The first chromosome-level gecko genome reveals dynamic sex chromosomes in Neotropical leaf-litter geckos (Sphaerodactylidae: Sphaerodactylus)

Sex chromosomes have evolved many times across eukaryotes, indicating both their importance and their evolutionary flexibility. Some vertebrate groups, such as mammals and birds, have maintained a single, conserved sex chromosome system across long evolutionary time periods. By contrast, many reptiles, amphibians, and fish have undergone frequent sex chromosome transitions, most of which remain to be catalogued. Among reptiles, gecko lizards (infraorder Gekkota) have shown an exceptional lability with regard to sex chromosome transitions and may possess the majority of transitions within squamates (lizards and snakes). However--across geckos--information about sex chromosome linkage is expressly lacking, leaving large gaps in our understanding of the evolutionary processes at play in this system. To address this gap, we assembled the first chromosome-level genome for a gecko and use this linkage information to survey six Sphaerodactylus species using a variety of genomic data, including whole-genome re-sequencing, RADseq, and RNAseq. Previous work has identified XY systems in two species of Sphaerodactylus geckos. We expand upon that work to identify between two and four sex chromosome cis-transitions (XY to XY) within the genus. Interestingly, we confirmed two linkage groups as XY sex chromosome systems that were previously unknown to act as sex chromosomes in tetrapods (syntenic with Gallus 3 and Gallus 18/30/33). We highlight the increasing evidence that most (if not all) linkage groups will likely be identified as a sex chromosome in future studies given thorough enough sampling.