High-quality genome assembly of channel catfish, Ictalurus punctatus.
High-quality genome assembly of channel catfish, Ictalurus punctatus.
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DOI：
10.1186/s13742-016-0142-5
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发表时间：
2016-08-22
期刊：
影响因子：
9.2
通讯作者：
Bian W
中科院分区：
文献类型：
--
作者：
Chen X;Zhong L;Bian C;Xu P;Qiu Y;You X;Zhang S;Huang Y;Li J;Wang M;Qin Q;Zhu X;Peng C;Wong A;Zhu Z;Wang M;Gu R;Xu J;Shi Q;Bian W
斑点叉尾鱼是原产于北美的物种，是世界上最重要的商业淡水鱼之一，特别是在美国的水产养殖业中。自1984年引入中国以来，该品种的养殖面积和产量都有了极大的提高，中国现在是斑点叉尾的主要生产国。为了帮助该物种的基因组研究，已经产生了诸如遗传连锁群、长插入文库、物理图谱、细菌人工克隆(BAC)末端序列(BES)、转录组组件和参考基因组序列等数据集。在这里，我们利用多样化的组装方法，从中国自交系三代以上的繁殖群体中，为最初从北美进口到中国的斑点叉尾鱼提供了可比的高质量基因组组装。通过Illumina HiSeq2000平台对大约201.6千兆碱基(GB)的基因组读数进行了测序。随后，我们用7.2Mb的支架N50和95.6%的完成率生成了高质量、高性价比和易于组装的斑点叉尾鱼基因组序列。我们还预测斑点叉尾鱼基因组包含21,556个蛋白质编码基因和275.3个百万碱基对的重复序列。我们报道了一种高质量的斑点叉尾鱼基因组组装，这与最近一份报告中的“可可”斑点叉尾鱼相当。这些产生的基因组数据可以作为利用基因组方法进行分子育种以获得新品种的初始平台。
The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world, especially in the United States’ aquaculture industry. Since its introduction into China in 1984, both cultivation area and yield of this species have been dramatically increased such that China is now the leading producer of channel catfish. To aid genomic research in this species, data sets such as genetic linkage groups, long-insert libraries, physical maps, bacterial artificial clones (BAC) end sequences (BES), transcriptome assemblies, and reference genome sequences have been generated. Here, using diverse assembly methods, we provide a comparable high-quality genome assembly for a channel catfish from a breeding stock inbred in China for more than three generations, which was originally imported to China from North America. Approximately 201.6 gigabases (Gb) of genome reads were sequenced by the Illumina HiSeq 2000 platform. Subsequently, we generated high quality, cost-effective and easily assembled sequences of the channel catfish genome with a scaffold N50 of 7.2 Mb and 95.6 % completeness. We also predicted that the channel catfish genome contains 21,556 protein-coding genes and 275.3 Mb (megabase pairs) of repetitive sequences. We report a high-quality genome assembly of the channel catfish, which is comparable to a recent report of the “Coco” channel catfish. These generated genome data could be used as an initial platform for molecular breeding to obtain novel catfish varieties using genomic approaches.