A draft genome assembly of southern bluefin tuna Thunnus maccoyii

TL;DR

This paper presents a draft genome assembly of the southern bluefin tuna, providing essential genetic data for conservation and comparative genomics, and includes genome sequences for five other tuna species.

Contribution

It reports the first draft genome assembly of the southern bluefin tuna and provides genome-wide data for multiple tuna species, aiding conservation and evolutionary studies.

Findings

Genome size estimated at 795 Mb.

Assembly scaffolds with N50 >174 kb.

High coverage of fish transcriptome with 91% of zebrafish mRNA matches.

Abstract

Tuna are large pelagic fish whose populations are close to panmixia. In addition, they are threatened species, so it is important for the maintenance and monitoring of genetic diversity that genetic information at a genome level be obtained. Here we report the draft assembly of the southern bluefin tuna genome and the collection of genome-wide sequence data for five other tuna species. We sampled five tuna species of the genus Thunnus, the northern and southern bluefin, yellowfin, albacore, and bigeye, as well as the skipjack (Katsuwonis pelamis), a tuna-like species. Genome assembly was facilitated at k-mer=25 while k-mer=51 generated assembly artefacts. The estimated size of the southern bluefin tuna genome was 795 Mb. We assembled two southern bluefin tuna individuals independently using both paired end and mate pair sequence. This resulted in scaffolds with N50>174,000 bp and maximum scaffold lengths>1.4 Mb. Our estimate of the size of the assembled genome was the scaffolded sequences in common to both assemblies, which amounted to 721 Mb of the 795 Mb of the southern bluefin tuna genome sequence. Using BLAST, there were matches between 13,039 of 14,341 (91%) refseq mRNA of the zebrafish Danio rerio to the tuna assembly indicating that most of a generic fish transcriptome was covered by the assembly.