Comparative genomic data of the Avian Phylogenomics Project.
Comparative genomic data of the Avian Phylogenomics Project.
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DOI：
10.1186/2047-217x-3-26
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发表时间：
2014
期刊：
影响因子：
9.2
通讯作者：
Avian Genome Consortium
中科院分区：
文献类型：
--
作者：
Zhang G;Li B;Li C;Gilbert MT;Jarvis ED;Wang J;Avian Genome Consortium
现代鸟类的进化关系是系统生物学中最难理解的问题之一，并且已经争论了几个世纪。为了应对这一挑战，我们组装或收集了48种鸟类的基因组，涵盖了大多数鸟类，包括所有的新颌目和五个古颌目中的两个，并使用基因组构建了一个基因组规模的鸟类系统发育树，并进行了比较基因组学分析（Jarvis et al. in press; Zhang et al. in press）。在这里，我们发布了与比较基因组分析相关的组件和数据集，其中包括38个新测序的鸟类基因组以及先前发布或同时发布的鸡，斑马雀，火鸡，鸽子，游隼，鸭，虎皮鹦鹉，阿德利企鹅，帝企鹅和中地雀的基因组。我们希望这一资源将服务于未来的研究工作，如基因组学和比较基因组学。使用Illumina HiSeq 2000平台对38个鸟类基因组进行测序，并使用全基因组鸟枪策略进行组装。根据组装体的N50支架大小，将48个基因组分为两组：高深度组，包括以高覆盖度（> 50 X）测序的23个物种，具有多个插入大小文库，导致N50支架大小大于1 Mb（除了白喉Tinamou和秃鹰）;和一个低深度组，包括25个在低覆盖度（~ 30倍）下测序的物种两个插入片段大小的文库产生约50 kb的平均N50支架大小。重复元件占鸟类基因组的4%-22%。组装的支架允许基于同源性的注释每个鸟类基因组中相对于鸡、斑胸草雀和人的13，000 ~ 17，000个蛋白质编码基因，以及比较和序列保守性分析。在这里，我们发布了38个新测序的鸟类物种的全基因组组装，链接了其余10个物种中7个的基因组组装下载，并提供了我们的鸟类系统基因组学项目中生成和使用的基因组数据指南。据我们所知，鸟类系统基因组学项目是迄今为止最大的脊椎动物比较基因组学项目。本文所提供的基因组数据有望加速许多领域的进一步分析，包括遗传学、比较基因组学、进化、神经生物学、发育生物学和其他相关领域。本文的在线版本（doi：10.1186/2047- 217 X-3-26）包含补充材料，可供授权用户使用。
The evolutionary relationships of modern birds are among the most challenging to understand in systematic biology and have been debated for centuries. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders, and used the genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomics analyses (Jarvis et al. in press; Zhang et al. in press). Here we release assemblies and datasets associated with the comparative genome analyses, which include 38 newly sequenced avian genomes plus previously released or simultaneously released genomes of Chicken, Zebra finch, Turkey, Pigeon, Peregrine falcon, Duck, Budgerigar, Adelie penguin, Emperor penguin and the Medium Ground Finch. We hope that this resource will serve future efforts in phylogenomics and comparative genomics. The 38 bird genomes were sequenced using the Illumina HiSeq 2000 platform and assembled using a whole genome shotgun strategy. The 48 genomes were categorized into two groups according to the N50 scaffold size of the assemblies: a high depth group comprising 23 species sequenced at high coverage (>50X) with multiple insert size libraries resulting in N50 scaffold sizes greater than 1 Mb (except the White-throated Tinamou and Bald Eagle); and a low depth group comprising 25 species sequenced at a low coverage (~30X) with two insert size libraries resulting in an average N50 scaffold size of about 50 kb. Repetitive elements comprised 4%-22% of the bird genomes. The assembled scaffolds allowed the homology-based annotation of 13,000 ~ 17000 protein coding genes in each avian genome relative to chicken, zebra finch and human, as well as comparative and sequence conservation analyses. Here we release full genome assemblies of 38 newly sequenced avian species, link genome assembly downloads for the 7 of the remaining 10 species, and provide a guideline of genomic data that has been generated and used in our Avian Phylogenomics Project. To the best of our knowledge, the Avian Phylogenomics Project is the biggest vertebrate comparative genomics project to date. The genomic data presented here is expected to accelerate further analyses in many fields, including phylogenetics, comparative genomics, evolution, neurobiology, development biology, and other related areas. The online version of this article (doi:10.1186/2047-217X-3-26) contains supplementary material, which is available to authorized users.