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Data released on December 20, 2016

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

Bian, C; Chen, J; Duan, J; Fang, D; He, J; Jiang, S; Li, J; Liu, K; Qiang, J; Xu, D; Xu, G; Xu, J; You, X; You, Y; Yu, H; Zhang, M; Zhou, Y; Shi, Q; Zhang, Z; Xu, P (2016): Supporting data for "Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius" GigaScience Database. http://dx.doi.org/10.5524/100262 RIS BibTeX Text

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.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/giw012

Accessions (data included in GigaDB):

BioProject: PRJNA328051

Keywords:

Clearhead icefish Protosalanx hyalocranius Whole genome sequencing Genome assembly Gene prediction Repetitive sequences 

Genomic

http://gigadb.org/images/data/cropped/100262.jpg

Funding:

  • Funding body - Natural Science Foundation of Jiangsu Province
  • Award ID - BK2012093
  • Comment - Dr. Kai Liu
  • Funding body - Taihu Basin Authority
  • Award ID - TH2016WT007
  • Comment - Dr. Kai Liu
  • Funding body - Chinese Academy of Fishery Sciences
  • Award ID - 2016DKA30470
  • Comment - Dr. Pao Xu
  • Funding body - Guangdong Provincial Department of Science and Technology
  • Award ID - 2013B090800017
  • Comment - Dr. Qiong Shi
  • Funding body - Chinese Academy of Fishery Sciences
  • Award ID - 2013JBFM07
  • Comment - Dr. Kai Liu

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN05363453418454Protosalanx hyalocranius Description:Whole genome sequencing of Protosalanx...
Species-a:FishbaseID:12236
Common name:Chinese clearhead icefish
...
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Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile 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).

History:

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