De novo assembly of a chromosome-level reference genome of red-spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C
De novo assembly of a chromosome-level reference genome of red-spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C
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DOI：
10.1111/1755-0998.13064
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发表时间：
2019-08-14
影响因子：
7.7
通讯作者：
Zheng, Leyun
中科院分区：
文献类型：
--
作者：
Ge, Hui;Lin, Kebing;Zheng, Leyun
赤点石斑鱼Epinealphus akaara（E.赤鲷（akaara）是中国、日本和东南亚最具经济价值的海洋鱼类之一，是一种受威胁的物种。该物种也被认为是研究性别反转，发育，遗传多样性和免疫力的良好模型。尽管E. Akaara仍然有限，迄今为止还没有发表参考基因组。本研究构建了大肠杆菌染色体水平的参考基因组。akaara通过利用牛津纳米孔技术（ONT）和Hi-C的长读单分子测序和从头组装。从总共106.29 Gb抛光的纳米孔序列（GridION，ONT）组装1.135 Gb的红斑石斑鱼基因组，相当于96倍的基因组覆盖率。组装的基因组代表96.8%的完整性（BUSCO），重叠群N50长度为5.25 Mb，最长重叠群为25.75 Mb。将重叠群聚类并排序到24个假染色体上，覆盖约95.55%的具有Hi-C数据的基因组组装，支架N50长度为46.03 Mb。该基因组含有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对23，808个（99.5%）基因进行了功能注释。高质量的染色体水平参考基因组。本研究首次构建了赤点石斑鱼基因组，为赤点石斑鱼的分子育种和功能基因组学研究提供了宝贵的资源。
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.