High-Quality Genome Assembly of Eriocheir japonica sinensis Reveals Its Unique Genome Evolution

被引：36

作者：

Tang, Boping ^{[1
]}

Wang, Zhongkai ^{[2
]}

Liu, Qiuning ^{[1
]}

Zhang, Huabin ^{[1
]}

Jiang, Senhao ^{[1
]}

Li, Xinzheng ^{[3
]}

Wang, Zhengfei ^{[1
]}

Sun, Yue ^{[1
]}

Sha, Zhongli ^{[3
]}

Jiang, Hui ^{[4
,5
]}

Wu, Xugan ^{[6
]}

Ren, Yandong ^{[2
]}

Li, Haorong ^{[2
]}

Xuan, Fujun ^{[1
]}

Ge, Baoming ^{[1
]}

Jiang, Wei ^{[3
]}

She, Shusheng ^{[7
]}

Sun, Hongying ^{[8
]}

Qiu, Qiang ^{[2
]}

Wang, Wen ^{[2
]}

Wang, Qun ^{[9
]}

Qiu, Gaofeng ^{[6
]}

Zhang, Daizhen ^{[1
]}

Li, Yongxin ^{[2
]}

机构：

[1] Yancheng Teachers Univ, Jiangsu Synthet Innovat Ctr Coastal Bioagr, Jiangsu Prov Key Lab Coastal Wetland Bioresources, Jiangsu Key Lab Bioresources Saline Soils, Yancheng, Peoples R China

[2] Northwestern Polytech Univ, Ctr Ecol & Environm Sci, Xian, Peoples R China

[3] Chinese Acad Sci, Inst Oceanol, Qingdao, Peoples R China

[4] Zhejiang Ocean Univ, Natl Engn Lab Marine Germplasm Resources Explorat, Zhoushan, Peoples R China

[5] Zhejiang Ocean Univ, Natl Engn Res Ctr Facilitated Marine Aquaculture, Zhoushan, Peoples R China

[6] Shanghai Ocean Univ, Key Lab Freshwater Aquat Genet Resources, Minist Agr & Rural Affairs, Shanghai, Peoples R China

[7] China Hong Kong Ecol Consultant Co, Hong Kong, Peoples R China

[8] Nanjing Normal Univ, Coll Life Sci, Nanjing, Peoples R China

[9] East China Normal Univ, Sch Life Sci, Dept Biol, Shanghai, Peoples R China

来源：

FRONTIERS IN GENETICS | 2020年 / 10卷

基金：

中国国家自然科学基金; 中国博士后科学基金;

关键词：

Eriocheir japonica sinensis; evolution; nanopore; crab; genome assembly and annotation; CHINESE MITTEN CRAB; MILNE-EDWARDS DECAPODA; PHYLOGENETIC ANALYSIS; LARVAL DEVELOPMENT; ALIGNMENT; SEQUENCE; INVASION; PROGRAM; BURROWS; ESTUARY;

D O I：

10.3389/fgene.2019.01340

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

As an important freshwater aquaculture species in China, the Chinese mitten crab (Eriocheir japonica sinensis) has high economic and nutritional value. However, limited genomic information is currently available for studying its basic development and genetic diversity. Here, we performed whole-genome sequencing on Oxford Nanopore Technologies Limited's platform using promethION. The assembled size of E. j.sinensis genome was approximately 1.27 Gb, which is close to the estimated size (1.19 Gb). Furthermore, based on assessment using Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simao et al., 2015), 94.00% of the expected eukaryotic genes were completely present in the genome assembly. In addition, repetitive sequences accounted for similar to 61.42% of the assembled genome, and 22,619 protein-coding genes were annotated. Comparative genomics analysis demonstrated that the Chinese mitten crab diverged from Penaeus vannamei similar to 373.6 million years ago, with a faster evolution rate than shrimp. We anticipate that the annotated high-quality genome of E. j. sinensis will promote research on its basic development and evolution and make substantial contributions to comparative genomic analyses of crustaceans.

引用

页数：9

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