Draft genome of the lined seahorse, Hippocampus erectus.
Draft genome of the lined seahorse, Hippocampus erectus.
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海马直立海马的基因组草图。
DOI：
10.1093/gigascience/gix030
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发表时间：
2017-06-01
期刊：
影响因子：
9.2
通讯作者：
Shi Q
中科院分区：
文献类型：
--
作者：
Lin Q;Qiu Y;Gu R;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
背景：条纹海马（Hippocampusectus）是大西洋物种，主要栖息在浅海床或珊瑚礁中。由于其在中药中的广泛应用，它在中国非常受欢迎。为了提高这种名贵鱼类的养殖产量，我们正在努力开发用于遗传育种辅助选择的基因组资源。在这里，我们提供了条纹海马的全基因组测序、组装和基因注释，可以丰富其基因组资源并进一步应用于其分子育种。结果：Illumina Hiseq2500 平台总共生成了 174.6 Gb (Gigabase) 的原始 DNA 序列。内衬海马基因组的最终组装约为 458 Mb，占估计基因组大小的 94%（k-mer 分析为 489 Mb）。重叠群 N50 和支架 N50 分别达到 14.57 kb 和 1.97 Mb。 BUSCO 评估了组装基因组的质量，预测了 85% 的已知脊椎动物基因，并使用从头组装的 RNA-seq 转录本进行了评估，以证明高映射率（超过 99% 的转录本可以映射到组装）。使用基于同源性、从头开始和基于转录组的预测方法，我们在生成的组装中预测了 20 788 个蛋白质编码基因，这少于我们之前报道的虎尾海马（H. comes）的基因数量（23 458）。结论：我们报告了条纹海马的基因组草案。这些生成的基因组数据将丰富这种经济上重要的鱼类的基因组资源，并为其标志性形态和雄性怀孕行为的遗传机制提供见解。
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.