Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang316022, China.
Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei 430075, China.
Gigascience. 2018 Sep 1;7(9):giy108. doi: 10.1093/gigascience/giy108.
Sillaginidae, also known as smelt-whitings, is a family of benthic coastal marine fishes in the Indo-West Pacific that have high ecological and economic importance. Many Sillaginidae species, including the Chinese sillago (Sillago sinica), have been recently described in China, providing valuable material to analyze genetic diversification of the family Sillaginidae. Here, we constructed a reference genome for the Chinese sillago, with the aim to set up a platform for comparative analysis of all species in this family.
Using the single-molecule real-time DNA sequencing platform Pacific Biosciences (PacBio) Sequel, we generated ∼27.3 Gb genomic DNA sequences for the Chinese sillago. We reconstructed a genome assembly of 534 Mb using a strategy that takes advantage of complementary strengths of two genome assembly programs, Canu and FALCON. The genome size was consistent with the estimated genome size based on k-mer analysis. The assembled genome consisted of 802 contigs with a contig N50 length of 2.6 Mb. We annotated 22,122 protein-coding genes in the Chinese sillago genomes using a de novo method as well as RNA sequencing data and homologies to other teleosts. According to the phylogenetic analysis using protein-coding genes, the Chinese sillago is closely related to Larimichthys crocea and Dicentrarchus labrax and diverged from their ancestor around 69.5-82.6 million years ago.
Using long reads generated with PacBio sequencing technology, we have built a draft genome assembly for the Chinese sillago, which is the first reference genome for Sillaginidae species. This genome assembly sets a stage for comparative analysis of the diversification and adaptation of fishes in Sillaginidae.
鯵科（也称为银汉鱼科）是印度-西太平洋地区底层沿海海洋鱼类的一个科，具有重要的生态和经济价值。中国的许多鯵科鱼类，包括中国银鯵（Sillago sinica），最近在中国被描述，为分析鯵科鱼类的遗传多样性提供了有价值的材料。在这里，我们构建了中国银鯵的参考基因组，旨在为该科所有物种的比较分析建立一个平台。
使用单分子实时 DNA 测序平台 Pacific Biosciences (PacBio) Sequel，我们为中国银鯵生成了约 27.3Gb 的基因组 DNA 序列。我们利用两种基因组组装程序 Canu 和 FALCON 的互补优势，采用一种策略重建了 534Mb 的基因组组装。基因组大小与基于 k-mer 分析估计的基因组大小一致。组装的基因组由 802 个 contigs 组成，contig N50 长度为 2.6Mb。我们使用从头预测方法以及 RNA 测序数据和与其他硬骨鱼的同源性，为中国银鯵基因组注释了 22122 个蛋白质编码基因。根据使用蛋白质编码基因进行的系统发育分析，中国银鯵与大黄鱼和欧洲鲈关系密切，与它们的祖先分化于 69.5-82.6 百万年前。
使用 PacBio 测序技术生成的长读长，我们构建了中国银鯵的基因组草图组装，这是 Sillaginidae 物种的第一个参考基因组。该基因组组装为比较分析 Sillaginidae 鱼类的多样性和适应性奠定了基础。
