Draft genome of the lined seahorse, Hippocampus erectus

Draft genome of the lined seahorse, Hippocampus erectus
Draft genome of the lined seahorse, Hippocampus erectus
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Publication Date:
22 April 2017
Qiang Lin, Ying Qiu, Ruobo Gu, Meng Xu, Jia Li, Chao Bian, Huixian Zhang, Geng Qin, Yanhong Zhang, Wei Luo, Jieming Chen, Xinxin You, Mingjun Fan, Min Sun, Pao Xu, Byrappa Venkatesh, Junming Xu, Hongtuo Fu, Qiong Shi, Draft genome of the lined seahorse, Hippocampus erectus, GigaScience, Volume 6, Issue 6, June 2017, gix030, https://doi.org/10.1093/gigascience/gix030
Background: 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. Findings: 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 and transcriptome-based prediction methods, we predicted 20 788 protein-coding genes in the generated assembly, which is less than our previously reported gene number (23 458) of the tiger tail seahorse (H. comes). Conclusion: 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.
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This work was supported by the Youth Foundation of National High Technology Research and Development Program (2015AA020909), the Outstanding Youth Foundation in Guangdong Province (S2013050014802), the Special Fund for Agro-scientific Research in the Public Interest (201403008), the National Natural Science Foundation of China (41576145), China National Natural Science Foundation (No. 31370047), Shenzhen Special Program for Future Industrial Development (No. JSGG20141020113728803), Special Project on the Integration of Industry, Education and Research of Guangdong Province (No. 2013B090800017), Shenzhen Science and Technology Program (No. SGLH20131010105856414 and GJHZ20160229173052805), and Shenzhen Dapeng Special Program for Industrial Development (No. KY20160307).
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