in all 41 genome) consists of 166 arCOGs. (beds.ac.uk)
- The Last Archaeal Common Ancestor (LACA) is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. (beds.ac.uk)
- The arCOGs provide a convenient, flexible framework for functional annotation of archaeal genomes, comparative genomics and evolutionary reconstructions. (beds.ac.uk)
Terms of genome size1
- Taking the average phylogeny of all genes in a genome isn't the way to get the best organismal phylogeny, and nobody really does this anyway. (blogspot.com)
- Maximum likelihood phylogeny of the Bacteroidetes was estimated using a concatenation of 38 conserved proteins identified in 41 complete and in-progress genomes (see Table S1 in the supplemental material). (asm.org)
- FIGURE 3-1 Phylogeny of wolf-like canids using 48,000 genome-wide single nucleotide polymorphisms (SNPs). (nap.edu)
- Gene content and order in the carboxysomal operon correlates well with the RubisCO phylogeny demonstrating that the complete carboxysomal operon was acquired by the common ancestor of the Paulinella chromatophore and the PS-clade through HGT. (beds.ac.uk)
Allowed us to reconstruct1
- Phylogenomic analysis focusing on chlamydial proteins with homology to plant proteins provided evidence for the acquisition of 53 chlamydial genes by a plant progenitor, lending further support for the hypothesis of an early interaction between a chlamydial ancestor and the primary photosynthetic eukaryote. (nih.gov)
- Moreover, they have a highly reduced metabolism, 70S ribosomes, and among the smallest known genomes of any eukaryote ( 4 , 28 , 60 , 62 ). (asm.org)
- We discuss the possible implications of these findings in the highly streamlined genome of this free-living eukaryote. (springer.com)
- and second, a hierarchical structure develops within the plastid, resulting in a eukaryote-like genome organization (e.g., intron invasion and the presence of maturases). (plantcell.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)
- Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. (pnas.org)
- There are taxon-specific differences in the change of dN / dS over time, which may indicate variation in selection, or in population genetics parameters such as population size or the rate of recombination. (pasteur.fr)
- Within-genome variation in SNP frequency is likely to occur at several different scales. (genetics.org)
- The early studies of genetic variation in wolves found such allelic differences at many loci throughout the genome. (nap.edu)
- What determines variation in genome size, gene content and genetic diversity at the broadest scales across the tree of life? (emergtoplifesci.org)
- One of the major challenges in evolutionary genetics is to explain the enormous variation in genome size and gene content across the tree of life in terms of basic evolutionary processes such as mutation, genetic drift and selection. (emergtoplifesci.org)
- However, the long-term evolutionary consequences of such variation in genome size among taxa remain poorly understood. (royalsocietypublishing.org)
- Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. (prolekare.cz)
- Here, we use this technique to investigate the genetic basis of natural variation in body size in Drosophila melanogaster . (prolekare.cz)
- Significant differentiation of hundreds of loci in replicate selection populations supports the hypothesis that the genetic basis of body size variation is very polygenic in D. melanogaster . (prolekare.cz)
- By using significantly associated polymorphisms as a priori candidates in follow-up studies, these data are expected to provide considerable power to determine the genetic basis of natural variation in body size. (prolekare.cz)
- Body size is also sexually dimorphic in D. melanogaster , yet genetic variation for size is correlated between the sexes, and differences in optimal size have been shown to result in sexual conflict . (prolekare.cz)
- Well-powered GWA and GS require a genome-wide assessment of genetic diversity, patterns of population structure, and the decay of linkage disequilibrium (LD). (pnas.org)
- We analyzed patterns of polymorphism and divergence at Z-linked and autosomal loci in the domestic chicken ( Gallus gallus ) to study the influence of mutation, effective population size, selection, and demography on levels of genetic diversity. (genetics.org)
- The 'orphan' Indian lions showed what the authors termed 'a nearly complete absence of genetic diversity,' consistent with their low population sizes in recent years. (patentdocs.org)
- This is the first genome-wide study - where we have population-level data, not just a few individuals - that spans 6,000 years," said University of Illinois anthropology professor Ripan Malhi , who co-led the new research with former graduate student John Lindo (now a postdoctoral researcher at the University of Chicago) and Pennsylvania State University biology professor Michael DeGiorgio . (popular-archaeology.com)
- Scientists at A*STAR's Institute of Molecular and Cell Biology (IMCB) led an international team of researchers that sequenced and analyzed the genome of the elephant shark. (technologynetworks.com)
- Joseph Felsenstein is Professor in the Departments of Genome Sciences and Biology and Adjunct Professor in the Departments of Computer Science and Statistics at the University of Washington in Seattle. (smbe.org)
- Integrating and analyzing heterogeneous genome-scale data is a huge algorithmic challenge for modern systems biology. (biomedcentral.com)
- These large genomes were primarily comprised of Transposable Elements (TE) with ~65% of the genome containing TE. (fungalgenomes.org)
- Increases in genome size may be driven by several processes, including whole genome duplications (WGDs), transposable element (TE) proliferation, intron expansion and tandem gene duplications [ 3 ]. (royalsocietypublishing.org)
- Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. (nih.gov)
- The demographic structure of human populations has changed dramatically over the last 200 years, resulting in major changes in the size and composition of gene pools. (biomedcentral.com)
- A predicted effect of the admixture of individuals from different genetic populations is an increase in average individual genome-wide heterozygosity, h , as previously reported for morphometric and biochemical parameters among younger Israelis [ 10 ]. (biomedcentral.com)
- Sharon Browning of the University of Washington and colleagues developed a method to estimate historical effective population size, which is the number of individuals who pass on their genes to the next generation, to reveal the shifting demographic history of U.S. populations during the last several thousand years. (eurekalert.org)
- In the current study, researchers developed a method for estimating past effective population size and used it to analzye data from nine populations enrolled in a Latino health study, and from African-American and European-American populations in Pittsburgh and Memphis. (eurekalert.org)
- The differences in historical effective sizes between these populations can be useful for understanding why individual groups face different health and disease risks. (eurekalert.org)
- Image Caption: In the African component, we see smaller estimated pre-admixture effective sizes for Cuba (150,000) and Mexico (100,000) than for the Dominican Republic (700,000), suggesting that the African ancestors of the former two populations came from smaller sub-populations of Africa than the African ancestors of the latter two populations. (eurekalert.org)
- Dense, genome-wide single-nucleotide polymorphism (SNP) data can be used to reconstruct the demographic history of human populations. (blogspot.com)
- In fact, according to the intensity of the selection process, the degree of change in populations can vary along a continuum from their wild ancestors to the domesticated populations, which cannot reproduce or survive without human intervention. (biomedcentral.com)
- Our comparative analysis of 6 strains of the spectacular Pandoraviridae family now suggests that their giant genomes may be actively breeding new proteins and functions. (nature.com)
- However, growth in interest in this topic has been particularly marked over the past decade, prompted by several factors: (i) the rise of large-scale comparative genomics, for which genome size data have practical importance (e.g. (royalsocietypublishing.org)
- Therefore, sequencing the genomes of reptiles would aid comparative studies on amniotes by providing more comprehensive coverage to help understand the molecular mechanisms underpinning evolutionary changes. (springer.com)
- There are also treats for the general purpose genome biologists with descriptions of next generation/2nd generation sequencing technologies, assembly methods, and comparative genomics. (fungalgenomes.org)
- Given the long-standing interest in this question, it is surprising that almost no data have been presented regarding genome size diversity among megabats (family Pteropodidae). (royalsocietypublishing.org)
- This study marks the first major survey, to our knowledge, of megabat genome size diversity and the single largest study of bats conducted to date. (royalsocietypublishing.org)
- Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. (biomedcentral.com)
- Understanding the role of these factors in shaping patterns of polymorphism within genomes is key to the interpretation of SNP data in, for example, association studies and for the quantification of linkage disequilibrium (LD) through analysis of haplotype diversity. (genetics.org)
- Free-living taxa with reduced genomes must however evolve strategies for generating functional diversity to support their independent lifestyles. (springer.com)
- Genome sizes and gene family copy numbers evolve at a higher rate in the former clade, and multi-copy genes were predominant in large genomes. (uio.no)
- It shows that typical genome size for (so far sampled) Pezizomycotina Ascomycetes in the ~40-50Mb range whereas these powdery mildew genomes here significantly large genomes in ~120-160 Mb range. (fungalgenomes.org)
- Microsatellites are repetitive segments of DNA that are widely distributed throughout the genome. (nap.edu)
- 20% of the genome is repetitive DNA: the majority of intergenic regions consist of numerous classes of short dispersed repeats (SDRs), which may have structural or evolutionary significance. (plantcell.org)
- Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. (royalsocietypublishing.org)
Genes in a genome1
- NEW YORK (GenomeWeb) − Researchers led by Dennis Lo at the Chinese University of Hong Kong have shown that size differences between fetal DNA and maternal DNA in the mother's plasma can be exploited for non-invasive prenatal testing, providing an alternative to methods used in commercial tests that might boost overall specificity. (genomeweb.com)