Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction.

Abstract

Background: 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. 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. Results: We generated 96.7 x 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 x 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. Conclusions: The 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.

Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional‐scale disturbance

“…They have broadly parapatric distributions (Figure 1). The south‐eastern highland and alpine taxon is of particular interest, because it has a system of sex determination that involves both differentiated sex chromosomes and sex reversal of the XX genotype to a male phenotype at a frequency that varies predictably with elevation and nest temperatures (Dissanayake et al, 2020, 2021; Dissanayake et al, 2021).…”

Temperature-Induced Sex Reversal in Reptiles: Prevalence, Discovery, and Evolutionary Implications

“…For example, in B. duperreyi, heteromorphic sex chromosomes were first detected using cytogenetic approaches [Shine et al, 2002] and then sex reversal was first demonstrated using PCR targeting a sequence unique to the Y chromosome [Radder et al, 2008], which was later refined using similar methods [Quinn et al, 2009]. New markers for this species have also been identified using an in silico whole genome subtraction approach [Dissanayake et al, 2020].…”

“…Identifying and confirming genotypic sex in reptiles can be challenging, requiring considerable time and resources to develop reliable assays. Homomorphic sex chromosomes are common in reptiles, necessitating the use of advanced cytological techniques [Ezaz et al, 2005] or sequencing technologies to identify sex-specific sequences [Sankovic et al, 2006;Chen et al, 2012;Traut et al, 2013;Palmer et al, 2019;Cornejo-Paramo et al, 2020;Dissanayake et al, 2020]. There is also limited understanding as to the individual-and population-level consequences of sex reversal in the wild, particularly under changing climatic regimes [Bókony et al, 2017;Schwanz et al, 2020].…”