Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly

Abstract

Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex determination to control sex ratio. Using a Restriction-site Associated DNA approach, we genotyped 18,214 single nucleotide polymorphism in 1,268 turbot individuals from 31 full-sibling families. Individual linkage maps were combined to obtain a male, female and species consensus maps. The turbot consensus map contained 11,845 markers distributed across 22 linkage groups representing a total normalised length of 3,753.9 cM. The turbot genome was anchored to this map, and scaffolds representing 96% of the assembly were ordered and oriented to obtain the expected 22 megascaffolds according to its karyotype. Recombination rate was lower in males, especially around centromeres, and pairwise comparison of 44 individual maps suggested chromosome polymorphism at specific genomic regions. Genome comparison across flatfish provided new evidence on karyotype reorganisations occurring across the evolution of this fish group.

Multiple evidences suggest sox2 as the main driver of a young and complex sex determining ZW/ZZ system in turbot (Scophthalmus maximus)

“…Illumina sequences matching to that 961.4 kb region were retrieved for assembly using the last version of the turbot genome (Maroso et al, 2018). A hybrid assembly was obtained separately for the W and Z chromosomes using Nanopore assembly as the backbone, which was then curated using the Illumina 150 bp PE reads of five WW females and five males, respectively.…”

“…A 2b-RAD method (Wang et al, 2012) was applied to genotype 18,214 SNPs in the 1181 fish used for GWAS and segregation analysis as reported by Maroso et al (2018).…”

“…Briefly, SNPs were filtered out according to SNP call-rate < 0.8, individual call-rate < 0.8, identity-by-state > 0.95 (both individuals removed) and minor allele frequency (MAF) < 0.01. The filtering done enabled to obtain a very consistent set of SNPs showing a genotyping error > 0.4 % estimated using family data (Maroso et al, 2018).…”

“…Only reads where both pairs were longer than 36 bp post-filtering were retained. Filtered reads were mapped to the most recent turbot genome assembly (ASM318616v1; Genbank accession GCA_003186165.1; Maroso et al, 2018) using Burrows-Wheeler aligner v.0.7.8 BWA-MEM algorithm (Li, 2013). Pileup files describing the base-pair information at each genomic position were generated from the alignment files using the mpileup function of samtools v1.6 (Li et al, 2009), discarding those aligned reads with a mapping quality < 30 and those bases with a Phred score < 30.…”

“…A de novo hybrid assembly with Illumina and Nanopore reads was carried out at the delimited SD region (see segregation analysis) using those reads matching at LG5 in that region using the last version of the turbot genome assembly (Maroso et al, 2018).…”