A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae
A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae
复制标题
DOI：
10.1093/gbe/evz269
复制
发表时间：
2020-01-01
影响因子：
3.3
通讯作者：
Ray, David A.
中科院分区：
文献类型：
--
作者：
Ghosh, Arnab;Johnson, Matthew G.;Ray, David A.
鳄鱼是一个经济，文化和生物学上重要的群体。为了提高研究人员研究基因组结构，进化和基因调控的能力，我们从基因组文库和体外邻近连接文库的Illumina短读数据中生成了咸水鳄鱼Crocodylus porosus的高质量从头基因组组装。组装的基因组为2，123.5 Mb，N50支架大小为17.7 Mb，N90支架大小为3.8 Mb。然后我们注释了这个新的集合，使注释的基因数量增加了74%。总的来说，23，242个注释的基因中有96%与功能蛋白质结构域相关。此外，多个非编码功能区和可定位的遗传标记被确定。通过对分支长度估计和位点选择试验的结果进行分析和重叠，我们发现鳄鱼中有16个可能受到正选择的基因，孔氏鳄鱼中有10个，密西西比扬子鳄中有6个。注释的C porosus基因组将作为一个重要的平台，调节，生理和性别决定的研究，以及在调查鳄鱼，鸟类和其他四足动物的系统发育关系的重要参考。
Crocodilians are an economically, culturally, and biologically important group. To improve researchers' ability to study genome structure, evolution, and gene regulation in the Glade, we generated a high-quality de novo genome assembly of the saltwater crocodile, Crocodylus porosus, from Illumina short read data from genomic libraries and in vitro proximity-ligation libraries. The assembled genome is 2,123.5 Mb, with N50 scaffold size of 17.7 Mb and N90 scaffold size of 3.8 Mb. We then annotated this new assembly, increasing the number of annotated genes by 74%. In total, 96% of 23,242 annotated genes were associated with a functional protein domain. Furthermore, multiple noncoding functional regions and mappable genetic markers were identified. Upon analysis and overlapping the results of branch length estimation and site selection tests for detecting potential selection, we found 16 putative genes under positive selection in crocodilians, 10 in C porosus and 6 in Alligator mississippiensis. The annotated C porosusgenome will serve as an important platform for osmoregulatory, physiological, and sex determination studies, aswell as an important reference in investigating the phylogenetic relationships of crocodilians, birds, and other tetrapods.