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Data released on April 12, 2017

Supporting data for "Draft genome of the lined seahorse, Hippocampus erectus"

Lin, Q; Gu, R; Qiu, Y; Xu, M; Li, J; Bian, C; Zhang, H; Qin, G; Zhang, Y; Luo, W; Chen, J; You, X; Fan, M; Sun, M; Xu, P; Venkatesh, B; Xu, J; Fu, H; Shi, Q (2017): Supporting data for "Draft genome of the lined seahorse, Hippocampus erectus" GigaScience Database. http://dx.doi.org/10.5524/100298 RIS BibTeX Text

The lined seahorse, Hippocampus erectus, is an Atlantic species and mainly inhabits shallow sea-beds or coral reefs. It has become very popular in China for its wide use in traditional Chinese medicine. In order to improve the aquaculture yield of this valuable fish species, we are trying to develop genomic resources for assistant selection in genetic breeding. Here, we provide whole genome sequencing, assembly and gene annotation of the lined seahorse, which can enrich genome resource and further application for its molecular breeding.
A total of 174.6-Gb (Gigabase) raw DNA sequences were generated by the Illumina Hiseq2500 platform. The final assembly of the lined seahorse genome is around 458 Mb, representing 94% of the estimated genome size (489 Mb by k-mer analysis). The contig N50 and scaffold N50 reached 14.57 kb and 1.97 Mb respectively. Quality of the assembled genome was assessed by BUSCO with prediction of 85% of the known vertebrate genes and evaluated using the de novo assembled RNA-seq transcripts to prove a high mapping ratio (more than 99% transcripts could be mapped to the assembly). Using homology-based, de novo annotation and transcriptome-based prediction methods, we predicted 20,788 protein-coding genes in the generated assembly, which is similar to our previously reported gene number (23,458) of the tiger tail seahorse (H. comes).
We report a draft genome of the lined seahorse. These generated genomic data are going to enrich genome resource of this economically important fish, and also provide insights into the genetic mechanisms of its iconic morphology and male pregnancy behavior.

Contact Submitter

Accessions (data included in GigaDB):

BioProject: PRJNA347499

Genomic

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Funding:

  • Funding body - National High Technology Research and Development Program of China-863 program
  • Location - China
  • Award ID - 2015AA020909
  • Comment - Youth Foundation of National High Technology Research and Development Program
  • Awardee - Dr. Qiang Lin
  • Funding body - Natural Science Foundation of Guangdong Province
  • Award ID - S2013050014802
  • Comment - Outstanding Youth Foundation in Guangdong Province
  • Awardee - Dr. Qiang Lin
  • Funding body - Ministry of agriculture science and technology
  • Award ID - 201403008
  • Comment - Special Fund for Agro-scientific Research in the Public Interest
  • Awardee - Dr. Qiang Lin
  • Funding body - National Natural Science Foundation of China
  • Award ID - 41576145
  • Comment - General Project of National Natural Science Foundation of China
  • Awardee - Dr. Qiang Lin
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31370047
  • Comment - General Project of National Natural Science Foundation of China
  • Awardee - Dr. Qiong Shi
  • Funding body - Shenzhen Science and Technology Innovation Committee
  • Award ID - JSGG20141020113728803
  • Comment - Shenzhen Special Program for Future Industrial Development
  • Awardee - Dr. Qiong Shi
  • Funding body - Guangdong Provincial Department of Science and Technology
  • Award ID - 2013B090800017
  • Comment - Special Project on the Integration of Industry Education and Research of Guangdong Province
  • Awardee - Dr. Qiong Shi
  • Funding body - Shenzhen Science and Technology Innovation Committee
  • Award ID - SGLH20131010105856414
  • Awardee - Dr. Qiong Shi
  • Funding body - Shenzhen Science and Technology Innovation Committee
  • Award ID - GJHZ20160229173052805
  • Awardee - Dr. Qiong Shi
  • Funding body - Shenzhen Dapeng New District Economic Service Bureau
  • Award ID - KY20160307
  • Comment - Shenzhen Dapeng Special Program for Industrial Development
  • Awardee - Dr. Qiong Shi

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Hippocampus erectus WGS109281 lined seahorseHippocampus erectus Description:Whole genome sequencing of Hippocampus...
Alternative names:seahorse
Life stage:adult
...
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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 
ReadmeTEXT0.03 KB2017-04-03
Phylogenetic treeNewick0.28 KB2017-04-03
otherUNKNOWN0.44 KB2017-04-03
ScriptTEXT0.55 KB2017-04-03
ScriptTEXT2.45 KB2017-04-03
annotationIPR2.26 MB2017-04-03
annotationIPR2.78 MB2017-04-03
protein sequenceFASTA14.38 MB2017-04-03
annotationGFF15.23 MB2017-04-03
AlignmentsUNKNOWN23.57 MB2017-04-03
Displaying 1-10 of 12 File(s).

History:

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