Abstract
BackgroundHomologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes.ResultsWe generated 96.7 × 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 109 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females.ConclusionsThe sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.
Highlights
Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog
What follows over time is a chain of mutational events on the hemizygous member of the Dissanayake et al BMC Genomics (2020) 21:667 sex chromosome pair, leading to the accumulation of genes that afford a fitness advantage to the heterogametic sex, a fitness disadvantage to the homogametic sex, suppression of recombination, the accumulation of repetitive sequence, and progressive loss of gene function unrelated to sex [5, 6]
For example, the nonrecombining region of the Y chromosome contains 78 protein coding genes encoding 27 proteins [7] compared with the 699 protein-coding genes with known function on the X [8]; the human Y is smaller than the X and highly heterochromatic
Summary
Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Most vertebrates reproduce sexually with distinct male and female phenotypes that arise from the complement of chromosomes that are inherited from their parents. These species are said to have their sex determined genotypically (GSD), and the influential genes reside on sex chromosomes that typically assort randomly during meiosis. For example, the nonrecombining region of the Y chromosome contains 78 protein coding genes encoding 27 proteins [7] compared with the 699 protein-coding genes with known function on the X [8]; the human Y is smaller than the X and highly heterochromatic
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