Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genome evolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,513 records · Page 84Linked to original sources
PubMed2000

Features of the mammal mar1 transposons in the human, sheep, cow, and mouse genomes and implications for their evolution.

Mariner-like elements (MLE) belong to the Tc1/ mariner superfamily of class II transposons. We have analyzed the mariner related to the cecropia subfamily, and called mammal mar1, in four mammalian genomes, Bos taurus (Bovidae), Homo sapiens (Primata), Mus musculus (Rodentia), and Ovis aries (Ovidae). Three kinds of MLE sequences were found in all these species: full-length 1.3-kbp elements, shorter elements 80 bp-1.2 kbp, and single inverted terminal repeats (ITRs). All the 1.3-kbp genomic copies sequenced had an open reading frame encoding a transposase interrupted by stop codons or frame shifts. Phylogenetic analysis of the full-length elements suggested at least two distinct populations of mammal mar1 elements in each species. This was confirmed by using a statistical method that allows defining populations. Finally, the evolutionary origin of the mammal mar1 elements and the paradoxes are discussed.

Animals↗
PubMed2005

The HSP90 family of genes in the human genome: insights into their divergence and evolution.

HSP90 proteins are important molecular chaperones. Transcriptome and genome analyses revealed that the human HSP90 family includes 17 genes that fall into four classes. A standardized nomenclature for each of these genes is presented here. Classes HSP90AA, HSP90AB, HSP90B, and TRAP contain 7, 6, 3, and 1 genes, respectively. HSP90AA genes mapped onto chromosomes 1, 3, 4, and 11; HSP90AB genes mapped onto 3, 4, 6, 13 and 15; HSP90B genes mapped onto 1, 12, and 15; and the TRAP1 gene mapped onto 16. Six genes, HSP90AA1, HSP90AA2, HSP90N, HSP90AB1, HSP90B1 and TRAP1, were recognized as functional, and the remaining 11 genes were considered putative pseudogenes. Amino acid polymorphic variants were detected for genes HSP90AA1, HSP90AA2, HSP90AB1, HSP90B1, and TRAP1. The structures of these genes and the functional motifs and polymorphic variants of their proteins were documented and the features and functions of their proteins were discussed. Phylogenetic analyses based on both nucleotide and protein data demonstrated that HSP90(AA+AB+B) formed a monophyletic clade, whereas TRAP is a relatively distant paralogue of this clade.

Amino Acid Sequence↗
PubMed1999

Genomic imprinting of the X chromosome: a novel mechanism for the evolution of sexual dimorphism.

Genomic imprinting is the differential marking of maternally and paternally inherited alleles of specific genes or chromosome regions during gametogenesis. The imprint silences the allele from 1 parent. A number of imprinted genes that are expressed in the brain have been identified in humans. They control the actions of other genes or regulate their products. Sexual dimorphism in the vertebrate brain is conventionally thought to be due to the epigenetic action of gonadal hormones. Sex differences could also reflect the actions of an imprinted X-linked locus. Until very recently no imprinted gene had been described on the X chromosome in humans. Here the implications of such a mechanism for the evolution of sexual dimorphism are discussed.

Adolescent↗
PubMed2000

The COG database: a tool for genome-scale analysis of protein functions and evolution.

Rational classification of proteins encoded in sequenced genomes is critical for making the genome sequences maximally useful for functional and evolutionary studies. The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on a phylogenetic classification of the proteins encoded in 21 complete genomes of bacteria, archaea and eukaryotes (http://www. ncbi.nlm. nih.gov/COG). The COGs were constructed by applying the criterion of consistency of genome-specific best hits to the results of an exhaustive comparison of all protein sequences from these genomes. The database comprises 2091 COGs that include 56-83% of the gene products from each of the complete bacterial and archaeal genomes and approximately 35% of those from the yeast Saccharomyces cerevisiae genome. The COG database is accompanied by the COGNITOR program that is used to fit new proteins into the COGs and can be applied to functional and phylogenetic annotation of newly sequenced genomes.

Database Management Systems↗
PubMed2005

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Insight into the diversity and evolution of the cryptomonad nucleomorph genome.

The cryptomonads are an enigmatic group of marine and freshwater unicellular algae that acquired their plastids through the engulfment and retention of a eukaryotic ("secondary") endosymbiont. Together with the chlorarachniophyte algae, the cryptomonads are unusual in that they have retained the nucleus of their endosymbiont in a miniaturized form called a nucleomorph. The nucleomorph genome of the cryptomonad Guillardia theta has been completely sequenced and with only three chromosomes and a total size of 551 kb, is a model of nuclear genome compaction. Using this genome as a reference, we have investigated the structure and content of nucleomorph genomes in a wide range of cryptomonad algae. In this study, we have sequenced nine new cryptomonad nucleomorph 18S ribosomal DNA (rDNA) genes and four heat shock protein 90 (hsp90) gene fragments, and using pulsed-field gel electrophoresis and Southern hybridizations, have obtained nucleomorph genome size estimates for nine different species. We also used long-range polymerase chain reaction to obtain nucleomorph genomic fragments from Hanusia phi CCMP325 and Proteomonas sulcata CCMP704 that are syntenic with the subtelomeric region of nucleomorph chromosome I in G. theta. Our results indicate that (1) the presence of three chromosomes is a common feature of the nucleomorph genomes of these organisms, (2) nucleomorph genome size varies dramatically in the cryptomonads examined, (3) unidentified cryptomonad species CCMP1178 has the largest nucleomorph genome identified to date at approximately 845 kb, (4) nucleomorph genome size reductions appear to have occurred multiple times independently during cryptomonad evolution, (5) the relative positions of the 18S rDNA, ubc4, and hsp90 genes are conserved in three different cryptomonad genera, and (6) interchromosomal recombination appears to be rapidly changing the size and sequence of a repetitive subtelomeric region of the nucleomorph genome between the 18S rDNA and ubc4 loci. These results provide a glimpse into the genetic diversity of nucleomorph genomes in cryptomonads and set the stage for more comprehensive sequence-based studies in closely and distantly related taxa.

Bayes Theorem↗
PubMed2005

Phylogeny of the Cucurbitales based on DNA sequences of nine loci from three genomes: implications for morphological and sexual system evolution.

The Cucurbitales are a clade of rosids with a worldwide distribution and a striking heterogeneity in species diversity among its seven family members: the Anisophylleaceae (29-40 species), Begoniaceae (1400 spp.), Coriariaceae (15 spp.), Corynocarpaceae (6 spp.), Cucurbitaceae (800 spp.), Datiscaceae (2 spp.), and Tetramelaceae (2 spp.). Most Cucurbitales have unisexual flowers, and species are monoecious, dioecious, andromonoecious, or androdioecious. To resolve interfamilial relationships within the order and to polarize morphological character evolution, especially of flower sexual systems, we sequenced nine plastids (atpB, matK, ndhF, rbcL, the trnL-F region, and the rpl20-rps12 spacer), nuclear (18S and 26S rDNA), and mitochondrial (nad1 b/c intron) genes (together approximately 12,000 bp) of 26 representatives of the seven families plus eight outgroup taxa from six other orders of the Eurosids I. Cucurbitales are strongly supported as monophyletic and are closest to Fagales, albeit with moderate support; both together are sister to Rosales. The deepest split in the Cucurbitales is that between the Anisophylleaceae and the remaining families; next is a clade of Corynocarpaceae and Coriariaceae, followed by Cucurbitaceae, which are sister to a clade of Begoniaceae, Datiscaceae, and Tetramelaceae. Based on this topology, stipulate leaves, inferior ovaries, parietal placentation, and one-seeded fruits are inferred as ancestral in Cucurbitales; exstipulate leaves, superior ovaries, apical placentation, and many-seeded fruits evolved within the order. Bisexual flowers are reconstructed as ancestral, but dioecy appears to have evolved already in the common ancestor of Begoniaceae, Cucurbitaceae, Datiscaceae, and Tetramelaceae, and then to have been lost repeatedly in Begoniaceae and Cucurbitaceae. Both instances of androdioecy (Datisca glomerata and Schizopepon bryoniifolius) evolved from dioecious ancestors, corroborating recent hypotheses about androdioecy often evolving from dioecy.

Begoniaceae↗
PubMed2006

Tempo and mode of ERV-K evolution in human and chimpanzee genomes.

Several families of endogenous retrovirus (ERV) exist in copious numbers in the genomes of primate species. Therefore, we undertook a systematic search for endogenous retrovirus sequences from the ERV-K family, comparing across both human (Homo sapiens) and chimpanzee (Pan troglodytes) genomes. Using conserved motifs of the ERV-K as query we identified and characterized 76 complete ERV-K elements, 54 in human (HERV-K), 34 of which were described previously, and 21 in the chimpanzee (CERV-K). Phylogenetic analysis using coding regions and LTRs showed the existence of two main branches. Group I was the most heterogeneous and had an average integration time of 18.3 MYBP (million years before present), using rates ranging from 1.5 to 4.0 x 10(-9) s/s/y (substitution per site per year). Group O/N integrated around 19.4 MYBP and nested Group N integrated about 14 MYBP. We found evidence for strong positive selection on the gag, pol and env coding regions and for A/T hypermutation. Our data suggest that the endogenous elements were possibly involved in chromosomal rearrangements and retained a great deal of information from their active stage, most likely as a consequence of host interactions. This study also contributes to the annotation effort of both human and chimpanzee genomes.

Animals↗
PubMed2024

Repeated evolution on oceanic islands: comparative genomics reveals species-specific processes in birds.

Understanding the interplay between genetic drift, natural selection, gene flow, and demographic history in driving phenotypic and genomic differentiation of insular populations can help us gain insight into the speciation process. Comparing patterns across different insular taxa subjected to similar selective pressures upon colonizing oceanic islands provides the opportunity to study repeated evolution and identify shared patterns in their genomic landscapes of differentiation. We selected four species of passerine birds (Common Chaffinch Fringilla coelebs/canariensis, Red-billed Chough Pyrrhocorax pyrrhocorax, House Finch  Haemorhous mexicanus and Dark-eyed/island Junco Junco hyemalis/insularis) that have both mainland and insular populations. Changes in body size between island and mainland populations were consistent with the island rule. For each species, we sequenced whole genomes from mainland and insular individuals to infer their demographic history, characterize their genomic differentiation, and identify the factors shaping them. We estimated the relative (Fst) and absolute (dxy) differentiation, nucleotide diversity (π), Tajima's D, gene density and recombination rate. We also searched for selective sweeps and chromosomal inversions along the genome. All species shared a marked reduction in effective population size (Ne) upon island colonization. We found diverse patterns of differentiated genomic regions relative to the genome average in all four species, suggesting the role of selection in island-mainland differentiation, yet the lack of congruence in the location of these regions indicates that each species evolved differently in insular environments. Our results suggest that the genomic mechanisms involved in the divergence upon island colonization-such as chromosomal inversions, and historical factors like recurrent selection-differ in each species, despite the highly conserved structure of avian genomes and the similar selective factors involved. These differences are likely influenced by factors such as genetic drift, the polygenic nature of fitness traits and the action of case-specific selective pressures.

Animals↗
PubMed2001

Determination of protein function, evolution and interactions by structural genomics.

The genome sequencing projects and knowledge of the entire protein repertoires of many organisms have prompted new procedures and techniques for the large-scale determination of protein structure, function and interactions. Recently, new work has been carried out on the determination of the function and evolutionary relationships of proteins by experimental structural genomics, and the discovery of protein-protein interactions by computational structural genomics.

Evolution, Molecular↗
PubMed2005

[Gene orders in genomes of alpha-proteobacteria: similarity and evolution].

The gene orders in the genomes of nine alpha-proteobacteria were compared using quantitative indices S (the relative number of common pairs of adjacent genes) and L (the mean difference between intergenic distances). A sample of 200 homologous genes, occurring in all 11 strains, was studied. In all of the genomes examined, 20 conserved, "uninterrupted" regions, including in total 63 out of 200 genes, were found. The rate of evolutionary change in the gene order widely varied in different evolutionary lineages. The highest rate (40 to 60 genome rearrangements per 100 Myr) was characteristic of the intercellular parasite Wolbachia (Rickettsiales). Computer simulation has showed that the S to L ratio observed in the sample testified that the probability of large genome rearrangements was somewhat lower than that of small ones.

Bacteria↗
PubMed2003

Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes.

Transposons are genetic elements that can move, and sometimes spread, within genomes, and that constitute an important fraction of eukaryote genomes. Two types of transposons, long terminal repeat (LTR)-retrotransposons and miniature inverted-repeat transposable elements (MITEs), are highly represented in plant genomes, and can account for as much as 50-80% of the total DNA content. In the last few years it has been shown that, in spite of their mutagenic capacity, both LTR-retrotransposons and MITEs can be found associated to genes, suggesting that their activity has influenced the evolution of plant genes. In this review we will summarise recent data on the control of the activity and the impact of both LTR-retrotransposons and MITEs on the evolution of plant genes and genomes.

DNA Transposable Elements↗
PubMed2006

Amphioxus: a peaceful anchovy fillet to illuminate Chordate Evolution (II).

The genome of the amphioxus is on the horizon. With Linda Holland and Jeremy Gibson-Brown at the forefront, with all the amphioxus community behind, and with the Joint Genome Institute, the amphioxus genome will see the light this year, 2006. Hope that it will reflect the "prototypical" preduplicative genome of vertebrates. It may answer definitively what the human genome did not: Are we vertebrates octaploid? Will it shed light on the novelties that helped non-chordates to be chordates? And more, will amphioxus, with a simpler genome, be developed to a senior "experimental model system", allowing the testing of molecular functions in a non-duplicated genome background and allowing genetic modification to "recapitulate" evolution? Thanks to an outstanding collaboration between labs, the laboratory culture of amphioxus is underway after years of hard work in the field. 2007 looks promising for amphioxus research.

Animals↗
PubMed2005

Size of the protein-coding genome and rate of molecular evolution.

In diploid populations of size N, there will be 2 Nmu mutations per nucleotide (nt) site (or per locus) per generation (mu stands for mutation rate). If either the population or the coding genome double in size, one expects 4 Nmu mutations. What is important is not the population size per se but the number of genes (coding sites), the two being often interconverted. Here we compared the total physical length of protein-coding genomes (n) with the corresponding absolute rates of synonymous substitution (K(S)), an empirical neutral reference. In the classical occupancy problem and in the coupons collector (CC) problem, n was expressed as the mean rate of change (K(CC)). Despite inherently very low power of the approaches involving averaging of rates, the mode of molecular evolution of the total size phenotype of the coding genome could be evidenced through differences between the genomic estimates of K(CC) [K(CC)=1/(ln n + 0.57721) n] and rate of molecular evolution, K(S). We found that (1) the estimates of n and K(S) are reciprocally correlated across taxa (r=0.812; p<< 0.001); (2) the gamete-cell division hypothesis (Chang et al. Proc Natl Acad Sci USA 91:827-831, 1994) can be confirmed independently in terms of K(CC)/K(S) ratios; (3) the time scale of molecular evolution changes with change in mutation rate, as previously shown by Takahata (Proc Natl Acad Sci USA 87:2419-2423, 1990), Takahata et al. (Genetics 130:925-938, 1992), and Vekemans and Slatkin (Genetics 137:1157-1165, 1994); (4) the generation time and population size (Lynch and Conery, Science 302:1401-1404, 2003) effects left their "signatures" at the level of the size phenotype of the protein-coding genome.

Codon↗
PubMed2006

Evolution of 2B and 2C genomic parts of species B Coxsackie viruses. Phylogenetic study and comparison with other regions.

Modern molecular approaches on the genome of enteroviruses' circulating strains have established new data about the mechanism and significance of its evolution. In the present study, 46 enteroviruses isolates, belonging to HEV-B species and exhibiting distinct origin in geographical or chronological terms, were investigated concerning their primary structure and phylogeny. Two regions of the aforementioned strains genome, which have not been thoroughly investigated (2B and 5' extreme of 2C) were amplified and sequenced for the first time. Phylogenetic and nucleotide analysis of the isolates' fragments, along with representative prototype sequences, demonstrate that the classification scheme of monophyly and accordance with the genotype, which characterizes VP1 region, is seriously disturbed. Moreover, the phylogenetic trees constructed from adjacent regions of the genome appear radically incongruent suggesting that the parameters that affect these portions are different or act in a different extent. Our study results an additional step in the study of enteroviruses evolution and inheritance, by investigating unstudied regions of newly sequenced strains and revealing that the primary structure and phylogeny of them is different not only comparably to the structural genome but also from one to another.

Enterovirus B, Human↗
PubMed2000

Genome gymnastics: unique modes of DNA evolution and processing in ciliates.

In some ciliates, the DNA sequences of the germline genomes have been profoundly modified during evolution, providing unprecedented examples of germline DNA malleability. Although the significance of the modifications and malleability is unclear, they may reflect the evolution of mechanisms that facilitate evolution. Because of the modifications, these ciliates must perform remarkable feats of cutting, splicing, rearrangement and elimination of DNA sequences to convert the chromosomal DNA in the germline genome (micronuclear genome) into gene-sized DNA molecules in the somatic genome (macronuclear genome). How these manipulations of DNA are guided and carried out is largely unknown. However, the organization and manipulation of ciliate DNA sequences are new phenomena that expand a general appreciation for the flexibility of DNA in evolution and development.

Animals↗