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

Abstract

BackgroundSiamese 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.FindingsFrist, 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.ConclusionsWe 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.

Improving the chromosome-level genome assembly of the Siamese fighting fish (Betta splendens) in a university Master’s course

“…Next, to further improve the resulting consensus quality, we carried out error correction using previously published Illumina paired-end short-read data (accession no. SRR6251365; [7]). For that, we first used Cutadapt v.1.18 [12] to remove adapter sequences as well as low-quality ends from the reads.…”

“…In order to achieve chromosome-level for our long-read based assembly, we removed all contigs matching to the mitochondrial genome, and subsequently mapped the previously published HiC reads (accession no. SRR6251367; [7]) onto the genome using BWA-MEM. Next, we scaffolded the assembly using the HiC reads with ALLHiC v.0.9.8 [16].…”

“…We then mapped the Illumina HiSeq2000 reads from the 5 Kbp insert-size mate pair library (accession no. SRR625353; [7]) to the assembly and investigated the distribution of insert sizes for the library (Supplementary Figure 2). We mapped the data using BWA-MEM, sorted the alignment files with SAMtools, marked duplicates using Picard 2.20.7 (https://broadinstitute.github.io/picard/), and then created a histogram based on the statistics obtained from GATK 4.1.4.1 (https://gatk.broadinstitute.org; CollectInsertSizeMetrics option).…”

“…Recently, [7] generated a chromosome-level B. splendens reference assembly. In order to do so, they first generated a baseline assembly using a combination of paired-end and mate pair libraries (sequenced on the Illumina HiSeq2000 platform), and then super-scaffolded the resulting assembly using a proximity-ligationbased HiC library (sequenced on the BGISEQ-500 platform).…”

“…In order to do so, they first generated a baseline assembly using a combination of paired-end and mate pair libraries (sequenced on the Illumina HiSeq2000 platform), and then super-scaffolded the resulting assembly using a proximity-ligationbased HiC library (sequenced on the BGISEQ-500 platform). To further improve this assembly and to provide a solid basis for future analyses on this important fish model, we generated a more continuous baseline assembly using long-read data generated with the MinION sequencing device from Oxford Nanopore Technologies (ONT), and subsequently carried out scaffolding using the published HiC data from [7].…”