title: High-quality genome assembly of channel catfish, Ictalurus punctatus.
abstract: 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.
authors.affiliation: Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, 210017, China.|The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210017, China.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Chen
authors.affiliation: Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, 210017, China.|The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210017, China.
authors.forename: Liqiang
authors.initials: L
authors.lastname: Zhong
authors.affiliation: Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen, 518083, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Bian
authors.affiliation: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
authors.forename: Pao
authors.initials: P
authors.lastname: Xu
authors.affiliation: Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen, 518083, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Qiu
authors.affiliation: Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen, 518083, China.
authors.forename: Xinxin
authors.initials: X
authors.lastname: You
authors.affiliation: Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, 210017, China.|The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210017, China.
authors.forename: Shiyong
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen, 518083, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen, 518083, China.
authors.forename: Jia
authors.initials: J
authors.lastname: Li
authors.affiliation: Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, 210017, China.|The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210017, China.
authors.forename: Minghua
authors.initials: M
authors.lastname: Wang
authors.affiliation: Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, 210017, China.|The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210017, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Qin
authors.affiliation: Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, 210017, China.|The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210017, China.
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Zhu
authors.affiliation: Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen, 518083, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Peng
authors.affiliation: BGI-Hong Kong, Hong Kong, 999077, China.
authors.forename: Alex
authors.initials: A
authors.lastname: Wong
authors.affiliation: BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000, China.|BGI Zhenjiang Fisheries Science and Technology Industrial Co. Ltd, Zhenjiang, 212000, China.
authors.forename: Zhifei
authors.initials: Z
authors.lastname: Zhu
authors.affiliation: Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen, 518083, China.|BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000, China.|BGI Zhenjiang Fisheries Science and Technology Industrial Co. Ltd, Zhenjiang, 212000, China.
authors.forename: Min
authors.initials: M
authors.lastname: Wang
authors.affiliation: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.|BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000, China.
authors.forename: Ruobo
authors.initials: R
authors.lastname: Gu
authors.affiliation: Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen, 518083, China. xujunmin@genomics.cn.|BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000, China. xujunmin@genomics.cn.|BGI Zhenjiang Fisheries Science and Technology Industrial Co. Ltd, Zhenjiang, 212000, China. xujunmin@genomics.cn.
authors.forename: Junmin
authors.initials: J
authors.lastname: Xu
authors.affiliation: Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen, 518083, China. shiqiong@genomics.cn.|BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000, China. shiqiong@genomics.cn.|BGI Zhenjiang Fisheries Science and Technology Industrial Co. Ltd, Zhenjiang, 212000, China. shiqiong@genomics.cn.|Laboratory of Aquatic Genomics, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China. shiqiong@genomics.cn.|Center for Marine Research, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China. shiqiong@genomics.cn.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Shi
authors.affiliation: Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, 210017, China. js6060@sina.com.|The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210017, China. js6060@sina.com.
authors.forename: Wenji
authors.initials: W
authors.lastname: Bian
mesh_terms: D000818:Animals; D002681:China; D020451:Contig Mapping / Q000379:methods*; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D007059:Ictaluridae / Q000235:genetics*; D058977:Molecular Sequence Annotation; D009656:North America; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*
keywords: Assembly; Channel catfish; Gene prediction; Repetitive sequence; Whole genome sequencing