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Gigascience. 2016 Aug 22;5(1):39. doi: 10.1186/s13742-016-0142-5.

High-quality genome assembly of channel catfish, Ictalurus punctatus.

Chen X1,2, Zhong L1,2, Bian C3, Xu P4, Qiu Y3, You X3, Zhang S1,2, Huang Y3, Li J3, Wang M1,2, Qin Q1,2, Zhu X1,2, Peng C3, Wong A5, Zhu Z6,7, Wang M3,6,7, Gu R4,6, Xu J8,9,10, Shi Q11,12,13,14,15, Bian W16,17.

Author information

1
Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, 210017, China.
2
The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210017, China.
3
Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen, 518083, China.
4
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
5
BGI-Hong Kong, Hong Kong, 999077, China.
6
BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000, China.
7
BGI Zhenjiang Fisheries Science and Technology Industrial Co. Ltd, Zhenjiang, 212000, China.
8
Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen, 518083, China. xujunmin@genomics.cn.
9
BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000, China. xujunmin@genomics.cn.
10
BGI Zhenjiang Fisheries Science and Technology Industrial Co. Ltd, Zhenjiang, 212000, China. xujunmin@genomics.cn.
11
Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen, 518083, China. shiqiong@genomics.cn.
12
BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000, China. shiqiong@genomics.cn.
13
BGI Zhenjiang Fisheries Science and Technology Industrial Co. Ltd, Zhenjiang, 212000, China. shiqiong@genomics.cn.
14
Laboratory of Aquatic Genomics, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China. shiqiong@genomics.cn.
15
Center for Marine Research, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China. shiqiong@genomics.cn.
16
Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, 210017, China. js6060@sina.com.
17
The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210017, China. js6060@sina.com.

Abstract

BACKGROUND:

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.

FINDINGS:

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.

CONCLUSIONS:

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.

KEYWORDS:

Assembly; Channel catfish; Gene prediction; Repetitive sequence; Whole genome sequencing

PMID:
27549802
PMCID:
PMC4994213
DOI:
10.1186/s13742-016-0142-5
[Indexed for MEDLINE]
Free PMC Article

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