Genomic characterization of sex‐identification markers inSebastes carnatusandSebastes chrysomelasrockfishes

Abstract

Fish have evolved a variety of sex-determining (SD) systems including male heterogamy (XY), female heterogamy (ZW) and environmental SD. Little is known about SD mechanisms of Sebastes rockfishes, a highly speciose genus of importance to evolutionary and conservation biology. Here, we characterize the sex determination system in the sympatrically distributed sister species Sebastes chrysomelas and Sebastes carnatus. To identify sex-specific genotypic markers, double digest restriction site - associated DNA sequencing (ddRAD-seq) of genomic DNA from 40 sexed individuals of both species was performed. Loci were filtered for presence in all of the individuals of one sex, absence in the other sex and no heterozygosity. Of the 74 965 loci present in all males, 33 male-specific loci met the criteria in at least one species and 17 in both. Conversely, no female-specific loci were detected, together providing evidence of an XY sex determination system in both species. When aligned to a draft reference genome from Sebastes aleutianus, 26 sex-specific loci were interspersed among 1168 loci that were identical between sexes. The nascent Y chromosome averaged 5% divergence from the X chromosome and mapped to reference Sebastes genome scaffolds totalling 6.9Mbp in length. These scaffolds aligned to a single chromosome in three model fish genomes. Read coverage differences were also detected between sex-specific and autosomal loci. A PCR-RFLP assay validated the bioinformatic results and correctly identified sex of five additional individuals of known sex. A sex-determining gene in other teleosts gonadal soma-derived factor (gsdf) was present in the model fish chromosomes that spanned our sex-specific markers.

Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral (Corallium rubrum)

“…The 435 male-specific loci detected here suggested at least 218 male-specific PstI sites, which is far higher than the number of sex-specific loci in other similar studies based on RAD-Seq [17,33,36]. However, considering the specificity of each study (genome size, frequency of the restriction site and parameters used for the loci assembly), we could not directly compare the number of sex-linked markers or the number of male-specific markers.…”

ZZ/ZW Sex Chromosomes in the Endemic Puerto Rican Leaf-Toed Gecko (<b><i>Phyllodactylus wirshingi</i></b>)

“…Sequencing paired-end reads, as we have done here, will generate larger RAD contigs, which in turn increases the probability of identifying genes Baxter et al, 2011;. Sex-specific RAD markers with gene fragments can be used to query genomic assemblies of related species to identify the sex chromosomes [Bruneaux et al, 2013;Fowler and Buonaccorsi, 2016;Qiu et al, 2016]. This is the approach we successfully applied here to identify synteny between the avian Z and the P. wirshingi ZZ/ZW.…”

How to identify sex chromosomes and their turnover

“…A solution might be to increase sample size; however, the number of shared loci decreases with sample numbers in RAD‐seq data (Mastretta‐Yanes et al, ). Several studies have had success by sampling ~5–20 individuals per sex (Fowler & Buonaccorsi, ; Gamble et al, ; Gamble & Zarkower, ; Jeffries et al, ); however, false positives can also be problematic with very small numbers of males and females, and greater skew in sample sexes. Implementing and developing approaches to quantify the false positive rate of identifying sex‐linked sequences is a future priority when using this approach (see Box 1).…”