Supporting data for "Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius"

Dataset type: Genomic
Data released on December 20, 2016

Liu K; Xu D; Li J; Bian C; Duan J; Zhou Y; Zhang M; You X; You Y; Chen J; Yu H; Xu G; Fang D; Qiang J; Jiang S; He J; Xu J; Shi Q; Zhang Z; Xu P (2016): Supporting data for "Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius" GigaScience Database.


Chinese clearhead icefish, Protosalanx hyalocranius, is a representative icefish species with economic importance and special appearance. Due to its great economic values 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 gigabases (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.
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.

Additional details

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Accessions (data generated as part of this study):

BioProject: PRJNA328051

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN05363453418454Protosalanx hyalocraniusProtosalanx hyalocranius Description:Whole genome sequencing of Protosalanx...
Common name:Chinese clearhead icefish
Displaying 1-1 of 1 Sample(s).

File NameSample IDData TypeFile FormatSizeRelease Date 
ScriptUNKNOWN11.54 KB2016-12-06
AlignmentsUNKNOWN328.87 KB2016-12-06
Repeat sequenceTAR30.87 MB2016-12-06
otherUNKNOWN0.4 KB2016-12-06
otherUNKNOWN0.4 KB2016-12-06
otherUNKNOWN1.3 KB2016-12-06
otherUNKNOWN0.64 KB2016-12-06
Sequence assemblyTAR97.51 MB2016-12-06
Coding sequenceTAR10.21 MB2016-12-06
annotationTAR1.99 MB2016-12-06
Displaying 1-10 of 16 File(s).
Funding body Awardee Award ID Comments
Natural Science Foundation of Jiangsu Province BK2012093 Dr. Kai Liu
Taihu Basin Authority TH2016WT007 Dr. Kai Liu
Chinese Academy of Fishery Sciences 2016DKA30470 Dr. Pao Xu
Guangdong Provincial Department of Science and Technology 2013B090800017 Dr. Qiong Shi
Chinese Academy of Fishery Sciences 2013JBFM07 Dr. Kai Liu
Date Action
December 20, 2016 Dataset publish
March 6, 2017 Manuscript Link added : 10.1093/gigascience/giw012