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A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes
Xu, Shengyong1; Xiao, Shijun2; Zhu, Shilin2; Zeng, Xiaofei2; Luo, Jing3; Liu, Jiaqi2; Gao, Tianxiang1; Chen, Nansheng4,5,6
2018-09-10
Source PublicationGIGASCIENCE
ISSN2047-217X
Volume7Issue:9Pages:8
Corresponding AuthorGao, Tianxiang(gaotianxiang0611@163.com) ; Chen, Nansheng(chenn@qdio.ac.cn)
AbstractBackground: 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.
KeywordSillaginidae Chinese sillago PacBio sequencing Canu FALCON genetic diversification
DOI10.1093/gigascience/giy108
Indexed BySCI
Language英语
Funding ProjectNational 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 Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000456724000001
PublisherOXFORD UNIV PRESS
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/157535
Collection海洋生态与环境科学重点实验室
Corresponding AuthorGao, Tianxiang; Chen, Nansheng
Affiliation1.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
Corresponding Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
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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