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

Dataset type: Genomic, Transcriptomic
Data released on June 08, 2018

Fan G; Chan J; Ma K; Yang B; Zhang H; Yang X; Shi C; Law H; Ren Z; Xu Q; Liu Q; Wang J; Chen W; Shao L; Gonçalves D; Ramos A; Cardoso SD; Guo M; Cai J; Xu X; Wang J; Yang H; Liu X; Wang Y (2018): Supporting data for "Chromosome-level reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression" GigaScience Database. http://dx.doi.org/10.5524/100433

DOI10.5524/100433

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 so far 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.
We first 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 heatmap and BUSCO. We also performed comparative chromosome analyses between Oryzias latipes and B. splendens, revealing a chromosome conservation evolution in B. splendens. We predicted a total of 23,981 genes assisted by RNA-seq data generated from brain, liver, muscle and heart tissues of Giant, and annotated 15% repetitive sequences in the genome. Additionally, we resequenced other five B. splendens varieties and detected ~3.4M single-nucleotide variations (SNVs) and 27,305 indels.
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.

Additional details

Accessions (data included in GigaDB):

BioProject: PRJNA416843





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Giant158456 Siamese fighting fishBetta splendens Description:DNA extracted from Giant Siemesse figh...
Alternative accession-BioSample:SAMN07955939
Analyte type:DNA
...
+
Half-moon158456 Siamese fighting fishBetta splendens Description:DNA extracted from Half-moon Siemesse ...
Alternative names:HM
Alternative accession-BioSample:SAMN07955940
...
+
Half-moon plakat158456 Siamese fighting fishBetta splendens Description:DNA extracted from Half-moon plakat Si...
Alternative names:HMPK
Alternative accession-BioSample:SAMN08972859
...
+
Fighter158456 Siamese fighting fishBetta splendens Description:DNA extracted from Fighter Siemesse fi...
Alternative accession-BioSample:SAMN08972862
Analyte type:DNA
...
+
Elephant Ear158456 Siamese fighting fishBetta splendens Description:DNA extracted from Elephant Ear Siemes...
Alternative names:EE
Alternative accession-BioSample:SAMN08972863
...
+
Brain158456 Siamese fighting fishBetta splendens Description:RNA extracted from Giant Siemesse figh...
Alternative accession-BioSample:SAMN07955939
Analyte type:RNA
...
+
Liver158456 Siamese fighting fishBetta splendens Description:RNA extracted from Giant Siemesse figh...
Alternative accession-BioSample:SAMN07955939
Analyte type:RNA
...
+
Heart158456 Siamese fighting fishBetta splendens Description:RNA extracted from Giant Siemesse figh...
Alternative accession-BioSample:SAMN07955939
Analyte type:RNA
...
+
Muscle158456 Siamese fighting fishBetta splendens Description:RNA extracted from Giant Siemesse figh...
Alternative accession-BioSample:SAMN07955939
Analyte type:RNA
...
+
Displaying 1-9 of 9 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
otherTEXT0.73 KB2018-06-01
otherTEXT0.75 KB2018-06-01
otherAGP335.87 KB2018-06-01
Sequence assemblyFASTA449.48 MB2018-06-01
Coding SequenceFASTA39.3 MB2018-06-01
Sequence assemblyFASTA451.35 MB2018-06-01
annotationGFF15.82 MB2018-06-01
protein sequenceFASTA14.61 MB2018-06-01
annotationGFF146.1 MB2018-06-01
SNPsVCF1.1 GB2018-06-01
Displaying 1-10 of 15 File(s).
Funding body Awardee Award ID Comments
Macau Science and Technology Development Fund SMY Lee 011/2014/A1
Shenzhen Municipal Government of China W Chen JCYJ20151015162041454
Shenzhen Municipal Government of China X Liu JCYJ20150529150505656

Protocols.io:

Date Action
June 8, 2018 Dataset publish
June 8, 2018 External Link added : https://www.protocols.io/widgets/protocol/high-quality-reference-genome-of-the-siamese-fight-qsvdwe6
June 11, 2018 External Link updated : https://www.protocols.io/widgets/protocol/high-quality-reference-genome-of-the-siamese-fight-qvddw26