Data from: De novo assembly of a chromosome-level reference genome of red spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C

The red spotted grouper Epinephelus akaara (E. akaara) is one of the most
economically important marine fish in China, Japan and Southeast 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 Technologies (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 pseudo-chromosomes 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
non-coding RNAs. Furthermore, after mining several RNA-seq datasets,
23,809 (99.5%) genes were functionally annotated from a total of 23,924
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.

赤点石斑鱼（Epinephelus akaara，E. akaara）是中国、日本及东南亚地区极具经济价值的海水鱼类之一，同时属于受威胁物种。该物种亦是性别反转、发育调控、遗传多样性与免疫研究的优良实验模型。尽管其具有重要的科研与经济价值，但目前赤点石斑鱼的分子研究资源仍较为匮乏，且截至目前尚无任何参考基因组发表。本研究依托牛津纳米孔科技（Oxford Nanopore Technologies, ONT）的长读长单分子测序技术，结合Hi-C技术进行从头组装，成功构建了赤点石斑鱼的染色体级参考基因组。研究共获取106.29 Gb经抛光校正的纳米孔测序序列（GridION, ONT），测序深度约为基因组的96倍，最终组装得到1.135 Gb的赤点石斑鱼基因组。该组装基因组的BUSCO（Benchmarking Universal Single-Copy Orthologs）完整度达96.8%，重叠群（contig）N50长度为5.25 Mb，最长重叠群长度达25.75 Mb。借助Hi-C数据，研究将所有重叠群聚类并锚定至24条假染色体上，覆盖约95.55%的基因组组装序列，最终支架序列（scaffold）N50长度为46.03 Mb。该基因组包含43.02%的重复序列与5480条非编码RNA。此外，通过挖掘多套RNA-seq数据集，从23924个预测的蛋白质编码序列中，成功注释得到23809个（占比99.5%）具备功能注释的基因。本研究首次获得高质量的赤点石斑鱼染色体级参考基因组，将为未来赤点石斑鱼的分子育种与功能基因组学研究提供宝贵的科研资源。