A Search for Sex-Linked Loci in the Agamid Lizard, <b><i>Calotes versicolor</i></b>

Abstract

The Indian garden lizard, &lt;i&gt;Calotes versicolor&lt;/i&gt;, lacks cytologically recognizable sex chromosomes, and its mechanism of sex determination is unclear. We evaluated genotype-to-sex-phenotype association using RAD-seq in wild-caught males and females, 30 of each sex. Of 210,736 unique, 96-nt long RAD-tags, 48% contained polymorphisms, 23% of which were present in at least 40 of 60 individuals. Twenty one RAD-tags neared, but none achieved, the inclusion criteria for sex enrichment, as expected if &lt;i&gt;C. versicolor&lt;/i&gt; lacks highly differentiated sex chromosomes. Three RAD-tags with alleles most strongly associated with sex tended to be heterozygous in females and to lack male-specific alleles, suggesting a ZW female/ZZ male system. Putative female alleles, however, were present in some males and lacking from some females, suggesting either recombination between these markers and the sex locus or sex reversal due to environmental or genetic factors. Paired-end, 250-nt reads from 1 male provided a fragmented draft genome assembly. Four sex-associated RAD-tags were identical to portions of 4 unique &lt;i&gt;C. versicolor &lt;/i&gt;genomic contigs rather than linked to a single putative sex-linked region. The lack of strongly sex-linked loci coupled with weak evidence for temperature-associated sex determination intensifies the need for further investigation of the puzzling sex determination mechanism in &lt;i&gt;C. versicolor&lt;/i&gt;.

Cytogenetic Analysis Did Not Reveal Differentiated Sex Chromosomes in Ten Species of Boas and Pythons (Reptilia: Serpentes)

“…The evolution of sex chromosomes and sex determination systems in henophidian and scolecophidian snakes should be further explored by genome-wide next generation sequencing approaches, such as restriction site associated DNA sequencing (RAD-seq) [25,50,51,52], which will allow the fine-tuned identification of sex-specific regions of the genome. Facultative parthenogenetic reproduction results in all-female homozygous progeny in Epicrates maurus [20], Epicrates cenchria cenchria [22], Malayopython reticulatus, and Python regius [23], which indicates that male heterogamety may be present in these species.…”

Draft genome of the oriental garden lizard (Calotes versicolor)

“…The remaining 0.7% and 1.3% were fragmented and missing, respectively (Supplementary Table S2). This was significantly improved when compared with the published assemblies (Wilson et al, 2019) (ASM2071127v1, genome size: 0.91 Gb, contig N50: 1.62 kb and BUSCO: 6.8%, Supplementary Table S1). The C. versicolor genome (43.79% GC content) has a much more homogenous GC distribution in 500 kb windows than either the green anole lizard (Anolis carolinensis), human (Homo sapiens) or chicken (Gallus Gallus) genome (Supplementary Figure S2).…”