SCSIO OpenIR  > 中科院海洋生物资源可持续利用重点实验室
Draft genome of the lined seahorse, Hippocampus erectus
Lin, Q; Qiu, Y; Gu, RB; Xu, M; Li, J; Bian, C; Zhang, HX; Qin, G; Zhang, YH; Luo, W; Chen, JM; You, XX; Fan, MJ; Sun, M; Xu, P; Venkatesh, B; Xu, JM; Fu, HT; Shi, Q; xujunming@genomics.cn; fuht@ffrc.cn; shiqiong@genomics.cn
2017
Source PublicationGIGASCIENCE
Volume6Issue:6Pages:-
AbstractBackground: 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.
Department[Lin, Qiang; Zhang, Huixian; Qin, Geng; Zhang, Yanhong; Luo, Wei] Chinese Acad Sci, CAS Key Lab Trop Marine Bioresources & Ecol, South China Sea Inst Oceanol, Guangzhou 510301, Guangdong, Peoples R China; [Qiu, Ying; Gu, Ruobo; Xu, Pao; Fu, Hongtuo] Chinese Acad Fishery Sci, Freshwater Fisheries Res Ctr, Wuxi 214081, Jiangsu, Peoples R China; [Qiu, Ying; Gu, Ruobo; Li, Jia; Bian, Chao; Chen, Jieming; You, Xinxin; Fan, Mingjun; Sun, Min; Xu, Junming; Shi, Qiong] BGI, Guangdong Prov Key Lab Mol Breeding Marine Econ A, BGI Acad Marine Sci, BGI Fisheries,Shenzhen Key Lab Marine Genom, Shenzhen 518083, Guangdong, Peoples R China; [Gu, Ruobo; Xu, Junming; Shi, Qiong] BGI Fisheries, BGI Zhenjiang Inst Hydrobiol, Zhenjiang 212000, Jiangsu, Peoples R China; [Xu, Meng] BGI, BGI Shenzhen, Shenzhen 518083, Guangdong, Peoples R China; [Bian, Chao; You, Xinxin; Xu, Pao; Xu, Junming; Fu, Hongtuo; Shi, Qiong] Chinese Acad Fishery Sci, BGI Res Ctr Aquat Genom, Shenzhen 518083, Guangdong, Peoples R China; [Bian, Chao] Univ Macau, Ctr Reprod Dev & Aging, Fac Hlth Sci, Taipa, Macau, Peoples R China; [Venkatesh, Byrappa] ASTAR, Inst Mol & Cell Biol, Biopolis 138673, Singapore; [Shi, Qiong] Sun Yat Sen Univ, Lab Aquat Genom, Coll Ecol & Evolut, Sch Life Sci, Guangzhou 510275, Guangdong, Peoples R China
KeywordGenome Assembly Annotation Hippocampus Erectus
Funding ProjectLMB
Document Type期刊论文
Identifierhttp://ir.scsio.ac.cn/handle/344004/16267
Collection中科院海洋生物资源可持续利用重点实验室
Corresponding Authorxujunming@genomics.cn; fuht@ffrc.cn; shiqiong@genomics.cn
Recommended Citation
GB/T 7714
Lin, Q,Qiu, Y,Gu, RB,et al. Draft genome of the lined seahorse, Hippocampus erectus[J]. GIGASCIENCE,2017,6(6):-.
APA Lin, Q.,Qiu, Y.,Gu, RB.,Xu, M.,Li, J.,...&shiqiong@genomics.cn.(2017).Draft genome of the lined seahorse, Hippocampus erectus.GIGASCIENCE,6(6),-.
MLA Lin, Q,et al."Draft genome of the lined seahorse, Hippocampus erectus".GIGASCIENCE 6.6(2017):-.
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