Heteromorphic ZZ/ZW sex chromosomes sharing gene content with mammalian XX/XY are conserved in Madagascan chameleons of the genus Furcifer

Abstract

Chameleons are well-known lizards with unique morphology and physiology, but their sex determination has remained poorly studied. Madagascan chameleons of the genus Furcifer have cytogenetically distinct Z and W sex chromosomes and occasionally Z₁Z₁Z₂Z₂/Z₁Z₂W multiple neo-sex chromosomes. To identify the gene content of their sex chromosomes, we microdissected and sequenced the sex chromosomes of F. oustaleti (ZZ/ZW) and F. pardalis (Z₁Z₁Z₂Z₂/Z₁Z₂W). In addition, we sequenced the genomes of a male and a female of F. lateralis (ZZ/ZW) and F. pardalis and performed a comparative coverage analysis between the sexes. Despite the notable heteromorphy and distinctiveness in heterochromatin content, the Z and W sex chromosomes share approximately 90% of their gene content. This finding demonstrates poor correlation of the degree of differentiation of sex chromosomes at the cytogenetic and gene level. The test of homology based on the comparison of gene copy number variation revealed that female heterogamety with differentiated sex chromosomes remained stable in the genus Furcifer for at least 20 million years. These chameleons co-opted for the role of sex chromosomes the same genomic region as viviparous mammals, lacertids and geckos of the genus Paroedura, which makes these groups excellent model for studies of convergent and divergent evolution of sex chromosomes.

Keywords: Chameleons; Homology; Karyotypes; Microdissection; Sex chromosomes; qPCR.

Figure 1

Chromosomal painting with probes from microdissected chromosomes. The probe derived from the W chromosome of F. oustaleti hybridized to metaphases from females of (a) F. oustaleti and (b) F. pardalis. (c) The hybridization of the probe from the Z₁ chromosome of F. pardalis to a female metaphase of the same species. Sex chromosomes are indicated.

Figure 2

Analysis of gene content of the microdissected chromosomes. Z₁ chromosome of F. pardalis, and Z and W chromosomes of F. oustaleti are enriched in genes with homologs linked to several chicken chromosomes, particularly 1, 4, 25, 33 and Z (a). The vast majority of these genes are probably pseudoautosomal, 42 genes with homologs linked mainly to chicken chromosome 4 could be Z-specific, because they were detected in both Z chromosome of F. oustaleti and Z₁ chromosome of F. pardalis, but not in the sequence of the microdissected W chromosome (b). Outer numbers correspond to chicken chromosomes, inner numbers to number of genes (b). All data are included in Table S2.

Figure 3

Log₂-transformed female to male ratios of DNA-seq read coverage per gene in F. lateralis and F. pardalis. Genes are illustrated based on the position of their orthologs in the chicken genome. The Z-specific genes are expected to show half female to male read coverage ratio (log₂-transformed ratios of ∼ − 1.00) than autosomal and pseudoautosomal genes (log₂-transformed ratios of ∼0.00). The genomic regions with putative Z-specific genes homologous to chicken chromosome 4 are indicated by arrows. All data are included in Table S3.

Figure 4

Mean relative gene dose ratios between female and male genomes in chameleons. Value 1.0 is expected for autosomal or pseudoautosomal genes, while 0.5 is consistent with Z-specificity. All data are included in Table S4. Phylogenetic relationships follow Pyron et al. and Tolley et al.. Please note that alternative topologies among species are presented in Tonini et al. and Mezzasalma et al.. Nevertheless, the monophyly of the genus Furcifer is supported in all above-mentioned phylogenies.