Chromosome-level reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression

被引：28

作者：

Fan, Guangyi ^{[1
,2
,3
,4
]}

Chan, Judy ^{[1
]}

Ma, Kailong ^{[3
,4
]}

Yang, Binrui ^{[1
]}

Zhang, He ^{[2
,3
,4
]}

Yang, Xianwei ^{[2
,3
,4
]}

Shi, Chengcheng ^{[2
,3
,4
]}

Law, Henry Chun-Hin ^{[1
]}

Ren, Zhitao ^{[1
]}

Xu, Qiwu ^{[2
,3
,4
]}

Liu, Qun ^{[2
,3
,4
]}

Wang, Jiahao ^{[2
,3
,4
]}

Chen, Wenbin ^{[3
,4
]}

Shao, Libin ^{[2
,3
,4
]}

Goncalves, David ^{[6
]}

Ramos, Andreia ^{[6
]}

Cardoso, Sara D. ^{[7
]}

Guo, Min ^{[1
]}

Cai, Jing ^{[1
]}

Xu, Xun ^{[2
,3
,4
]}

Wang, Jian ^{[3
,5
]}

Yang, Huanming ^{[3
,5
]}

Liu, Xin ^{[2
,3
,4
]}

Wang, Yitao ^{[1
]}

机构：

[1] Univ Macau, Inst Chinese Med Sci, State Key Lab Qual Res Chinese Med, Ave Univ, Taipa, Macau, Peoples R China

[2] BGI Shenzhen, BGI Qingdao, Sino German Ecopk,2877 Tuanjie Rd, Qingdao 266555, Shandong, Peoples R China

[3] BGI Shenzhen, Bldg 11,Beishan Ind Zone, Shenzhen 518083, Peoples R China

[4] BGI Shenzhen, China Natl GeneBank, Jinsha Rd, Shenzhen 518120, Peoples R China

[5] James D Watson Inst Genome Sci, Hangzhou 310058, Zhejiang, Peoples R China

[6] Univ St Joseph, Inst Sci & Environm, Rua Londres 16, Macau, Macao, Peoples R China

[7] Inst Gulbenkian Ciencias, Rua Quinta Grande 6, P-2780156 Oeiras, Portugal

来源：

GIGASCIENCE | 2018年 / 7卷 / 11期

关键词：

Betta splendens; fish genome; aggression; Hi-C; chromosomal genome assembly; resequencing; HI-C; PREDICTION; GENE;

D O I：

10.1093/gigascience/giy087

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Background: Siamese fighting fish Betta splendens are notorious for their aggressiveness and accordingly have been widely used to study aggression. However, the lack of a reference genome has, to date, limited the understanding of the genetic basis of aggression in this species. Here, we present the first reference genome assembly of the Siamese fighting fish. Findings: Frist, we sequenced and de novo assembled a 465.24-Mb genome for the B. splendens variety Giant, with a weighted average (N50) scaffold size of 949.03 Kb and an N50 contig size of 19.01 Kb, covering 99.93% of the estimated genome size. To obtain a chromosome-level genome assembly, we constructed one Hi-C library and sequenced 75.24 Gb reads using the BGISEQ-500 platform. We anchored approximately 93% of the scaffold sequences into 21 chromosomes and evaluated the quality of our assembly using the high-contact frequency heat map and Benchmarking Universal Single-Copy Orthologs. We also performed comparative chromosome analyses between Oryzias latipes and B. splendens, revealing a chromosome conservation evolution in B. splendens. We predicted 23,981 genes assisted by RNA-sequencing data generated from brain, liver, muscle, and heart tissues of Giant and annotated 15% repetitive sequences in the genome. Additionally, we resequenced five other B. splendens varieties and detected similar to 3.4 M single-nucleotide variations and 27,305 insertions and deletions. Conclusions: We provide the first chromosome-level genome for the Siamese fighting fish. The genome will lay a valuable foundation for future research on aggression in B. splendens.

引用

页码：1 / 7

页数：7

共 23 条

[21] AUGUSTUS:: ab initio prediction of alternative transcripts [J].