Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius

• Published in: Gigascience Vol. 6; no. 4; pp. 1 - 6
• Main Authors: Liu, Kai, Xu, Dongpo, Li, Jia, Bian, Chao, Duan, Jinrong, Zhou, Yanfeng, Zhang, Minying, You, Xinxin, You, Yang, Chen, Jieming, Yu, Hui, Xu, Gangchun, Fang, Di-an, Qiang, Jun, Jiang, Shulun, He, Jie, Xu, Junmin, Shi, Qiong, Zhang, Zhiyong, Xu, Pao
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 01.04.2017
• Subjects: Animals; Assembly; Computational Biology - methods; Data Note; Economic importance; Fish; Gene sequencing; Genome; Genomes; Genomics - methods; Germplasm; High-Throughput Nucleotide Sequencing; Molecular modelling; Molecular Sequence Annotation; Nucleotide sequence; Osmeriformes - classification; Osmeriformes - genetics; Phenotype; Phylogeny; Protosalanx hyalocranius; Sequence Analysis, DNA; Whole genome sequencing; Gene prediction; Clearhead icefish; Genome assembly; Whole genome sequencing; Repetitive sequences; Protosalanx hyalocranius
• ISSN: 2047-217X; 2047-217X
• DOI: 10.1093/gigascience/giw012

Abstract Background: 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. Findings: 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. Conclusion: 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.