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6 results for “ancient genome duplication”
Autopolyploidy Genome Duplication Preserves Other Ancient Genome Duplications in Atlantic Salmon (Salmo salar) Supplementary Datasets
<p>For various species, alignments were found between a protein database (produced from Zebrafish) and the sequenced genome of that species. Using Perl scripts and the alignments, gene models were identified in the various species based on the protein sequences. </p> <ul> <li>The gene models, for the various species, can be found in the .gff3 files. Some of the .gff3 files have had ribosomal proteins removed. </li> <li>Homeologous regions were then identified using Perl scripts and can be found in .gff3 files as well. They have Homeologous_Regions.gff3 in their title. </li> <li>Homeologous genes in these regions were counted (named XX_XX_Homeologous_Regions.txt), and compared to all of the genes (not just homeologous genes) in these regions (named Gene_Count_Homeolgous_XX_XX_XX.txt) to find the density. </li> <li>Homeologous gene sequences were compared to each other to identify the Ps values between them using a program called SNAP (Files with _Homeologous_region_analysis_version_1.2.txt at the end). </li> <li>The analyses of these files are summarized in "Pn_Ps_Values_Vertebrate_Homeologous_Regions.ods." </li> <li>The synteny between species can be found in the files with .seg extensions (These can be opened in IGV). </li> <li>A comparison between the gene density and Ps value for each homeologous region can be found in the file, "Gene_Density_Compared_to_Ps_Values.ods."</li> </ul> <p>Included is an extended readme file and Perl scripts (.pl extension) in a compressed file (Final_Scripts.tar.gz).</p>
Data from: Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes
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Data from: Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon
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Chromosome-level genome of Capitulum mitella reveals an ancient whole-genome duplication event and intertidal adaptation of barnacles
<p><span>Barnacles are the only sessile crustaceans inhabiting intertidal zone, an extremely stressful environment for sessile organisms. Herein, we report the chromosome-level genome of a stalked barnacle, <em>Capitulum</em> <em>mitella</em>, which is a dominant intertidal cirripede of the west Pacific Ocean coast. After comprehensive comparative genomic analyses, it is the first time to find an ancient whole-genome duplication (WGD) event that preceded the divergence of Lepadomorpha and Sessilia approximately </span><span>237 million years ago. </span><span>The retained duplicated genes of WGD are primarily enriched in many environmental information processing pathways, shedding light on its adaptive evolution of intertidal sessile life. In addition, transcriptomic and metabolomic sequencing and analyses of <em>C</em>. <em>mitella</em> indicated that the upregulation of some expanded anti-stress factors and accumulation of acyl-carnitines help barnacles adapt to stressful intertidal conditions. Therefore, this study provides a valuable resource for understanding the unique intertidal adaptation mechanism of sessile crustaceans and reveals novel WGD events in invertebrates.</span></p>
Chromosome-level genome of Capitulum mitella reveals an ancient whole-genome duplication event and intertidal adaptation of barnacles
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Ancient genomic regulatory blocks are a major source for gene deserts in vertebrates after whole genome duplications
GEO Series GSE136554. Branchiostoma lanceolatum; Danio rerio; Mus musculus. 12 samples. Type: Other.
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