A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes

doi:10.1093/gigascience/giy108

	A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes
	Xu, Shengyong 1; Xiao, Shijun 2; Zhu, Shilin 2; Zeng, Xiaofei 2; Luo, Jing 3; Liu, Jiaqi 2; Gao, Tianxiang 1; Chen, Nansheng 4,5,6
	2018-09-10
发表期刊	GIGASCIENCE
ISSN	2047-217X
卷号	7 期号:9 页码:8
通讯作者	Gao, Tianxiang(gaotianxiang0611@163.com) ; Chen, Nansheng(chenn@qdio.ac.cn)
摘要	Background: 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. Findings: Using the single-molecule real-time DNA sequencing platform Pacific Biosciences (PacBio) Sequel, we generated similar to 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. Conclusions: 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.
关键词	Sillaginidae Chinese sillago PacBio sequencing Canu FALCON genetic diversification
DOI	10.1093/gigascience/giy108
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[41776171] ; National Natural Science Foundation of China[31572227] ; National Natural Science Foundation of China[31602207] ; Scientific Startup Foundation of Zhejiang Ocean University[Q1505] ; Open Foundation from Fishery Sciences in the First-Class Subjects of Zhejiang[20160001] ; CAS Pioneer Hundred Talents Program ; National Natural Science Foundation of China[41776171] ; National Natural Science Foundation of China[31572227] ; National Natural Science Foundation of China[31602207] ; Scientific Startup Foundation of Zhejiang Ocean University[Q1505] ; Open Foundation from Fishery Sciences in the First-Class Subjects of Zhejiang[20160001] ; CAS Pioneer Hundred Talents Program
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000456724000001
出版者	OXFORD UNIV PRESS
引用统计	被引频次：25[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/157535
专题	海洋生态与环境科学重点实验室
通讯作者	Gao, Tianxiang; Chen, Nansheng
作者单位	1.Zhejiang Ocean Univ, Fishery Coll, Zhoushan 316022, Zhejiang, Peoples R China 2.Wuhan Frasergen Bioinformat Co Ltd, Wuhan 430075, Hubei, Peoples R China 3.Yunnan Univ, Sch Life Sci, Kunming 650500, Yunnan, Peoples R China 4.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, Qingdao 266071, Shandong, Peoples R China 5.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao 266237, Shandong, Peoples R China 6.Simon Fraser Univ, Dept Mol Biol & Biochem, Burnaby, BC, Canada
通讯作者单位	中国科学院海洋研究所
推荐引用方式 GB/T 7714	Xu, Shengyong,Xiao, Shijun,Zhu, Shilin,et al. A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes[J]. GIGASCIENCE,2018,7(9):8.
APA	Xu, Shengyong.,Xiao, Shijun.,Zhu, Shilin.,Zeng, Xiaofei.,Luo, Jing.,...&Chen, Nansheng.(2018).A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes.GIGASCIENCE,7(9),8.
MLA	Xu, Shengyong,et al."A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes".GIGASCIENCE 7.9(2018):8.

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文件名称/大小	文献类型	版本类型	开放类型	使用许可
A draft genome assem（1655KB）	期刊论文	出版稿	限制开放	CC BY-NC-SA	浏览