Improvement of the Pacific bluefin tuna (Thunnus orientalis) reference genome and development of male-specific DNA markers

Abstract

The Pacific bluefin tuna, Thunnus orientalis, is a highly migratory species that is widely distributed in the North Pacific Ocean. Like other marine species, T. orientalis has no external sexual dimorphism; thus, identifying sex-specific variants from whole genome sequence data is a useful approach to develop an effective sex identification method. Here, we report an improved draft genome of T. orientalis and male-specific DNA markers. Combining PacBio long reads and Illumina short reads sufficiently improved genome assembly, with a 38-fold increase in scaffold contiguity (to 444 scaffolds) compared to the first published draft genome. Through analysing re-sequence data of 15 males and 16 females, 250 male-specific SNPs were identified from more than 30 million polymorphisms. All male-specific variants were male-heterozygous, suggesting that T. orientalis has a male heterogametic sex-determination system. The largest linkage disequilibrium block (3,174 bp on scaffold_064) contained 51 male-specific variants. PCR primers and a PCR-based sex identification assay were developed using these male-specific variants. The sex of 115 individuals (56 males and 59 females; sex was diagnosed by visual examination of the gonads) was identified with high accuracy using the assay. This easy, accurate, and practical technique facilitates the control of sex ratios in tuna farms. Furthermore, this method could be used to estimate the sex ratio and/or the sex-specific growth rate of natural populations.

Methods for identifying and interpreting sex‐linked SNP markers and carrying out sex assignment: application to thornback ray (Raja clavata)

“…Validation of sex‐linked loci can be achieved in several ways: (a) cross‐validation using part of the data set used for identifying sex‐linked loci and/or (b) predicting sex for an independent sample with morphologically determined sex. Certain authors have also developed specific assays for DNA sequences including the putative sex‐linked identified SNPs and then used them to identify the sex for an independent sample to be compared with morphologically determined sex (Carmichael et al, 2013; Drinan et al, 2018; Shi et al, 2018; Suda et al, 2019; Utsunomia et al, 2017).…”

Prediction of the sex-determination gene in tunas (Thunnus fishes)

“…In 2019, Suda et al sequenced the genome of female PBT, compared the assembled scaffold with that of the male genome, and explored sex-associated regions from the scaffold sequences by resequencing 31 PBT individuals (15 males and 16 females) (Suda et al, 2019). They performed a genome-wide association (GWA) study focusing on sex-associated single nucleotide variants (SNVs) between males and females, and identified several regions carrying male-specific alleles.…”

Transcriptome characterization of BPG axis and expression profiles of ovarian steroidogenesis-related genes in the Japanese sardine

“…As recent examples, RNA-seq analyses were conducted on carp, eel, perch, and salmonid species [1][2][3][4][5]. For important target species of fisheries, the application of large-scale genomic approaches has mostly been conducted to investigate population structure and genetic differentiation (e.g., for cod [6] and tuna species [7]). Accordingly, the current understanding of large-scale transcriptome data for fish reproduction is considered to be biased towards aquaculture species.…”