Independent Evolution of Sex Chromosomes in Eublepharid Geckos, A Lineage with Environmental and Genotypic Sex Determination

Abstract

Geckos demonstrate a remarkable variability in sex determination systems, but our limited knowledge prohibits accurate conclusions on the evolution of sex determination in this group. Eyelid geckos (Eublepharidae) are of particular interest, as they encompass species with both environmental and genotypic sex determination. We identified for the first time the X-specific gene content in the Yucatán banded gecko, Coleonyx elegans, possessing X₁X₁X₂X₂/X₁X₂Y multiple sex chromosomes by comparative genome coverage analysis between sexes. The X-specific gene content of Coleonyx elegans was revealed to be partially homologous to genomic regions linked to the chicken autosomes 1, 6 and 11. A qPCR-based test was applied to validate a subset of X-specific genes by comparing the difference in gene copy numbers between sexes, and to explore the homology of sex chromosomes across eleven eublepharid, two phyllodactylid and one sphaerodactylid species. Homologous sex chromosomes are shared between Coleonyx elegans and Coleonyx mitratus, two species diverged approximately 34 million years ago, but not with other tested species. As far as we know, the X-specific gene content of Coleonyx elegans / Coleonyx mitratus was never involved in the sex chromosomes of other gecko lineages, indicating that the sex chromosomes in this clade of eublepharid geckos evolved independently.

Keywords: DNA-seq; Gekkota; qPCR; reptiles; sex chromosomes; sex determination.

Figure 1

Log₂-transformed male to female ratios of DNA-seq read coverage per gene in Coleonyx elegans. The X-specific genes have half male to female read coverage ratio than autosomal and pseudoautosomal genes, i.e., log₂-transformed ratios about −1.0. The position of gene orthologs in chicken chromosomes is presented. X-specific genes with homologs linked to GGA1, GGA6 and GGA11 chromosomes are indicated by arrows.

Figure 2

Average relative gene dose ratios between sexes of autosomal (blue bars) and X-specific genes (red bars), identified from the comparative genome coverage analysis in Coleonyx elegans and tested by qPCR across 12 eublepharid, two phyllodactylid and one sphaerodactylid species. Among all tested species of geckos, only Coleonyx elegans and Coleonyx mitratus share the same X-specific genes. Phylogeny follows [17]. All data are presented in Table S3.