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

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.