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 883 records · Page 49Linked to original sources
PubMed2005

A trajectory of increasing activity and the elaboration of chemosensory modality: a new perspective on vertebrate origins.

This article reviews recent advances in comparative biological studies of vertebrate origins, with the aim of revisiting the long-standing controversy concerning these origins. Since early vertebrate evolution is paralleled by an evolutionary trend towards increasing activity, I focus on the evolution of respiratory and circulatory systems and discuss their potential roles in early vertebrate evolution. I give particular attention to the nasohypophyseal duct, an orifice characteristically found in agnathan vertebrates, and hypothesize that this duct originally functioned to convey oxygen dissolved in seawater to the respiratory gills. The chemosensory cell population that originated from the wall of the duct became the incipient olfactory organ and played a role in the organization of feeding behavior. An increase in chemosensory receptor genes via large-scale genomic evolution in the vertebrate lineage caused the repertoire of chemosensory cells to diversify and led to the appearance of the integrative center, including telencephalic structures typically lacking in protochordates.

Animals↗
PubMed1996

Single base-pair substitutions in pathology and evolution: two sides to the same coin.

Relative single base-pair substitution rates in human genes, derived from a collection of > 2,700 point mutations causing human genetic disease, were related to the results of an evolutionary gene/pseudogene comparison. At the mononucleotide level, notable differences between the two datasets were confined to C-to-T and G-to-A transitions, both being rarer in gene/pseudogene alignments than among disease-associated lesions. Relative nearest neighbour-dependent substitution rates were found to be similar in the two datasets, indicating the long-term stability of these parameters during human genome evolution. Allowing for the 5' and 3' nucleotides flanking mutated sites, the primary likelihood of mutation generation could be demonstrated to be biased toward the avoidance of replacements that: (1) change the chemical characteristics of the encoded amino acid residue substantially, and (2) have a high chance of resulting in genetic disease in humans. A similar bias is also reflected in the evolutionary history of human and rodent proteins: amino acid replacements that currently exhibit a high likelihood of coming to clinical attention have been less likely to be accepted during protein evolution.

Base Composition↗
PubMed1994

DNA sequence divergence among derivatives of Escherichia coli K-12 detected by arbitrary primer PCR (random amplified polymorphic DNA) fingerprinting.

Derivatives of Escherichia coli K-12 of known ancestry were characterized by random amplified polymorphic DNA (RAPD) fingerprinting to better understand genome evolution in this family of closely related strains. This sensitive method entails PCR amplification with arbitrary primers at low stringency and yields arrays of anonymous DNA fragments that are strain specific. Among 150 fragments scored, eight were polymorphic in that they were produced from some but not all strains. Seven polymorphic bands were chromosomal, and one was from the F-factor plasmid. Five of the six mapped polymorphic chromosomal bands came from just 7% of the genome, a 340-kb segment that includes the terminus of replication. Two of these were from the cryptic Rac prophage, and the inability to amplify them from strains was attributable to deletion (excision) or to rearrangement of Rac. Two other terminus-region segments that resulted in polymorphic bands appeared to have sustained point mutations that affected the ability to amplify them. Control experiments showed that RAPD bands from the 340-kb terminus-region segment and also from two plasmids (P1 and F) were represented in approximate proportion to their size. Optimization experiments showed that the concentration of thermostable polymerase strongly affected the arrays of RAPD products obtained. Comparison of RAPD polymorphisms and positions of strains exhibiting them in the pedigree suggests that many sequence changes occurred in these historic E. coli strains during their storage. We propose that the clustering of such mutations near the terminus reflects errors during completion of chromosome replication, possibly during slow growth in the stab cultures that were often used to store E. coli strains in the early years of bacterial genetics.

Base Sequence↗
PubMed2000

Genomic exploration of the hemiascomycetous yeasts: 5. Saccharomyces bayanus var. uvarum.

Saccharomyces bayanus var. uvarum investigated here is the species closest to Saccharomyces cerevisiae. Random sequence tags (RSTs) allowed us to identify homologues to 2789 open reading frames (ORFs) in S. cerevisiae, ORFs duplicated in S. uvarum but not in S. cerevisiae, centromeres, tRNAs, homologues of Ty1/2 and Ty4 retrotransposons, and a complete rDNA repeat. Only 13 RSTs seem to be homologous to sequences in other organisms but not in S. cerevisiae. As the synteny between the two species is very high, cases in which synteny is lost suggest special mechanisms of genome evolution. The corresponding RSTs revealed that S. uvarum can exist without any S. cerevisiae DNA introgression. Accession numbers are from AL397139 to AL402278 in the EMBL databank.

Ascomycota↗
PubMed2006

Homeologous recombination plays a major role in chromosome rearrangements that occur during meiosis of Brassica napus haploids.

Chromosomal rearrangements can be triggered by recombination between distinct but related regions. Brassica napus (AACC; 2n = 38) is a recent allopolyploid species whose progenitor genomes are widely replicated. In this article, we analyze the extent to which chromosomal rearrangements originate from homeologous recombination during meiosis of haploid B. napus (n = 19) by genotyping progenies of haploid x euploid B. napus with molecular markers. Our study focuses on three pairs of homeologous regions selected for their differing levels of divergence (N1/N11, N3/N13, and N9/N18). We show that a high number of chromosomal rearrangements occur during meiosis of B. napus haploid and are transmitted by first division restitution (FDR)-like unreduced gametes to their progeny; half of the progeny of Darmor-bzh haploids display duplications and/or losses in the chromosomal regions being studied. We demonstrate that half of these rearrangements are due to recombination between regions of primary homeology, which represents a 10- to 100-fold increase compared to the frequency of homeologous recombination measured in euploid lines. Some of the other rearrangements certainly result from recombination between paralogous regions because we observed an average of one to two autosyndetic A-A and/or C-C bivalents at metaphase I of the B. napus haploid. These results are discussed in the context of genome evolution of B. napus.

Alleles↗
PubMed2000

Genomic variations in echovirus 30 persistent isolates recovered from a chronically infected immunodeficient child and comparison with the reference strain.

Seven sequential isolates of echovirus type 30 (EV30) were recovered over 22 months from a child with severe combined immune deficiency syndrome. The nucleotide sequences of the 5' halves of the genomes (4,400 nucleotides) of the first (S1) and last (S7) isolates were determined and compared with that of the EV30 Bastianni reference strain, also determined in this study. In genome regions P1 and P2, 101 variations were identified between the two isolates. Synonymous differences far outnumbered nonsynonymous differences. Amino acid changes affected both capsid and nonstructural polypeptides (particularly 2B). The VP1 nucleotide sequences of the seven isolates were determined to analyze genome evolution during the chronic infection. In the phylogenetic tree, the seven isolates were directly related to the prototype strain in an individual monophyletic group, strongly suggesting that the chronic infection in the child arose from a single persistent EV30 isolate. Four lineages were observed in the persistent isolates. Isolates S2, S4, S5, and S6 were close relatives of one another, whereas isolates S1 and S3 formed individual lineages. Isolate S7, distantly related to all other isolates, formed the fourth lineage. These findings suggest the quasispecies nature of the genomes of the seven sequential EV30 isolates. Grouping of persistent isolates on the basis of replicative capacities was consistent with phylogenetic relationships. Overall, the results indicate that genetically related EV30 variants with different replicative capacities coexisted in a carrier state, probably in the gastrointestinal tract, during the infection of the child.

5' Untranslated Regions↗
PubMed2002

Sequence variation in the gene encoding the 10-kDa prolamin in Oryza (Poaceae). I. Phylogenetic Implications.

Oryza L. (Poaceae) contains approximately 20 wild and two domesticated species and nine genomes. Major disagreements exist on its systematics and genome evolution. Sequence polymorphism in the gene that encodes the 10-kDa prolamin polypeptide (a seed storage protein) was used to determine phylogenetic relationships and evaluate current systematics for 19 Oryza species. This gene in Oryza is approximately 402-bp long, and includes a 72-bp signal peptide region. A strict consensus tree shows Oryza brachyantha (FF) as the most basal species, followed by a polytomy of three clades that can be delineated based on genome composition: (1) the GG clade: Oryza granulata and Oryza meyeriana, (2) the EE clade: Oryza australiensis, and (3) the ABCD clade: the remaining Oryza species. Two subclades within the ABCD clade emerge, one containing species with the AA genome, the other with components of the BC and D genomes. Members of the AA subclade form a polytomy and were delineated by a single 3-base deletion. The African species Oryza punctata (BB) and the South American-endemic CCDD genome species form a strong lineage, pointing to a close genetic affinity of O. punctata to the missing DD genome donor. The strong association between the CC and BBCC species implies convergence at the gene level. The study supports the following sectional units of Oryza: Section Oryza (Series sativae and officinaliae), Section australiensis, Section Granulata, Section Brachyantha.

Journal Article↗
PubMed2005

A genomic population genetics analysis of the pathogenic enterocyte effacement island in Escherichia coli: the search for the unit of selection.

Comparative genomic analysis is a powerful tool for understanding the history and organization of complete genomes. The mathematical tools of population genetics combined with genomic analysis provide a powerful approach to dissect heterogeneities in genome evolution. This study presents a hierarchical analysis of the enterocyte and effacement island (35 kb), which is found in the enteropathogenic and enterohemorrhagic strains in Escherichia coli and in Citrobacter rodentium. The locus of enterocyte and effacement in E. coli is considered to be a clonal unit inside a clonal organism and is expected to evolve as a single unit. This analysis examines the clonal assumption by determining genetic diversity, GC content, and the substitution rates at the different functional levels of (i) the complete pathogenic island, (ii) the five operons in which the island is organized, and (iii) for each of the individual 41 genes that comprise the locus. We find that there is a conserved region that is composed of genes that belong to the type III secretion system and that may be products of horizontal transfer. A more diverse region is composed of genes for secreted proteins and genes that we infer to be original components of the E. coli genome. This genetic mosaic seems to be differentially affected by selection and mutation. Our results suggest that recombination and selection may be breaking this structure so that different elements are, at best, weakly coupled in their evolution. These observations suggest that the units of selection are not the complete island, but rather, much smaller units that comprise the island.

Codon↗
PubMed2004

A genome sequence survey of the filarial nematode Brugia malayi: repeats, gene discovery, and comparative genomics.

Comparative nematode genomics has thus far been largely constrained to the genus Caenorhabditis, but a huge diversity of other nematode species, and genomes, exist. The Brugia malayi genome is approximately 100 Mb in size, and distributed across five chromosome pairs. Previous genomic investigations have included definition of major repeat classes and sequencing of selected genes. We have generated over 18,000 sequences from the ends of large-insert clones from bacterial artificial chromosome libraries. These end sequences, totalling over 10 Mb of sequence, contain just under 8 Mb of unique sequence. We identified the known Mbo I and Hha I repeat families in the sequence data, and also identified several new repeats based on their abundance. Genomic copies of 17% of B. malayi genes defined by expressed sequence tags have been identified. Nearly one quarter of end sequences can encode peptides with significant similarity to protein sequences in the public databases, and we estimate that we have identified more than 2700 new B. malayi genes. Importantly, 459 end sequences had homologues in other organisms, but lacked a match in the completely sequenced genomes of Caenorhabditis briggsae and Caenorhabditis elegans, emphasising the role of gene loss in genome evolution. B. malayi is estimated to have over 18,500 protein-coding genes.

Animals↗
PubMed1994

The marsupial mitochondrial genome and the evolution of placental mammals.

The entire nucleotide sequence of the mitochondrial genome of the American opossum, Didelphis virginiana, was determined. Two major features distinguish this genome from those of other mammals. First, five tRNA genes around the origin of light strand replication are rearranged. Second, the anticodon of tRNA(Asp) is posttranscriptionally changed by an RNA editing process such that its coding capacity is altered. When the complete protein-coding region of the mitochondrial genome is used as an outgroup for placental mammals it can be shown that rodents represent an earlier branch among placental mammals than primates and artiodactyls and that artiodactyls share a common ancestor with carnivores. The overall rates of evolution of most of the mitochondrial genome of placentals are clock-like. Furthermore, the data indicate that the lineages leading to the mouse and rat may have diverged from each other as much as 35 million years ago.

Amino Acid Sequence↗
PubMed2026

Overcoming cancer resistance in pancreatic cancer: toward dynamic precision oncology.

Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal malignancy, largely because of its profound and evolving therapeutic resistance. Resistance is not determined by a single molecular alteration but arises from interconnected mechanisms, including intrinsic resistance, treatment-induced adaptive resistance, acquired resistance, genomic evolution, clonal selection, cancer stemness, phenotypic plasticity, metabolic adaptation, and tumor microenvironment-mediated effects. Emerging therapeutic approaches targeting KRAS/RAS signaling, stromal and immune components, metabolic dependencies, and DNA damage repair pathways offer opportunities to address these mechanisms, although durable efficacy remains limited by biological heterogeneity and adaptive responses. In this review, we examine therapeutic resistance as an evolutionary and multidimensional process and summarize emerging strategies for overcoming resistance. We further propose a Dynamic Precision Oncology (DPO) framework that extends conventional precision oncology beyond baseline molecular profiling by integrating longitudinal assessment of tumor genomics, circulating tumor DNA, CA19-9, imaging, radiomics, and clinical characteristics. This framework emphasizes iterative detection and characterization of emerging resistance, mechanism-informed treatment adaptation, and subsequent reassessment rather than automatic treatment modification based on a single biomarker. DPO may provide a conceptual framework for integrating evolving tumor biology into treatment decision-making, while prospective studies are needed to validate biomarkers, define actionable thresholds, and determine whether longitudinal resistance-guided strategies improve clinical outcomes in PDAC.

Humans↗
PubMed2006

Genetic map-based analysis of genome structure in the homosporous fern Ceratopteris richardii.

Homosporous ferns have extremely high chromosome numbers relative to flowering plants, but the species with the lowest chromosome numbers show gene expression patterns typical of diploid organisms, suggesting that they may be diploidized ancient polyploids. To investigate the role of polyploidy in fern genome evolution, and to provide permanent genetic resources for this neglected group, we constructed a high-resolution genetic linkage map of the homosporous fern model species, Ceratopteris richardii (n = 39). Linkage map construction employed 488 doubled haploid lines (DHLs) that were genotyped for 368 RFLP, 358 AFLP, and 3 isozyme markers. Forty-one linkage groups were recovered, with average spacing between markers of 3.18 cM. Most loci (approximately 76%) are duplicated and most duplicates occur on different linkage groups, indicating that as in other eukaryotic genomes, gene duplication plays a prominent role in shaping the architecture of fern genomes. Although past polyploidization is a potential mechanism for the observed abundance of gene duplicates, a wide range in the number of gene duplicates as well as the absence of large syntenic regions consisting of duplicated gene copies implies that small-scale duplications may be the primary mode of gene duplication in C. richardii. Alternatively, evidence of past polyploidization(s) may be masked by extensive chromosomal rearrangements as well as smaller-scale duplications and deletions following polyploidization(s).

Chromosome Mapping↗
PubMed2026

A marine-derived fungal genome of Annulohypoxylon annulatoides reveals AT-rich isochores with putative regulatory functions.

Marine and coastal fungi experience intense environmental variability, yet the genomic features associated with tolerance to such conditions remain unclear. From 56 fungal isolates collected along the Lailai rocky shore in northern Taiwan, we selected the coastal isolate Annulohypoxylon annulatoides RYS0019 for phenotypic and genomic investigation because of its prevalence and distinctive stress-response profile. Compared with 5 bark-derived conspecific strains, RYS0019 showed distinct growth and recovery dynamics under salinity, temperature, and UV-associated stress treatments. We generated a high-quality 41.8 Mb de novo genome assembly with 11,523 predicted proteins and compared it with 15 other Hypoxylaceae genomes. Across Annulohypoxylon genomes, we identified variably sized and dispersed AT-rich isochores that are repeat-enriched and gene-poor. Despite variation in AT content, core gene content and Pfam domain profiles remained broadly conserved. Most AT-rich isochores were embedded within syntenically conserved regions and showed limited positional conservation across species, supporting recurrent, lineage-specific formation or expansion after species divergence. These regions also exhibit several sequence and structural features consistent with scaffold/matrix attachment regions, raising the possibility that they influence higher-order genome organization or context-dependent regulation. Together, our findings identify repeat-rich genome architecture as a dynamic feature of Annulohypoxylon genome evolution and provide a framework for testing how such regions may contribute to fungal environmental flexibility.

Genome, Fungal↗
PubMed2002

Comparative mapping of human Chromosome 19 with the chicken shows conserved synteny and gives an insight into chromosomal evolution.

Human Chromosome 19 (HSA19) is virtually completely sequenced. A complete physical contig map made up of BACs and cosmids is also available for this chromosome. It is, therefore, a rich source of information that we have used as the basis for a comparative mapping study with the chicken. Various orthologs of genes known to map to HSA19 have been mapped in the chicken. Five chicken microchromosomes (two of which were previously undefined) are seen to show conserved synteny with this chromosome, along with individual gene homologs on Chr 1 and another tiny microchromosome. Compared with the mouse, which has 12 chromosomal regions homologous to HSA19, the chicken genotype displays fewer evolutionary rearrangements. The ancestral nature of the chicken karyotype is demonstrated and may prove to be an excellent tool for studying genome evolution.

Animals↗
PubMed2005

Polydnavirus genomes reflect their dual roles as mutualists and pathogens.

Symbionts often exhibit significant reductions in genome complexity while pathogens often exhibit increased complexity through acquisition and diversification of virulence determinants. A few organisms have evolved complex life cycles in which they interact as symbionts with one host and pathogens with another. How the predicted and opposing influences of symbiosis and pathogenesis affect genome evolution in such instances, however, is unclear. The Polydnaviridae is a family of double-stranded (ds) DNA viruses associated with parasitoid wasps that parasitize other insects. Polydnaviruses (PDVs) only replicate in wasps but infect and cause severe disease in parasitized hosts. This disease is essential for survival of the parasitoid's offspring. Thus, a true mutualism exists between PDVs and wasps as viral transmission depends on parasitoid survival and parasitoid survival depends on viral infection of the wasp's host. To investigate how life cycle and ancestry affect PDVs, we compared the genomes of Campoletis sonorensis ichnovirus (CsIV) and Microplitis demolitor bracovirus (MdBV). CsIV and MdBV have no direct common ancestor, yet their encapsidated genomes share several features including segmentation, diversification of virulence genes into families, and the absence of genes required for replication. In contrast, CsIV and MdBV share few genes expressed in parasitized hosts. We conclude that the similar organizational features of PDV genomes reflect their shared life cycle but that PDVs associated with ichneumonid and braconid wasps have likely evolved different strategies to cause disease in the wasp's host and promote parasitoid survival.

Animals↗
PubMed2006

Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.).

Intron length polymorphisms (ILPs) have been used as genetic markers in some studies. However, a systematic investigation and large-scale exploitation of ILP markers has not been reported. In this study, we performed a genome-wide search of ILPs between two subspecies (indica and japonica) in rice using the draft genomic sequences of cultivars 93-11 (indica) and Nipponbare (japonica) and 32,127 full-length cDNA sequences of Nipponbare obtained from public databases. We identified 13,308 putative ILPs. Based on these putative ILPs, we developed 5811 candidate ILP markers via electronic-PCR with primers designed in flanking exons. We further conducted experiment to verify the candidate ILP markers. Out of 215 candidate ILP markers tested on 93-11, Nipponbare and their hybrid, we successfully exploited 173 codominant ILP markers. Further analyses on 10 rice accessions showed that these ILP markers were widely applicable and most (71.1%) exhibited subspecies specificity. This feature suggests that ILPs would be useful for the studies of genome evolution and inter-subspecies heterosis and for cross-subspecies marker-assisted selection in rice. In addition, by testing 51 pairs of the ILP primers on five Gramineae plants and three dicot plants, we found another desirable characteristic of rice ILP markers that they have high transferability to other plants.

Base Sequence↗
PubMed2005

A two-edged role for the transposable element Kiddo in the rice ubiquitin2 promoter.

Miniature inverted repeat transposable elements (MITEs) are thought to be a driving force for genome evolution. Although numerous MITEs are found associated with genes, little is known about their function in gene regulation. Whereas the rice ubiquitin2 (rubq2) promoter in rice (Oryza sativa) line IR24 contains two nested MITEs (Kiddo and MDM1), that in line T309 has lost Kiddo, providing an opportunity to understand the role of MITEs in promoter function. No difference in endogenous rubq2 transcript levels between T309 and IR24 was evident using RT-PCR. However, promoter analysis using both transient and stably transformed calli revealed that Kiddo contributed some 20% of the total expression. Bisulfite genomic sequencing of the rubq2 promoters revealed specific DNA methylation at both symmetric and asymmetric cytosine residues on the MITE sequences, possibly induced by low levels of homologous transcripts. When methylation of the MITEs was blocked by 5-azacytidine treatment, a threefold increase in the endogenous rubq2 transcript level was detected in IR24 compared with that in T309. Together with the observed MITE methylation pattern, the detection of low levels of transcripts, but not small RNAs, corresponding to Kiddo and MDM1 suggested that RNA-dependent DNA methylation is induced by MITE transcripts. We conclude that, although Kiddo enhances transcription from the rubq2 promoter, this effect is mitigated by sequence-specific epigenetic modification.

Base Sequence↗
PubMed2000

Amphidiploid Brassica juncea contains conserved progenitor genomes.

To perform a detailed study of genome evolution in the natural Brassica amphidiploid B. juncea, we have constructed two linkage maps based on RFLP (restriction fragment length polymorphism) markers; one generated from a cross between a resynthesized B. juncea (a chromosome doubled interspecific B. rapa x B. nigra hybrid) and a natural B. juncea cultivar, the other from a cross between two B. juncea cultivars. By using a common cultivar in both crosses, the two maps could be unambiguously integrated. All loci exhibited disomic inheritance of parental alleles in the natural x resynthesized cross, showing that B. rapa chromosomes paired exclusively with their A-genome homologues in B. juncea and that B. nigra chromosomes likewise paired with their B-genome homologues. The maps derived from the two crosses were also perfectly collinear. Furthermore, these maps were collinear with maps of the diploid progenitor species (B. nigra and B. rapa) produced using the same set of RFLP probes. These data indicate that the genome of B. juncea has remained essentially unchanged since polyploid formation. Our observations appear to refute the suggestion that the formation of polyploid genomes is accompanied by rapid change in genome structure.

Brassica↗