Genome complexity reduction and high throughput sequencing of green iguana (Iguana iguana) cause a paradigm shift in understanding sex chromosomal linkages on homomorphic X and Y sex chromosomes

Most lizards in the Superfamily Iguanoidea have an XX/XY sex determination
system in which sex chromosomal linkage has homology with chicken (Gallus
gallus) chromosome 15 (GGA15); however, sex chromosome genomics remains
largely unexplored due to the presence of homomorphic sex chromosomes in
many species. Recent advances in high-throughput sequencing with genome
complexity reduction now provide an effective approach to identify
sex-specific loci in both single nucleotide polymorphisms (SNPs) and
restriction fragment presence/absence (PA), and a better understanding of
sex chromosome dynamics in this lineage. Here, we applied Diversity Arrays
Technology (DArTseq™) in 29 phenotypic sex assignments of green iguana
(Iguana iguana). We confirmed a male heterogametic (XX/XY) sex
determination mode in this species, identifying 29 perfectly sex-linked
SNP/PA loci and 164 moderately sex-linked SNP/PA loci, likely serving as
evidence indicative of XY recombination. 3 loci from perfectly sex-linked
SNP/PA loci showed partial homology with several amniote sex chromosomal
linkages. Our results support the hypothesis of an ancestral super-sex
chromosome with overlaps of partial sex chromosomal linkages. However,
only one locus from moderately sex-linked loci had homology with GGA15,
suggesting that the specific region homologous to GGA15 was located
outside the non-recombination region but very close to this region of sex
chromosome in the green iguana. The location of GGA15 might, therefore, be
further apart from the putative sex-determining locus in green iguana. The
DArTseq platform provides an easy to use strategy for future research on
sex chromosome evolution of lizards in Iguanoidea, particularly for
non-model species with homomorphic or very cryptic sex chromosomes.