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479 results for “genomic evolution”
Data from: Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.
Recent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found dominant among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes concludes to the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the Microvirus. In addition, a peptidase gene was found in 11 Microviridae and its analysis concludes to a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in microviruses. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin.
Data from: Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints
It is generally believed that the organization of avian genomes remains highly conserved in evolution as chromosome number is constant and comparative chromosome painting demonstrated there to be very few interchromosomal rearrangements. The recent sequencing of the zebra finch (Taeniopygia guttata) genome allowed an assessment of the number of intra-chromosomal rearrangements between it and the chicken (Gallus gallus) genome, revealing a surprisingly high number of intra-chromosomal rearrangements. With the publication of the turkey (Meleagris gallopavo) genome it has become possible to describe intrachromosomal rearrangements between these three important avian species, gain insight into the direction of evolutionary change and assess whether breakpoint regions are reused in birds. To this end, we aligned entire chromosomes between chicken, turkey and zebra finch, identifying syntenic blocks of at least 250kb. Potential optimal pathways of rearrangements between each of the three genomes were determined, as was a potential Galliform ancestral organization. From this, our data suggest that around one third of chromosomal breakpoint regions may recur during avian evolution, with 10% of breakpoints apparently recurring in different lineages. This agrees with our previous hypothesis that mechanisms of genome evolution are driven by hotspots of non-allelic homologous recombination.
Plastid genome evolution in leafless members of the orchid subfamily Orchidoideae, with a focus on Degranvillea dermaptera
<p><strong>Premise</strong>: Leafless, heterotrophic plants are prime examples of organismal modification, the genomic consequences of which have received considerable interest. In particular, plastid genomes (plastomes) are being sequenced at a high rate, allowing continual refinement of conceptual models of reductive evolution in heterotrophs. Yet, numerous sampling gaps exist, hindering the ability to conduct comprehensive phylogenomic analyses in these plants. </p><p><strong>Methods</strong>: We sequenced and analyzed the plastome of <i>Degranvillea dermaptera</i>, a rarely collected, leafless orchid species from South America about which little is known, including its phylogenetic affinities. </p><p><strong>Key Results</strong>: We revealed the most reduced plastome sequenced to date among the orchid subfamily Orchidoideae. <i>Degranvillea</i> has lost the majority of genes found in leafy autotrophic species, is structurally rearranged, and has similar gene content to the most reduced plastomes among the orchids. We found strong evidence for the placement of <i>Degranvillea</i> within the subtribe Spiranthinae using models that explicitly account for heterotachy, or lineage-specific evolutionary rate variation over time. We further found evidence of relaxed selection on several genes and correlations among substitution rates and several other "traits" of the plastome among leafless members of orchid subfamily Orchidoideae. </p><p><strong>Conclusions</strong>: Our findings advance knowledge on the phylogenetic relationships and paths of plastid genome evolution among the orchids, which have experienced more independent transitions to heterotrophy than any other plant family. This study demonstrates the importance of herbarium collections in comparative genomics of poorly known species of conservation concern. </p>
Three reference genomes for freshwater diatom ecology and evolution
<p>This repository contains the genome assemblies and gene models provided for "Three reference genomes for freshwater diatom ecology and evolution"</p> <p>Authors:</p> <p>Wade R. Roberts (email: wader [at] uark [dot] edu)</p> <p>Andrew J. Alverson (email: aja [at] uark [dot] edu)</p> <p> </p> <p>The Whole Genome Shotgun (WGS) projects are available from NCBI GenBank under accession JALLPB020000000 (C. tholiformis), JALLBG020000000 (D. pseudostelligera), and JALLAZ020000000 (P. triporus).<strong></strong></p> <p><br>The following files are included:</p> <p>Cyclostephanos tholiformis strain AJA228-03</p> <p> aja228-03.consensus.fasta</p> <p> aja228-03.consensus.gff3<br> <br> aja228-03.consensus.proteins.fasta</p> <p> aja228-03.consensus.combined_uniprot_annotation.csv</p> <p> aja228-03.consensus.panther_annotation.csv</p> <p> aja228-03.consensus.pfam_annotation.csv</p> <p> </p> <p>Discostella pseudostelligera strain AJA232-27</p> <p> aja232-27.consensus.fasta</p> <p> aja232-27.consensus.gff3<br> <br> aja232-27.consensus.proteins.fasta</p> <p> aja232-27.consensus.combined_uniprot_annotation.csv</p> <p> aja232-27.consensus.panther_annotation.csv</p> <p> aja232-27.consensus.pfam_annotation.csv</p> <p> </p> <p>Praestephanos triporus strain AJA276-08</p> <p> aja276-08.consensus.fasta</p> <p> aja276-08.consensus.gff3<br> <br> aja276-08.consensus.proteins.fasta</p> <p> aja276-08.consensus.combined_uniprot_annotation.csv</p> <p> aja276-08.consensus.panther_annotation.csv</p> <p> aja276-08.consensus.pfam_annotation.csv</p> <p> </p> <p>R code and phylogenetic tree to reproduce Figure 1 in the manuscript</p> <p> plot-figure-1.R</p> <p> busc.prot.concat.partition.rooted.tree</p> <p> </p>
Homology-based classification of accessory proteins in coronavirus genomes uncovers extremely dynamic evolution of gene content
<p>Fasta files of ORF sequences for all orthogroups generated in the study.</p>
Evolution of binding preferences among whole-genome duplicated transcription factors
<p>Throughout evolution, new transcription factors (TFs) emerge by gene duplication, promoting growth and rewiring of transcriptional networks. How TF duplicates diverge is known for only a few studied cases. To provide a genome-scale view, we considered the 35% of budding yeast TFs, classified as whole-genome duplication (WGD)-retained paralogs. Using high-resolution profiling, we find that ~60% of paralogs evolved differential binding preferences. We show that this divergence results primarily from variations outside the DNA binding domains (DBDs), while DBD preferences remain largely conserved. Analysis of non-WGD orthologs revealed that ancestral preferences are unevenly split between duplicates, while new targets are acquired preferentially by the least conserved paralog (biased sub/neo-functionalization). Dimer-forming paralogs evolved mostly one-sided dependency, while other paralogs interacted through low-magnitude DNA-binding competition that minimized paralog interference. We discuss the implications of our findings for the evolutionary design of transcriptional networks.</p>
Genome size drives morphological evolution in organ-specific ways
<p class="MsoNormal">Morphogenesis is an emergent property of biochemical and cellular interactions during development. Genome size and the correlated trait of cell size can influence these interactions through effects on developmental rate and tissue geometry, ultimately driving the evolution of morphology. We tested whether variation in genome and body size is related to morphological variation in the heart and liver using nine species of the salamander genus <em>Plethodon</em> (genome sizes 29–67 gigabases). Our results show that overall organ size is a function of body size, whereas tissue structure changes dramatically with evolutionary increases in genome size. In the heart, increased genome size is correlated with a reduction of myocardia in the ventricle, yielding proportionally less force–producing mass and greater intertrabecular space. In the liver, increased genome size is correlated with fewer and larger vascular structures, positioning hepatocytes farther from the circulatory vessels that transport key metabolites. Although these structural changes should have obvious impacts on organ function, their effects on organismal performance and fitness may be negligible because low metabolic rates in salamanders relax selective pressure on function of key metabolic organs. Overall, this study suggests large genome and cell size influence the developmental systems involved in heart and liver morphogenesis.</p>
Figure 8 in Comparative genomics reveals the evolutionary history of the unicellular eukaryote class Litostomatea and its adaptive evolution based on biochemical metabolic capacity
Figure 8. RSCU of 14 newly sequenced litostomatean genomes/transcriptomes. Each codon is ploưed.
Data from: Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations
The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug–resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.
Data from: Disruptive selection without genome-wide evolution across a migratory divide
Transcontinental migration is a fascinating example of how animals can respond to climatic oscillation. Yet, quantitative data on fitness components are scarce, and the resulting population genetic consequences are poorly understood. Migratory divides, hybrid zones with a transition in migratory behaviour, provide a natural setting to investigate the micro-evolutionary dynamics induced by migration under sympatric conditions. Here, we studied the effects of migratory programme on survival, trait evolution and genome-wide patterns of population differentiation in a migratory divide of European barn swallows. We sampled a total of 824 individuals from both allopatric European populations wintering in central and southern Africa, respectively, along with two mixed populations from within the migratory divide. While most morphological characters varied by latitude consistent with Bergmann's rule, wing length co-varied with distance to wintering grounds. Survival data collected during a 5-year period provided strong evidence that this covariance is repeatedly generated by disruptive selection against intermediate phenotypes. Yet, selection-induced divergence did not translate into genome-wide genetic differentiation as assessed by microsatellites, mtDNA and >20 000 genome-wide SNP markers; nor did we find evidence of local genomic selection between migratory types. Among breeding populations, a single outlier locus mapped to the BUB1 gene with a role in mitotic and meiotic organization. Overall, this study provides evidence for an adaptive response to variation in migration behaviour continuously eroded by gene flow under current conditions of nonassortative mating. It supports the theoretical prediction that population differentiation is difficult to achieve under conditions of gene flow despite measurable disruptive selection.
The hornwort genome and early land plant evolution
<p>Hornworts, liverworts, and mosses are three early diverging clades of land plants, together composing the bryophytes. Here we report the draft genome sequence of the hornwort <a name="_Hlk532977332"><i>Anthoceros</i></a><i> angustus</i>. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the <i>Anthoceros</i> genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of <i>A. angustus</i> bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to life on land.</p> <p> </p>
Data from: Horizontal gene transfer and genome evolution in Methanosarcina
Background: Genomes of Methanosarcina spp. are among the largest archaeal genomes. One suggested reason for that is massive horizontal gene transfer (HGT) from bacteria. Genes of bacterial origin may be involved in the central metabolism and solute transport, in particular sugar synthesis, sulfur metabolism, phosphate metabolism, DNA repair, transport of small molecules etc. Horizontally transferred (HT) genes are considered to play the key role in the ability of Methanosarcina spp. to inhabit diverse environments. At the moment, genomes of three Methanosarcina spp. have been sequenced, and while these genomes vary in length and number of protein-coding genes, they all have been shown to accumulate HT genes. However, previous estimates had been made when fewer archaeal genomes were known. Moreover, several Methanosarcinaceae genomes from other genera have been sequenced recently. Here, we revise the census of genes of bacterial origin in Methanosarcinaceae. Results: About 5 % of Methanosarcina genes have been shown to be horizontally transferred from various bacterial groups to the last common ancestor either of Methanosarcinaceae, or Methanosarcina, or later in the evolution. Simulation of the composition of the NCBI protein non-redundant database for different years demonstrates that the estimates of the HGT rate have decreased drastically since 2002, the year of publication of the first Methanosarcina genome. The phylogenetic distribution of HT gene donors is non-uniform. Most HT genes were transferred from Firmicutes and Proteobacteria, while no HGT events from Actinobacteria to the common ancestor of Methanosarcinaceae were found. About 50 % of HT genes are involved in metabolism. Horizontal transfer of transcription factors is not common, while 46 % of horizontally transferred genes have demonstrated differential expression in a variety of conditions. HGT of complete operons is relatively infrequent and half of HT genes do not belong to operons. Conclusions: While genes of bacterial origin are still more frequent in Methanosarcinaceae than in other Archaea, most HGT events described earlier as Methanosarcina-specific seem to have occurred before the divergence of Methanosarcinaceae. Genes horizontally transferred from bacteria to archaea neither tend to be transferred with their regulators, nor in long operons.
The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution
<p class="Body">Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the <i>Pachyrhynchus sulphureomaculatus </i>genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. This large amount of reshuffling within chromosomes with few inter-chromosomal events contrasts with patterns seen in mammals in which the chromosomes tend to exchange larger blocks of material more readily. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta in a phylogenetic framework. For the first time, we find that synteny decays at an exponential rate relative to phylogenetic distance. Additionally, there are significant differences in decay rates between insect orders, this pattern was not driven by Lepidoptera alone which has a substantially different rate.</p>
Figure 1 from: Minton RL, Martinez Cruz MA, Farman ML, Perez KE (2016) Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). ZooKeys 626: 137-154. https://doi.org/10.3897/zookeys.626.9633
Figure 1 - Mitochondrial genome of Praticolella mexicana UTRGV and McAllen illustrated with an image of the species holotype (ANSP 426031). Gene order and sizes are shown relative to one another, not including non-coding regions. Genes are color coded by H (black) or L (red) strand. IUPAC single letter codes are used to identify tRNA genes.
Figure 3 from: Minton RL, Martinez Cruz MA, Farman ML, Perez KE (2016) Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). ZooKeys 626: 137-154. https://doi.org/10.3897/zookeys.626.9633
Figure 3 - Maximum likelihood phylogeny of gene order. Analysis in MLGO yielded a single tree. Branch support >50% is shown based on 100 bootstrap replicates. Bradybaenidae and Helicidae were recovered as monophyletic, but Helicoidea was not.
Figure 4 from: Minton RL, Martinez Cruz MA, Farman ML, Perez KE (2016) Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). ZooKeys 626: 137-154. https://doi.org/10.3897/zookeys.626.9633
Figure 4 - Ancestral gene order reconstructions for Helicoidea. Columns (A–E) correspond to labeled nodes in Figure 2. IUPAC single letter codes are used to identify tRNA genes. Rearrangements in red and blue are unique to Helicidae. The convergent rearrangement seen in Bradybaenidae, Camaena, and Praticolella is shown in yellow. The green rearrangement is unique to Aegista.
Figure 2 from: Minton RL, Martinez Cruz MA, Farman ML, Perez KE (2016) Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). ZooKeys 626: 137-154. https://doi.org/10.3897/zookeys.626.9633
Figure 2 - Maximum likelihood phylogeny of Stylommatophora protein coding genes. Analysis in IQTREE yielded a single tree (log likelihood = -89104.188) under the mtZOA+F+I+G4 model. Branch support >50% is shown based on 10,000 ultra-fast bootstrap replicates. Helicoidea, Bradybaenidae, and Helicidae were recovered as monophyletic. Nodes A-E refer to rearrangements shown in Figure 4.
Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica
<p>Plant cells arose through the endosymbiotic engulfment of a cyanobacterium that subsequently formed the chloroplast genome, enabling plants to develop new critical functions. Almost all chloroplast proteins are now encoded in the nucleus, but some chloroplast protein complexes are jointly encoded by both nuclear and chloroplast genes, which interact to facilitate essential plant functions, such as the photosystems. Allopolyploidy, resulting from the hybridization and genome doubling of two divergent species, can disrupt these fine-tuned cytonuclear interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with a uniparental organelle inheritance. Such unequal genome inheritance may affect the conformation of the five cytonuclear complexes in allopolyploids. We used <em>Brassica</em> as a model to study the effects of paleopolyploidy and dichotomic divergence in parental species, as well as the effects of recent allopolyploidy in <em>Brassica napus</em>, on genes implicated in cytonuclear complexes. Because the <em>B. napus</em> parental diploid species are paleohexaploids, we first identified paleologous copies of cytonuclear complex genes. We found that these genes are preferentially retained in duplicates, are nearly all transcribed and are undergoing strong purifying selection, in accordance with the ‘gene balance hypothesis’. Subsequently, we compared expression patterns of cytonuclear complex homoeolog genes between resynthesized <em>B. napus </em>individuals and their respective diploid parents. The neo-polyploids showed neither biased sub-genome expression nor homogenization of homoeologs, due to highly conserved parental chloroplast genomes. These findings provide new insights and an innovative framework to understand the impact of cytonuclear interactions on interspecific hybridization and allopolyploid speciation.</p>
Grasshopper genome reveals long-term conservation of the X chromosome and temporal variation in X chromosome evolution
<p>We present the first chromosome-level genome assembly of the grasshopper, <em>Locusta migratoria</em>, one of the largest insect genomes. We use coverage differences between females (XX) and males (X0) to identify the X chromosome gene content, and find that the X chromosome shows both complete dosage compensation in somatic tissues and an underrepresentation of testes-expressed genes. Remarkably, X-linked gene content from <em>L. migratoria </em>is highly conserved across four insect orders, namely Orthoptera, Hemiptera, Coleoptera and Diptera, and the 800 Mb grasshopper X chromosome is homologous to the fly ancestral X chromosome despite 400 million years of divergence, suggesting either repeated origin of sex chromosomes with highly similar gene content, or long-term conservation of the X chromosome. We use this broad conservation of the X chromosome to test for temporal dynamics to Fast-X evolution, and find evidence of a recent burst evolution for new X-linked genes in contrast to slow evolution of X-conserved genes. Additionally, our results reveal the X chromosome represents a hotspot for adaptive protein evolution related migration and the locust swarming phenotype. Overall, our results reveal a remarkable case of conservation and adaptation on the X chromosome.</p>
Evolution of Rosaceae chloroplast genomes highlights unique Cerasus diversification and independent origins of fruit cherry
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