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

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.<br>
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). <br>
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.

线纹海马（Hippocampus erectus）是大西洋分布物种，主要栖息于浅海海床或珊瑚礁海域。由于在传统中医药中用途广泛，该物种在国内备受青睐。为提升这一高经济价值鱼类的养殖产量，我们着手开发基因组资源以辅助遗传育种选择。本研究完成了线纹海马的全基因组测序、基因组组装及基因注释工作，相关成果可丰富该物种的基因组资源，并为其分子育种的后续应用提供支撑。

研究通过Illumina Hiseq2500测序平台共产出174.6 Gb（吉碱基）的原始DNA序列数据。最终组装的线纹海马基因组大小约为458 Mb，占k-mer分析预估基因组大小（489 Mb）的94%。重叠群N50与支架N50分别达到14.57 kb与1.97 Mb。我们采用Benchmarking Universal Single-Copy Orthologs（BUSCO）评估组装质量，结果显示可覆盖85%的已知脊椎动物单拷贝同源基因；同时利用从头组装的RNA-seq转录本进行比对验证，超过99%的转录本可匹配至该基因组组装结果，证明组装质量优异。本研究通过同源预测、从头注释及转录组辅助预测三种方法，共注释得到20788个蛋白编码基因，与此前报道的虎尾海马（H. comes）基因数量（23458）相近。

本研究报道了线纹海马的基因组草图。本次生成的基因组数据将丰富这一经济鱼类的基因组资源库，同时为解析其标志性形态特征与雄性妊娠行为的遗传机制提供重要研究线索。