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Gigascience. 2018 Nov 1;7(11). doi: 10.1093/gigascience/giy087.

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

Fan G1,2,3,4, Chan J1, Ma K3,4, Yang B1, Zhang H2,3,4, Yang X2,3,4, Shi C2,3,4, Chun-Hin Law H1, Ren Z1, Xu Q2,3,4, Liu Q2,3,4, Wang J2,3,4, Chen W3,4, Shao L2,3,4, Gonçalves D5, Ramos A5, Cardoso SD6, Guo M1, Cai J1, Xu X2,3,4, Wang J3,7, Yang H3,7, Liu X2,3,4, Wang Y1.

Author information

1
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
Institute of Science and Environment, University of Saint Joseph, Rua de Londres 16, Macao SAR, China.
6
Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
7
James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.

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 ∼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.

PMID:
30010754
PMCID:
PMC6251983
DOI:
10.1093/gigascience/giy087
[Indexed for MEDLINE]
Free PMC Article

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