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Data released on February 08, 2018

Supporting data for ‘Draft Genome of the Protandrous Chinese Black Porgy, Acanthopagrus schlegelii’

Zhang, Z; Zhang, K; Chen, S; Zhang, Z; Zhang, J; You, X; Bian, C; Xu, J; Jia, C; Qiang, J; Zhu, F; Li, H; Liu, H; Shen, D; Ren, Z; Chen, J; Li, J; Gao, T; Gu, R; Xu, J; Shi, Q; Xu, P (2018): Supporting data for ‘Draft Genome of the Protandrous Chinese Black Porgy, Acanthopagrus schlegelii’ GigaScience Database. http://dx.doi.org/10.5524/100409 RIS BibTeX Text

As one of the most popular and valuable commercial marine fishes in China and East Asian countries, the Chinese black porgy (Acanthopagrus schlegelii) also known as the blackhead seabream, has some attractive characteristics, such as fast growth rate, good meat quality, resistance to diseases and excellent adaptability to various environments. Furthermore, the black porgy is a good model for investigating sex changes in fish due to its protandrous hermaphrodite. Here, we obtained a high-quality genome assembly of this interesting teleost species and performed a genomic survey on potential genes associated with the sex-change phenomenon. We generated 175.4 gigabases (Gb) of clean sequence reads using a whole-genome shotgun sequencing strategy. The final genome assembly is approximately 688.1 megabases (Mb), accounting for 93% of the estimated genome size (739.6 Mb). The achieved scaffold N50 is 7.6 Mb, reaching a relatively high level among sequenced fish species. Meanwhile, we identified 19,465 protein-coding genes, which had an average transcript length of 17.3 kb. By performing a comparative genomic analysis, we found three types of genes potentially associated with sex change, which are useful for the prediction of related genetic basis for the interesting protandrous hermaphrodite. We provided a draft genome assembly of the Chinese black porgy and discussed about the potential genetic mechanisms of sex change. These data are also an important resource for studying the biology and facilitating the molecular breeding of this economically important fish.

Contact Submitter

Accessions (data included in GigaDB):

BioProject: PRJNA377579
BioProject: PRJNA394769

Accessions (data not in GigaDB):

BioProject: PRJNA183073

Keywords:

chinese black porgy acanthopagrus schlegelii whole genome sequencing genome assembly sex-change related genes 

Genomic, Transcriptomic

http://gigadb.org/images/data/cropped/100409.jpg

Funding:

  • Funding body - Jiangsu Ocean and Fisheries Burea
  • Award ID - D2015-17
  • Comment - Aquatic Sanxin Engineering Major Project of Jiangsu Province
  • Awardee - Zhiyong Zhang
  • Funding body - Jiangsu Ocean and Fisheries Burea
  • Award ID - BE2016326
  • Comment - Key Research and Development (Modern Agriculture) Program of Jiangsu Province
  • Awardee - Zhiwei Zhang
  • Funding body - Jiangsu Ocean and Fisheries Burea
  • Award ID - CX(17)2021
  • Comment - Fund for Independent Innovation of Agricultural Science and Technology of Jiangsu Province
  • Awardee - Zhiwei Zhang
  • Funding body - Jiangsu Ocean and Fisheries Burea
  • Award ID - Y2016-23
  • Comment - Aquatic Sanxin Engineering Project of Jiangsu Province
  • Awardee - Zhiwei Zhang
  • Funding body - Jiangsu Ocean and Fisheries Burea
  • Award ID - BM2015017
  • Comment - Jiangsu Innovation Ability Construction Program
  • Awardee - Zhiyong Zhang
  • Funding body - Science and Technology Bureau of Nantong City
  • Award ID - MS12015071
  • Comment - Nantong Applied Basic Research Program
  • Awardee - Zhiwei Zhang
  • Funding body - Science and Technology Bureau of Nantong City
  • Award ID - MS12015070
  • Comment - Nantong Applied Basic Research Program
  • Awardee - Zhiyong Zhang
  • Funding body - Science and Technology Bureau of Nantong City
  • Award ID - MS12016029
  • Comment - Nantong Applied Basic Research Program
  • Awardee - Zhiyong Zhang
  • Funding body - Science and Technology Bureau of Zhenjiang City
  • Comment - Zhenjiang Leading Talent Program for Innovation and Entrepreneurship
  • Awardee - Qiong Shi

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN0646337872011black sea breamblack porgyAcanthopagrus schlegelii Description:Genomic DNA extracted from the muscle ...
Alternative accession-BioProject:PRJNA377579
Sex:female
...
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SAMN0735926572011black sea breamblack porgyAcanthopagrus schlegelii Description:RNA extracted from a mixture of liver,...
Alternative accession-BioProject:PRJNA394769
Sex:female
...
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Displaying 1-2 of 2 Sample(s).

Files: (FTP site) Table Settings

Columns:

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

File NameSample IDData TypeFile FormatSizeRelease Date 
annotationGFF15.49 MB2018-02-01
Coding SequenceFASTA37 MB2018-02-01
Coding SequenceFASTA87.12 KB2018-02-01
otherTEXT0.92 KB2018-02-01
otherTEXT0.9 KB2018-02-01
Phylogenetic treezip68.62 KB2018-02-08
Phylogenetic treeJPG9.42 MB2018-02-01
protein sequenceFASTA29.39 KB2018-02-01
protein sequenceFASTA13.61 MB2018-02-01
ReadmeTEXT2.89 KB2018-02-01
Displaying 1-10 of 14 File(s).

History:

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