• Cladistic analyses based on chloroplast protein coding genes rbcL and rps 4, and the chloroplast encoded trnL (UAA) intron were conducted (1) to investigate phylogenetic relationships among basal peristomate mosses, especially the nematodontous mosses (Tetraphidaceae and Polytrichaceae), and the arthrodontous mosses with pleated endostomes (Buxbaumiaceae and Diphysciaceae), and (2) to make inferences on evolution of the peristome. (bioone.org)
  • Though most chloroplast genes are believed to have been transferred to the nucleus during evolution, their genomes have maintained fairly conserved structures and gene contents throughout their evolutionary lineage 1 . (plos.org)
  • The cp genomes of land plants usually contain approximately 110-120 genes, which mostly participate in photosynthesis or gene expression 4 , 5 . (plos.org)
  • Under this theory, symbiotic organelles gradually transferred their genes to the eukaryotic genome, implying that mtDNA was gradually integrated into the nuclear genome. (wikipedia.org)
  • All plastomes are highly conserved in genome structure and gene order, with a total length of 158-159 kb and 122 genes. (biomedcentral.com)
  • Horizontal gene transfer happens when foreign genetic material jumps into genomes, creating new combinations (recombination) of genes, or new genomes. (i-sis.org.uk)
  • In this study, we analyzed all genes from sequenced plastid genomes to unearth any neglected cases of HGT and to obtain a measure of the overall extent of HGT to the plastid. (biomedcentral.com)
  • Finally, we'll take a quick look at sex-linked genes, lethal alleles, and non-nuclear inheritance (mtDNA and chloroplast DNA). (biologydictionary.net)
  • Our proposal also includes comparisons with Arabidopsis, whose complete genome was recently sequenced Spruce and poplar (Populus spp. (bcgsc.ca)
  • The small genome of poplar makes construction of integrated physical and genetic maps feasible, and its relative closeness to species such as Arabidopsis makes the large-scale conservation of gene order (synteny) more likely. (bcgsc.ca)
  • In this study, chloroplast DNA sequence variability was used to infer phylogenetic relationships among Arabidopsis thaliana accessions from around the world, with the emphasis on samples from China. (biomedcentral.com)
  • Natural selection on the Arabidopsis thaliana genome in present and future climates. (mpg.de)
  • Biswal D, Konhar R, Debnath M, Parameswaran S, Sundar D, Tandon P. Chloroplast Genome Sequence Annotation of Dendrobium nobile (Asparagales: Orchidaceae), an Endangered Medicinal Orchid from Northeast India. (plos.org)
  • Here, we report the complete cp genome sequence of Dendrobium nobile from Northeast India (Orchidaceae, Asparagales), bearing the GenBank accession number KX377961, which will provide valuable information for future research on orchid genomics and evolution, as well as the medicinal value of orchids. (plos.org)
  • the evidence of such translocation has been seen through the comparison of mitochondrial DNA sequence with the genome sequence of the counterparts. (wikipedia.org)
  • In contrast to the well-delimitated species boundary inferred from the nuclear ITS sequence variations, three of the four species are non-monophyletic in the plastome trees, which is consistent with previous studies based on a few chloroplast markers. (biomedcentral.com)
  • Previous study failed to discern the four Ostrya species based on four chloroplast (cp) fragments ( rps16 , trnG (UCC) intron, trnH-psbA , and trnL-trnF ) while the ITS sequence variations did [ 5 ]. (biomedcentral.com)
  • In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona , and allotetraploid E. oryzicola ) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. (nature.com)
  • Three chloroplast microsatellites (cpSSRs), previously sequence characterized and for which paternal inheritance was tested and confirmed, were used to assess their usefulness as informative markers for phylogeographic studies in Norway spruce ( Picea abies K.) and to detect spatial genetic differentiation related to the possible recolonization processes in the postglacial period. (lib4ri.ch)
  • Further taxon sampling of clpP and ycf2 resulted in rejection of HGT due to long-branch attraction and a serious error in the published plastid genome sequence of Oenothera elata , respectively. (biomedcentral.com)
  • The SIPs were the first to be unraveled via genome sequence analysis and are generally localized in the endoplasmic reticulum (ER). (biomedcentral.com)
  • PolyMarker generates a multiple alignment between the target SNP sequence and the selected reference genome (from the drop off menu in green below). (polymarker.info)
  • Applied to whole-genome sequence data from Plasmodium parasites, Anopheles mosquitoes, and global human populations, this approach yields median test errors of 16.9km, 5.7km, and 85km, respectively. (elifesciences.org)
  • While the complete plastid genomes of tobacco and liverworts were the first to be determined, as of April 2017, the complete chloroplast (cp) genomes of 1161 GenBank accessions from land plants have been reported in the National Centre for Biotechnology Information (NCBI) Organelle Genome Resources (http://www.ncbi.nlm.nih.gov/genome/browse/?report=5) 2 . (plos.org)
  • To quantify the overall extent of HGT in plastid genomes, we searched exhaustively for HGT among the 42 sequenced plastid genomes available when this study began. (biomedcentral.com)
  • More and more NUMT sequences, with different size and length, in the diverse number of Eukaryotes, have been detected as more whole genome sequencing of different organisms accumulates. (wikipedia.org)
  • 66 thousand whole-genome sequences indicate this currently occurs as frequent as once in every ~4,000 human births. (wikipedia.org)
  • Studies on the GM process have shown that the foreign gene inserts invariably damages the genome, scrambling and rearranging DNA sequences, resulting in inappropriate gene expression that can trigger cancer [3, 4]. (i-sis.org.uk)
  • The phylogenetic distance between spruce and angiosperms makes evolutionary comparisons of spruce sequences informative. (bcgsc.ca)
  • These authors found considerable variation existed among the non-coding single-copy sequences in the chloroplast genome of A. thaliana . (biomedcentral.com)
  • The relationships of the rare Mesoamerican fern Campyloneurum anetioides are inferred by comparing sequences of trnL UAA -trnF GAA intergenic spacer of the plastid genome. (bioone.org)
  • Sequences have been ordered using POPSEQ data and Hi-C (chromosome conformation capture) to generate 21 pseudomolecules representing the majority of the wheat genome. (polymarker.info)
  • We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades of Ficus . (nature.com)
  • However, studies based on limited informative sites of several chloroplast markers failed to resolve interspecific delimitation and relationships among the four Chinese species. (biomedcentral.com)
  • We assembled and annotated 33 complete chloroplast genomes (plastomes) of the four Chinese species, representing 17 populations across most of their geographical distributions. (biomedcentral.com)
  • In addition, the plastomes with more informative sites compared with a few chloroplast markers still failed to resolve the phylogenetic relationships of the four species, and further studies involving population genomic data may be needed to better understand their evolutionary histories. (biomedcentral.com)
  • It has been suggested that the traditionally accepted cpDNA barcodes own limited resolution in delimitating closely related species due to the insufficient informative variations [ 8 , 9 , 10 ]. (biomedcentral.com)
  • Furthermore, GMDNA is designed - albeit crudely - to cross species barriers and to jump into genomes. (i-sis.org.uk)
  • The analysis of chloroplast SSR variation detected the presence of two main gene pools (Sarmathic-Baltic and Alpine - Centre European) and a relatively low degree of differentiation ( R ST of about 10%), characteristic of tree species with large distribution and probably influenced by an intensive human impact on this species. (lib4ri.ch)
  • Most, if not all of these transfers seem to be the result of a gene being transferred from the mitochondrial genome of one species to that of another. (biomedcentral.com)
  • A short phylogenetically informative cpDNA fragment for the identification of Pinus species. (uu.se)
  • To clarify the monophyly and phylogenetic position of the species, a molecular study using the internal transcribed spacer region of nuclear ribosomal DNA and chloroplast DNA ( trn L-F) data was conducted. (e-kjpt.org)
  • First, in a number of species, genomes are hard to assemble with classical methods because of an heterogeneous chromosomal structure or difficulties to perform classical assembly. (biomedcentral.com)
  • NUMTs have been reported in all studied eukaryotes, and nearly all mitochondrial genome regions can be integrated into the nuclear genome. (wikipedia.org)
  • These parts of the mitochondrial genome have been reported to be the most frequently employed. (wikipedia.org)
  • Initial evidence that DNA could move among cell compartments came when fragments of chloroplast DNA were found in the maize mitochondrial genome with the help of cross-hybridization, between chloroplast and mitochondrial DNA, and physical mapping of homologous regions. (wikipedia.org)
  • I present evidence from reciprocal crosses, cytoplasmic substitution lines, and cell fusion lines that hybrid weakness and sterility often arise from interactions between the nuclear genome and the chloroplast and mitochondrial genomes. (bioone.org)
  • NUMT, pronounced "new might", is an acronym for "nuclear mitochondrial DNA" segment or genetic locus coined by evolutionary geneticist, Jose V. Lopez, which describes a transposition of any type of cytoplasmic mitochondrial DNA into the nuclear genome of eukaryotic organisms. (wikipedia.org)
  • In addition, De novo integration of NUMT pseudogenes into the nuclear genome has an adverse effect in some cases, promoting various disorders and aging. (wikipedia.org)
  • The first application of the NUMT term in the domestic cat (Felis catus) example was striking, since mitochondrial gene number and content were amplified 38-76X in the cat nuclear genome, besides being transposed from the cytoplasm. (wikipedia.org)
  • The possible presence of organelle DNA inside the nuclear genome was suggested after the finding of homologous structure to the mitochondrial DNA, which was shortly after the discovery of the presence of an independent DNA within the organelles in 1967. (wikipedia.org)
  • Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and mitochondrial-based phylogenies, none of which correspond with any published phylogenies of the associated pollinator wasps. (nature.com)
  • The scaffolds where assigned to their corresponding genome by comparing the diploid progenitors and the scaffolds where anchored with the aid of genetic maps. (polymarker.info)
  • Five chloroplast DNA regions, i.e. atpH-I, matK, rpoB, rpoC and trnL-F, were used in an attempt to study the molecular diversity of C. caulecsens. (ndltd.org)
  • A cloned, 500 base pair (bp) restriction fragment from the chloroplast genome of Pinus contorta hybridized to restriction fragments of a previously known polymorphism when used in molecular mapping experiments with total cellular DNAs of P. banksiana and P. contorta. (researchgate.net)
  • Variation in the size of cp genomes among plant lineages is generally observed in the mutable IR region. (plos.org)
  • Further analysis demonstrated that cryptic chloroplasts are common in apicomplexan parasites, including in lineages where they were not previously known to exist. (elifesciences.org)
  • However, at least three lineages of apicomplexans have independently lost their cryptic chloroplasts. (elifesciences.org)
  • It is not dissimilar to the gradient of proliferation and differentiation along developing roots [ 2 ] but, in contrast, it provides a unique opportunity to study chloroplast biogenesis and differentiation. (biomedcentral.com)
  • Although previously unrecognized, plastids in deep-branching apicomplexans are common, and they contain some of the most divergent and AT-rich genomes ever found. (elifesciences.org)
  • The two einkorn wheats, Triticum boeoticum and Triticum urartu, that known as 'A' genome donor to cultivated wheat are the main elements of many wheat breeding programs. (innspub.net)
  • The poplar genome will add to the numerous mamallian and other genomes already mapped by the Genome Sciences Centre. (bcgsc.ca)
  • Design features include changes in the genetic code and special ends that enhance recombination, i.e., breaking into genomes and rejoining. (i-sis.org.uk)
  • Genetic modification is essentially horizontal gene transfer and recombination, speeded up enormously, and totally unlimited in the source of genetic material recombined to make the GMDNA that's inserted into the genomes plants, animals and livestock to create genetically modified organisms (GMOs). (i-sis.org.uk)
  • In natural populations, local mate selection and dispersal create correlations between geographic location and genetic variation - each individual's genome is a mosaic of material inherited from recent ancestors that are usually geographically nearby. (elifesciences.org)
  • Stepwise regression analysis between molecular data as predictors and each morphological traits data as dependent variables was performed to identify informative markers associated with the studied traits. (innspub.net)
  • Because subcellular constructions go through substantial morphological adjustments in response to reprogramming also, evaluating the structural shifts on the subcellular level could possibly be informative for analyzing the amount TGX-221 inhibition of pluripotency TGX-221 inhibition equally. (tam-receptor.com)
  • Taking advantage of the developmental gradient in the bread wheat leaf, we provide a simultaneous quantitative analysis for the development of mesophyll cells and of chloroplasts as a cellular compartment. (biomedcentral.com)
  • Our analysis generates both the first wheat leaf transcriptional map and one of the most comprehensive descriptions to date of the developmental history of chloroplasts in higher plants. (biomedcentral.com)
  • Independent wheat B and G genome origins in outcrossing Aegilops progenitorhaplotypes. (innspub.net)
  • We leverage Locator's computational efficiency to predict locations separately in windows across the genome, which allows us to both quantify uncertainty and describe the mosaic ancestry and patterns of geographic mixing that characterize many populations. (elifesciences.org)
  • The uniparental inheritance and non-recombinant nature of cp genomes make them potentially useful tools for inferring evolutionary and ancient phylogenetic relationships. (plos.org)
  • Not only has any correlation been found between the fraction of noncoding DNA and NUMT abundance in the genome but NUMTs are also proven to have non-random distribution and a higher likelihood of being inserted in the certain location of genome compare to others. (wikipedia.org)
  • During the last decade, a huge amount of new genomes have been sequenced, leading to an abundance of available DNA resources. (biomedcentral.com)
  • Previous studies explored its phylogenetic relationships and historical biogeography using limited loci, which might result in biased molecular dating due to insufficient parsimony-informative sites. (biomedcentral.com)
  • It reveals functionally distinct plastid and chloroplast development stages, identifies processes occurring in each of them, and highlights our very limited knowledge of the earliest drivers of plastid biogenesis, while providing a basis for their future identification. (biomedcentral.com)
  • Chloroplast microsatellite analysis reveals the presence of population subdivision in Norway spruce (Picea abies K. (lib4ri.ch)
  • Chloroplast microsatellite analysis reveals the presence of population subdivision in Norway spruce ( Picea abies K.). Genome , 43 , 68-78. (lib4ri.ch)
  • thus, traits determined by chloroplast and mitochondrial DNA do not follow simple Mendelian rules. (biologydictionary.net)
  • as such, mitochondria-determined and chloroplast-determined traits are maternally inherited. (biologydictionary.net)
  • However, the relationships of tribes Cinnamomeae and Laureae remained unresolved due to insufficient informative sites. (biomedcentral.com)
  • Regions of the genome reflect correlated sets of genealogical relationships ( A ), each of which represents a set of ancestors with varying spatial positions back in time. (elifesciences.org)
  • However, we also could provide other type of information to compute the weight on the edges, like for instance ancestral support in a phylogenetic context, or comparison to other extent genomes which could be used as multiple references. (biomedcentral.com)
  • Another reason is that producing a complete genome, or an as-complete-as-possible-genome is a difficult task. (biomedcentral.com)
  • Traditionally, producing a complete genome consists of three steps, each of them computationally or financially difficult: the assembly, the scaffolding, and the finishing. (biomedcentral.com)
  • Chloroplast biogenesis involves a multiplicity of processes. (biomedcentral.com)
  • Sciences), this project involves mapping the poplar genome as well as carrying out BAC end sequencing to add to the utility of the map. (bcgsc.ca)
  • However, it remains unclear how widespread cryptic chloroplasts are in these parasites, largely because few apicomplexans have been successfully grown in the laboratory. (elifesciences.org)
  • shed new light on the importance of chloroplasts in the evolution of life and may help develop new treatments for diseases caused by apicomplexan parasites. (elifesciences.org)
  • Several drugs targeting the cryptic chloroplasts in malaria parasites are currently in clinical trials, and this work suggests that these drugs may also have the potential to be used against other apicomplexan parasites in the future. (elifesciences.org)
  • Typically, the cp genomic size of land plants varies between 120 and 220 kb, with a pair of inverted repeats (IRs) that separate the genome into a large single copy (LSC) region and a small single copy (SSC) region 3 . (plos.org)
  • Within the NIP subfamily, the presence of a NIP2 in both genomes supports a conserved ability to absorb Si within plants of the genus. (biomedcentral.com)
  • This study reports the first case of drastic IR expansion in tribe Cinnamomeae, and indicates that plastomes have sufficient parsimony-informative sites for molecular dating. (biomedcentral.com)
  • The Department of Biotechnology (DBT), Government of India, funded this work under the DBT-NER Twinning program "Next Generation Sequencing (NGS)-based de novo assembly of expressed transcripts and genome information of Orchids in North-East India" (Grant ID BT/325/NE/TBP/2012 dated August 07, 2014). (plos.org)
  • Using a network reconstruction algorithm, we predict that known chloroplast gene expression regulators are differentially involved across those developmental stages. (biomedcentral.com)
  • The uniparentally inherited chloroplast genome has been utilized in many studies in plant population and evolutionary genetics. (biomedcentral.com)
  • However, the relationship between the two is barely understood, which limits the value of transcriptome data to understand the process of chloroplast development. (biomedcentral.com)
  • Analysis of RNA-seq data from A. hypogea revealed a similar expression pattern for the different AQP paralogs of AA and BB genomes. (biomedcentral.com)
  • The present study reports the identification and structural and expression analysis of the AQPs found in the diploid progenitor genomes of A. hypogea i.e. (biomedcentral.com)
  • The large genome of spruce mandates more functional approaches, while the small genome of poplar makes structural approaches possible. (bcgsc.ca)