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Data released on June 08, 2018

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

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, S, D; 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 RIS BibTeX Text

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.

Contact Submitter

Protocols.io:

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Accessions (data included in GigaDB):

BioProject: PRJNA416843

Keywords:

betta splendens fish genome aggression hi-c chromosomal genome assembly resequencing 

Genomic, Transcriptomic

http://gigadb.org/images/data/cropped/100433.jpg

Funding:

  • Funding body - Macau Science and Technology Development Fund
  • Award ID - 011/2014/A1
  • Awardee - SMY Lee
  • Funding body - Shenzhen Municipal Government of China
  • Location - China
  • Award ID - JCYJ20151015162041454
  • Awardee - W Chen
  • Funding body - Shenzhen Municipal Government of China
  • Location - China
  • Award ID - JCYJ20150529150505656
  • Awardee - X Liu

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
Coding SequenceFASTA39.3 MB2018-06-01
otherAGP335.87 KB2018-06-01
SNPsVCF1.1 GB2018-06-01
otherTEXT0.73 KB2018-06-01
otherTEXT0.75 KB2018-06-01
Expression dataEXCEL3.98 MB2018-06-01
AlignmentsFASTA329.05 MB2018-06-01
otherUNKNOWN0.26 KB2018-06-01
ReadmeTEXT2.99 KB2018-06-01
Phylogenetic treeUNKNOWN0.26 KB2018-06-01
Displaying 1-10 of 15 File(s).

History:

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