Evolution and conservation of Characidium sex chromosomes

Abstract

Fish species exhibit substantial variation in the degree of genetic differentiation between sex chromosome pairs, and therefore offer the opportunity to study the full range of sex chromosome evolution. We used Restriction site Associated DNA sequencing (RAD-seq) to study the sex chromosomes of Characidium gomesi, a species with conspicuous heteromorphic ZW/ZZ sex chromosomes. We screened 9,863 SNPs, corresponding to ~1 marker/100 kb distributed across the genome for sex-linked variation. With this dataset, we identified 26 female-specific RAD loci, putatively located on the W chromosome, as well as 148 sex-associated SNPs showing significant differentiation (average F ST = 0.144) between males and females, and therefore in regions of more recent divergence between the Z and W chromosomes. Additionally, we detected 25 RAD loci showing extreme heterozygote deficiency in females but which were in Hardy-Weinberg equilibrium in males, consistent with degeneration of the W chromosome and therefore female hemizygosity. We validated seven female-specific and two sex-associated markers in a larger Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the Europe PMC Funders Author ManuscriptsEurope PMC Funders Author Manuscripts sample of C. gomesi, of which three localised to the W chromosome, thereby providing useful markers for sexing wild samples. Validated markers were evaluated in other populations and species of the genus Characidium, this exploration suggesting a rapid turnover of W-specific repetitive elements. Together, our analyses point to a complex origin for the sex chromosome of C. gomesi and highlight the utility of RAD-seq for studying the composition and evolution of sex chromosomes systems in wild populations.

RADSex: a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data

“…an allele specific to one sex in a polymorphic locus) (Utsunomia et al, 2017) . In addition, the lack of visualization tools for RAD-Seq data makes the interpretation of results from some datasets difficult, for instance, datasets containing individuals with mis-assigned sex, strong population structure, or sex-bias in sequencing depth.…”

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

“…These loci would correspond to sequences absent from the other sex because they occur only on the Y or W chromosome. Loci only present in females were identified for the neotropical fish Characidium gomesi (Utsunomia et al, 2017…”

“…To move from sex-correlated SNPs to gene function, comparison and alignment of the loci including the putative sex-linked SNPs with known interpreted genomes is needed (e.g. Benestan et al, 2017;Carmichael et al, 2013;Utsunomia et al, 2017). The most common tool for this is BLAST (basic local alignment search tool) first developed by Altschul, Gish, Miller, Myers, and Lipman (1990), and available from the National Centre for Biotechnology Information (NCBI).…”

Dispersion of transposable elements and multigene families: Microstructural variation in Characidium (Characiformes: Crenuchidae) genomes

“…The genus Characidium (Characiformes: Crenuchidae) presents a diversified karyotype microstructure despite its conserved karyotype macrostructure and prevalent diploid number (2n) of 50 ( Centofante et al , 2001 , 2003 ; Vicari et al , 2008 ; Pazian et al , 2013 ; Scacchetti et al , 2015a ; Pucci et al , 2016 ; Serrano et al , 2017 ). The Characidium species studied to date exhibited differences mainly in the number of ribosomal DNA sites and sex chromosomes ( Pansonato-Alves et al , 2010 , 2011 , 2014 ; Pucci et al , 2014 ; Scacchetti et al , 2015a , Utsunomia et al , 2017 ), as well as an interesting dynamic of repetitive DNAs ( Scacchetti et al , 2015b ; Pucci et al , 2016 ).…”