UM  > 中藥質量研究國家重點實驗室(澳門大學)
Chromosome-level reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression
Guangyi Fan1,2,3,4; Judy Chan1; Kailong Ma3,4; Binrui Yang1; He Zhang2,3,4; Xianwei Yang2,3,4; Chengcheng Shi2,3,4; Henry Chun-Hin Law1; Zhitao Ren1; Qiwu Xu2,3,4; Qun Liu2,3,4; Jiahao Wang2,3,4; Wenbin Chen3,4; Libin Shao2,3,4; David Goncalves6; Andreia Ramos6; Sara D. Cardoso7; Min Guo1; Jing Cai1; Xun Xu2,3,4; Jian Wang3,5; Huanming Yang3,5; Xin Liu2,3,4; Yitao Wang1
2018-07-11
Source PublicationGIGASCIENCE
ISSN2047-217X
Volume7Issue:11
Abstract

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.

KeywordBetta Splendens Aggression Hi-c Chromosomal Genome Assembly Resequencing Fish Genome
DOI10.1093/gigascience/giy087
Language英语
WOS Research AreaLife Sciences & Biomedicine - Other Topics ; Science & Technology - Other Topics
WOS SubjectBiology ; Multidisciplinary Sciences
WOS IDWOS:000456729300001
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Cited Times [WOS]:2   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionTHE STATE KEY LABORATORY OF QUALITY RESEARCH IN CHINESE MEDICINE (UNIVERSITY OF MACAU)
Institute of Chinese Medical Sciences
Corresponding AuthorYitao Wang
Affiliation1.State Key Laboratory of Quality Research of Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China
2.BGI-Qingdao, BGI-Shenzhen, Sino-German Ecopark, No.2877, Tuanjie Road, Huangdao District, Qingdao, Shandong Province, 266555, China
3.BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
4.China National GeneBank, BGI-Shenzhen, Jinsha Road, Dapeng New District, Shenzhen 518120, China
5.James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
6.Institute of Science and Environment, University of Saint Joseph, Rua de Londres 16, Macao SAR, China
7.Instituto Gulbenkian de Ciencia, Rua da ˆ Quinta Grande 6, 2780-156 Oeiras, Portugal
First Author AffilicationInstitute of Chinese Medical Sciences
Corresponding Author AffilicationInstitute of Chinese Medical Sciences
Recommended Citation
GB/T 7714
Guangyi Fan,Judy Chan,Kailong Ma,et al. Chromosome-level reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression[J]. GIGASCIENCE,2018,7(11).
APA Guangyi Fan.,Judy Chan.,Kailong Ma.,Binrui Yang.,He Zhang.,...&Yitao Wang.(2018).Chromosome-level reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression.GIGASCIENCE,7(11).
MLA Guangyi Fan,et al."Chromosome-level reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression".GIGASCIENCE 7.11(2018).
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