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

Dataset type: Genomic
Data released on April 12, 2017

Bian C; Chen J; Fan M; Gu R; Li J; Lin Q; Luo W; Qin G; Qiu Y; Sun M; Venkatesh B; Xu J; Xu M; Xu P; You X; Zhang H; Zhang Y; 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

DOI10.5524/100298

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.

Additional details

Read the peer-reviewed publication(s):

Lin, Q., Qiu, Y., Gu, R., Xu, M., Li, J., Bian, C., … Shi, Q. (2017). Draft genome of the lined seahorse, Hippocampus erectus. GigaScience, 6(6). doi:10.1093/gigascience/gix030

Accessions (data included in GigaDB):

BioProject: PRJNA347499





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
...
+
Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
AlignmentsUNKNOWN23.57 MB2017-04-03
ScriptTEXT2.45 KB2017-04-03
ScriptTEXT0.55 KB2017-04-03
Phylogenetic treeNewick0.28 KB2017-04-03
ReadmeTEXT0.03 KB2017-04-03
otherUNKNOWN0.44 KB2017-04-03
Coding sequenceFASTA38.76 MB2017-04-03
annotationGFF15.23 MB2017-04-03
protein sequenceFASTA14.38 MB2017-04-03
annotationIPR2.78 MB2017-04-03
Displaying 1-10 of 12 File(s).
Funding body Awardee Award ID Comments
National High Technology Research and Development Program of China-863 program Dr. Qiang Lin 2015AA020909 Youth Foundation of National High Technology Research and Development Program
Natural Science Foundation of Guangdong Province Dr. Qiang Lin S2013050014802 Outstanding Youth Foundation in Guangdong Province
Ministry of agriculture science and technology Dr. Qiang Lin 201403008 Special Fund for Agro-scientific Research in the Public Interest
National Natural Science Foundation of China Dr. Qiang Lin 41576145 General Project of National Natural Science Foundation of China
National Natural Science Foundation of China Dr. Qiong Shi 31370047 General Project of National Natural Science Foundation of China
Shenzhen Science and Technology Innovation Committee Dr. Qiong Shi JSGG20141020113728803 Shenzhen Special Program for Future Industrial Development
Guangdong Provincial Department of Science and Technology Dr. Qiong Shi 2013B090800017 Special Project on the Integration of Industry Education and Research of Guangdong Province
Shenzhen Science and Technology Innovation Committee Dr. Qiong Shi SGLH20131010105856414
Shenzhen Science and Technology Innovation Committee Dr. Qiong Shi GJHZ20160229173052805
Shenzhen Dapeng New District Economic Service Bureau Dr. Qiong Shi KY20160307 Shenzhen Dapeng Special Program for Industrial Development
Date Action
April 12, 2017 Dataset publish
October 2, 2017 Manuscript Link added : 10.1093/gigascience/gix030