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DupScan：脊椎动物基因组重复预测与可视化数据库。

DupScan: predicting and visualizing vertebrate genome duplication database.

机构信息

School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China.

Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China.

出版信息

Nucleic Acids Res. 2023 Jan 6;51(D1):D906-D912. doi: 10.1093/nar/gkac718.

DOI:10.1093/nar/gkac718
PMID:36018807
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9825427/
Abstract

Duplicated genes prevail in vertebrates and are important in the acquisition of new genes and novelties. Whole genome duplication (WGD) is one of the sources of duplicated genes. It can provide raw materials for natural selection by increasing the flexibility and complexity of the genome. WGDs are the driving force for the evolution of vertebrates and contribute greatly to their species diversity, especially in fish species with complicated WGD patterns. Here, we constructed the DupScan database (https://dupscan.sysumeg.com/) by integrating 106 chromosomal-level genomes, which can analyze and visualize synteny at both the gene and genome scales, visualize the Ka, Ks, and 4DTV values, and browse genomes. DupScan was used to perform functional adaptation for the intricate WGD investigation based on synteny matching. DupScan supports the analysis of five WGD rounds (R): VGD2 (vertebrate genome duplication 2), Ars3R (Acipenser-ruthenus-specific 3R), Pss3R (Polyodon-spathula-specific 3R), Ts3R (teleost-specific duplication 3R), Ss4R (salmonid-specific 4R), and Cs4R (carp-specific 4R). DupScan serves as one-stop analysis platform for synteny and WGD research in which users can analyze and predict synteny and WGD patterns across 106 species of whole genome sequences. This further aided us in elucidating genome evolutionary patterns across over 60,000 vertebrate species with synteny and WGD events.

摘要

重复基因在脊椎动物中普遍存在，对获得新基因和新特性具有重要作用。全基因组复制（Whole genome duplication，WGD）是重复基因的来源之一。它可以通过增加基因组的灵活性和复杂性为自然选择提供原材料。WGD 是脊椎动物进化的驱动力，对它们的物种多样性做出了巨大贡献，尤其是在具有复杂 WGD 模式的鱼类物种中。在这里，我们通过整合 106 个染色体水平的基因组，构建了 DupScan 数据库（https://dupscan.sysumeg.com/），可以在基因和基因组尺度上分析和可视化同线性，可视化 Ka、Ks 和 4DTV 值，并浏览基因组。DupScan 用于基于同线性匹配进行复杂 WGD 调查的功能适应。DupScan 支持 5 轮 WGD（R）的分析：VGD2（脊椎动物基因组复制 2）、Ars3R（Acipenser-ruthenus 特异性 3R）、Pss3R（Polyodon-spathula 特异性 3R）、Ts3R（硬骨鱼特异性复制 3R）、Ss4R（鲑鱼特异性 4R）和 Cs4R（鲤鱼特异性 4R）。DupScan 是同线性和 WGD 研究的一站式分析平台，用户可以在 106 个全基因组序列物种中分析和预测同线性和 WGD 模式。这进一步帮助我们阐明了超过 60,000 个具有同线性和 WGD 事件的脊椎动物物种的基因组进化模式。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/126f/9825427/1166c1031b2b/gkac718fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/126f/9825427/667fa90996e8/gkac718fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/126f/9825427/eafcc9df2e7f/gkac718fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/126f/9825427/b5898591d12f/gkac718fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/126f/9825427/1166c1031b2b/gkac718fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/126f/9825427/667fa90996e8/gkac718fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/126f/9825427/eafcc9df2e7f/gkac718fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/126f/9825427/b5898591d12f/gkac718fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/126f/9825427/1166c1031b2b/gkac718fig4.jpg

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