Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius.
Chinese clearhead icefish, Protosalanx hyalocranius , is a representative icefish species with economic importance and special appearance. Due to its great economic value in China, the fish was introduced into Lake Dianchi and several other lakes from the Lake Taihu half a century ago. Similar to the Sinocyclocheilus cavefish, the clearhead icefish has certain cavefish-like traits, such as transparent body and nearly scaleless skin. Here, we provide the whole genome sequence of this surface-dwelling fish and generated a draft genome assembly, aiming at exploring molecular mechanisms for the biological interests. A total of 252.1 Gb of raw reads were sequenced. Subsequently, a novel draft genome assembly was generated, with the scaffold N50 reaching 1.163 Mb. The genome completeness was estimated to be 98.39 % by using the CEGMA evaluation. Finally, we annotated 19 884 protein-coding genes and observed that repeat sequences account for 24.43 % of the genome assembly. We report the first draft genome of the Chinese clearhead icefish. The genome assembly will provide a solid foundation for further molecular breeding and germplasm resource protection in Chinese clearhead icefish, as well as other icefishes. It is also a valuable genetic resource for revealing the molecular mechanisms for the cavefish-like characters.
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
Kai
K
Liu
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
Dongpo
D
Xu
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China.
Jia
J
Li
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China.
Chao
C
Bian
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
Jinrong
J
Duan
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
Yanfeng
Y
Zhou
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
Minying
M
Zhang
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China.
Xinxin
X
You
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
Yang
Y
You
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China.
Jieming
J
Chen
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China.
Hui
H
Yu
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
Gangchun
G
Xu
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
Di-An
DA
Fang
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
Jun
J
Qiang
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
Shulun
S
Jiang
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
Jie
J
He
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China.|BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, Jiangsu 212000, China.|BGI Research Center for Aquatic Genomics, Chinese Academy of Fishery Sciences, Shenzhen, Guangdong 518083, China.
Junmin
J
Xu
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China.|BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, Jiangsu 212000, China.|BGI Research Center for Aquatic Genomics, Chinese Academy of Fishery Sciences, Shenzhen, Guangdong 518083, China.|Laboratory of Aquatic Genomics, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China.
Qiong
Q
Shi
Institute of Oceanology & Marine Fisheries, Nantong, Jiangsu 226007, China.
Zhiyong
Z
Zhang
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.|BGI Research Center for Aquatic Genomics, Chinese Academy of Fishery Sciences, Shenzhen, Guangdong 518083, China.
Pao
P
Xu
D000818:Animals; D019295:Computational Biology / Q000379:methods; D016678:Genome; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D036441:Osmeriformes / Q000145:classification / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D017422:Sequence Analysis, DNA
Clearhead icefish; Gene prediction; Genome assembly; Protosalanx hyalocranius; Repetitive sequences; Whole genome sequencing