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17 results for “genome reduction”
Genome alignments for the article "Targeted reduction of highly abundant transcripts with pseudo-random primers"
<p>Sequence alignment (Moirai workflow management) for the article "Targeted reduction of highly abundant transcripts with pseudo-random primers". File names indicate unique run identifiers. In the manuscript, shorter names are used:</p> <ul> <li>NC12: NC12_1.CAGEscan_short-reads.20150629125015</li> <li>NC17: NC16-17_1.CAGEscan_short-reads.20150625154740</li> <li>NC22b: NC22b.CAGEscan_short-reads.20150625152335</li> <li>NCki: NCms10058_1.CAGEscan_short-reads.20150625154711</li> </ul>
Genome streamlining: effect of mutation rate and population size on genome size reduction: simulated data
<p>Lineages data of populations simulated with Aevol (<a href="https://gitlab.inria.fr/aevol/aevol">https://gitlab.inria.fr/aevol/aevol</a>), and the Wild-Types sequences used for that.</p> <p>Conditions: change of mutation rate, population size, or both.<br>Mutational bias: none, insertion bias or deletion bias</p>
Let There Be Light: Genome-reduction Enables Bacillus subtilis to Produce Disulfide-bonded Gaussia Luciferase
<p>Supplemental Material:</p> <ul> <li>Plasmid Maps in PNG format</li> <li>Plasmid Sequences in GB format</li> <li>Plasmid Sequences in DNA format (SnapGene)</li> </ul>
Genome sequence and characterization of a freshwater photoarsenotroph, Cereibacter azotoformans strain ORIO, isolated from sediments capable of cyclic light-dark arsenic oxidation and reduction
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A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component
<p>Over the last six decades, populations of the bumblebees <em>Bombus sylvicola</em> and <em>Bombus balteatus</em> in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations.</p> <p>We analysed whole-genome sequencing data and morphometric measurements of 580 samples of both species from seven high-altitude localities. Out of 281 samples originally identified as <em>B</em>. <em>sylvicola</em>, 67 formed a separate genetic cluster comprising a newly-discovered cryptic species ("incognitus"). However, an absence of genetic structure within species suggests that gene flow is common between mountains. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme was implicated in body size variation. We identified evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is possible that shared environmental effects between colonies are responsible. Our results provide evidence for ongoing modification of a morphological trait important for pollination and indicate that this trait probably has a complex genetic and environmental basis.</p> <p>This archive contains genetic variation data derived from genome sequencing of 580 bumblebee samples collected from high-elevation locations in Colorado. The species are Bombus sylvicola (n=214), Bombus balteatus (n=299) and "incognitus" (n=67).</p>
Parallel dynamics of bacterial genome reduction across independent transitions to endosymbiosis.
<p>The establishment of symbiosis dramatically alters the evolution of the associated species, making symbiotic systems ideal models for studying the impact of lifestyle changes on genomes. Here, we focused on Enterobacterales, a large and ancient bacterial lineage that includes endosymbionts with diverse host associations, ranging from gut inhabitants to intracellular environments, and from horizontal to vertical transmission. Leveraging over two hundred genomes, along with cutting-edge single-copy gene concatenation and multi-copy gene family approaches, we inferred a robust phylogenetic framework that supports eleven independent transitions to endosymbiosis. Inferences on patterns of genome evolution confirm previous hypotheses about the processes underlying genome reduction: a substantial spike in gene loss always occurs simultaneously with the establishment of endosymbiosis, while a reduction in gene acquisition mechanisms is associated with the subsequent genome erosion. Furthermore, gene family loss frequencies were correlated across independent endosymbiotic clades; genes with more conserved functions and stronger constraints on sequence evolution are lost less frequently, suggesting that differences in gene essentiality and dispensability drive the observed parallelism. Our analyses contribute to the coming of age of the theory of genome evolution in symbiotic associations and provide novel insights into the importance of recombination as an opposing force against genome erosion.</p>
A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component
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Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence - between species core gene alignments
<p><span>Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of <i>Streptococcus suis</i>, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of <i>S. suis</i>). While genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, i.e. host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of non-functional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a predictive marker of pathogenicity in bacteria.</span></p>
Data from: Harvest-associated size reductions and genomic changes within two generations in wild walleye populations
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Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence - between species core gene alignments
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Genome complexity reduction and high throughput sequencing of green iguana (Iguana iguana) cause a paradigm shift in understanding sex chromosomal linkages on homomorphic X and Y sex chromosomes
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Data from: Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology
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Genome-wide reductions in active chromatin, paused RNA Polymerase II and nucleosome turnover during heat shock
GEO Series GSE30755. Drosophila melanogaster. 18 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Data from: Genome reduction and microbe-host interactions drive adaptation of a sulfur-oxidizing bacterium associated with a cold seep sponge
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Data from: Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum
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Development of a potent epigenetic editor targeting human PCSK9 with durable reduction of cholesterol in mice and non-human primates [whole genome methyl-seq]
GEO Series GSE282521. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genome-wide reduction in chromatin accessibility and unique transcription factor footprints in endothelial cells and fibroblasts in scleroderma skin
GEO Series GSE163199. Homo sapiens. 24 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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OpenNeuro
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