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 × 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. 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.

Lizards as Model Organisms of Sex Chromosome Evolution: What We Really Know from a Systematic Distribution of Available Data?

“…For example, fluorescence in situ hybridization (FISH) using the sex-determining SRY gene finds consistent applications in mammals (e.g., References [ 161 , 162 ]). However, because sex-determining genes are not known in lizards, the identification of sex chromosomes with molecular cytogenetics involves the chromosomal mapping of other markers, including satellite repeats (which can preferentially accumulate on degenerated heteromorphic chromosomes), various sex-specific sequences (whose occurrence and localization may vary among different taxa) and painting techniques (e.g., with chromosome-specific probes) (e.g., References [ 71 , 99 , 104 , 163 ]).…”

“…In silico whole-genome subtraction (ISWGS), which has recently been performed on the skink Acritoscincus duperreyi [ 163 ], also has the potential to isolate sex-specific markers from heterogametic chromosomes (Y/W) and will probably help to open new perspectives in the study of sex chromosome evolution in squamate reptiles.…”

Sex-Determination Mechanisms among Populations within Cryptic Species Complex of Calotes (Squamata: Agamidae: Draconinae)

“…These contradicting results could originate from a possible sex reversal caused by temperature that overrides the original sex-determination system, as recorded in other agamid lizards such as in Pogona vitticeps [18,61,62] and the skink Bassiana duperreyi [17], or the existence of multiple sex-determination systems within the same species, as in the Japanese wrinkled frog G. rugosa [3,4]. In previous studies, most C. versicolor samples were from India, while in this study, the samples were from Bangladesh and Thailand.…”

“…In these cases, the development of sex-linked markers can provide valuable insights by enabling genetic sex to be identified and correlated with phenotypic sex. Such markers have been successfully identified in several reptilian taxa [8,11,12,[14][15][16][17], where they have been used to identify sex-determination modes and cases of sex reversal [18,19].…”

Pleistocene divergence in the absence of gene flow among populations of a viviparous reptile with intraspecific variation in sex determination

“…Although transitions among these systems were initiated as an intraspecific polymorphism, it is unknown whether they were accompanied by genetic isolation. Within squamates, the family Scincidae shows evidence of conserved sex chromosomal regions between some lineages (Cornejo-Paramo et al, 2020;Dissanayake et al, 2020) in addition to temperature sensitivity in sex determination (Holleley et al, 2016). However, variation in the degree of sex chromosome differentiation, number of sex chromosomes (Ezaz et al, 2009), and system of heterogamety (Patawang et al, 2018) exists, and our understanding of the mechanisms of evolutionary transitions in sex determination and how they impact demographics remains poor.…”