Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.
Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China.
Mol Ecol Resour. 2019 Nov;19(6):1461-1469. doi: 10.1111/1755-0998.13064. Epub 2019 Aug 14.
The red-spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and South-East Asia and is a threatened species. The species is also considered a good model for studies of sex inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome-level reference genome of E. akaara by taking advantage of long-read single-molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi-C. A red-spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96-fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudochromosomes covering approximately 95.55% of the genome assembly with Hi-C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 noncoding RNAs. Furthermore, combined with several RNA-seq data sets, 23,808 (99.5%) genes were functionally annotated from a total of 23,923 predicted protein-coding sequences. The high-quality chromosome-level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red-spotted grouper in the future.
鞍带石斑鱼 Epinephelus akaara（E. akaara）是中国、日本和东南亚地区最具经济价值的海洋鱼类之一，也是一种受到威胁的物种。该物种也被认为是性反转、发育、遗传多样性和免疫研究的良好模型。尽管其重要性不言而喻，但 E. akaara 的分子资源仍然有限，迄今为止尚未发表参考基因组。在本研究中，我们利用长读长单分子测序和 Oxford Nanopore Technology（ONT）和 Hi-C 的从头组装，构建了鞍带石斑鱼的染色体水平参考基因组。总共从 106.29Gb 抛光纳米孔序列（GridION，ONT）中组装了一个 1.135Gb 的鞍带石斑鱼基因组，相当于基因组覆盖度的 96 倍。组装的基因组具有 96.8%的完整性（BUSCO），contig N50 长度为 5.25Mb，最长的 contig 为 25.75Mb。通过 Hi-C 数据，将 contigs 聚类并排列在 24 条假染色体上，覆盖了基因组组装的约 95.55%，支架 N50 长度为 46.03Mb。基因组包含 43.02%的重复序列和 5,480 个非编码 RNA。此外，结合几个 RNA-seq 数据集，从总共 23,923 个预测的蛋白质编码序列中，功能注释了 23,808 个（99.5%）基因。鞍带石斑鱼的高质量染色体水平参考基因组首次组装成功，将成为未来石斑鱼分子育种和功能基因组学研究的宝贵资源。
