Chromosome-Level Genome Assembly Reveals Dynamic Sex Chromosomes in Neotropical Leaf-Litter Geckos (Sphaerodactylidae: Sphaerodactylus)

Abstract

Sex determination is a critical element of successful vertebrate development, suggesting that sex chromosome systems might be evolutionarily stable across lineages. For example, mammals and birds have maintained conserved sex chromosome systems over long evolutionary time periods. Other vertebrates, in contrast, have undergone frequent sex chromosome transitions, which is even more amazing considering we still know comparatively little across large swaths of their respective phylogenies. One reptile group in particular, the gecko lizards (infraorder Gekkota), shows an exceptional lability with regard to sex chromosome transitions and may possess the majority of transitions within squamates (lizards and snakes). However, detailed genomic and cytogenetic information about sex chromosomes is lacking for most gecko species, leaving large gaps in our understanding of the evolutionary processes at play. To address this, we assembled a chromosome-level genome for a gecko (Sphaerodactylidae: Sphaerodactylus) and used this assembly to search for sex chromosomes among six closely related 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 a new XY) within the genus. Interestingly, we confirmed two different linkage groups as XY sex chromosome systems that were previously unknown to act as sex chromosomes in tetrapods (syntenic with Gallus chromosome 3 and Gallus chromosomes 18/30/33), further highlighting a unique and fascinating trend that most linkage groups have the potential to act as sex chromosomes in squamates.

Keywords: genome evolution; genomics; herpetology; sex chromosomes; sex determination.

Figure 1.

Overview of the study system: Time-calibrated phylogenetic tree (Daza et al. 2019) for Sphaerodactylus geckos from within the Puerto Rican Bank and an outgroup (S. notatus; node ~20 mya) with previously identified sex chromosome sex systems in grey; new information identified here in black.

Figure 2.

Whole-genome M/F F_ST scan in 500 Kb windows using RADseq data for 4 taxa: (A) S. townsendi, (B) S. nicholsi, (C) S. inigoi, and (D) S. notatus.

Figure 3.

Confirmation of the Sphaerodactylus townsendi sex chromosome on LG3. (A) RADseq M/F F_ST scan in 500 kb windows (zoomed in on LG3 from Figure 2); (B) M/F read depth differences across the length of LG3; (C) male and female nucleotide diversity (π) along LG3. The same set of male-specific RADtags mapped to LG3 are denoted by orange ticks along the bottom of each graph (same in each panel). (D) Gel images from a subset of these markers illustrate that they are located on the Y chromosome. Picture of an adult male S. townsendi scaled with a penny, USA currency (diameter = 19.05 mm).

Figure 4.

Comparative genomics of the S. townsendi sex chromosome (LG3) across multiple Sphaerodactylus species in 500 kb windows. (A and B) S. nicholsi M/F F_ST values (RADseq) and M and F nucleotide diversity (WGS), respectively; (C) S. klauberi M and F nucleotide diversity (WGS); (D and E) S. inigoi M/F F_ST values (RADseq) and M and F nucleotide diversity (RNAseq), respectively; (F) S. macrolepis M and F nucleotide diversity (RNAseq); (G and H) S. notatus M/F F_ST values (RADseq) and M and F nucleotide diversity (WGS), respectively. Sex-specific RADtags mapped to S. nicholsi (A and B) and S. inigoi (D and E) along the X axis (orange ticks). Note: slight shifts on the X-axis are due to the differences in programs used to calculate values, i.e., WGS used pixy, while RADseq and RNAseq used vcftools.

Figure 5.

Comparative genomics of the S. notatus sex chromosome (LG1) across multiple Sphaerodactylus species in 500kb windows. (A and B) S. townsendi M/F F_ST values (RADseq) and M and F nucleotide diversity (WGS), respectively; (C and D) S. nicholsi M/F F_ST values (RADseq) and M and F nucleotide diversity (WGS), respectively; (E) S. klauberi M and F nucleotide diversity (WGS); (F and G) S. inigoi M/F F_ST values (RADseq) and M and F nucleotide diversity (RNAseq), respectively; (H) S. macrolepis M and F nucleotide diversity (RNAseq); (I and J) S. notatus M/F F_ST values (RADseq) and M and F nucleotide diversity (WGS), respectively. Sex-specific RADtags mapped to S. inigoi (F and G) and S. notatus (I and J) along the X axis (orange ticks). Note: slight shifts on the X-axis are due to the differences in programs used to calculate values, i.e., WGS used pixy, while RADseq and RNAseq used vcftools.

Figure 6.

Genome-wide patterns of GC content across representative squamate taxa, orange line representing the genomic mean. Broadly, pattern of GC content appears most similar, both in chromosome patterns and mean per-window GC content (~0.2), between (A) Sphaerodactylus and (D) Naja. Both (B) Podarcis and (C) Anolis have a considerably higher mean per-window GC (~0.4), and Podarcis shows an inverse pattern to Sphaerodactylus and Naja in that GC goes up at the tips of chromosomes instead of down. We believe that the Anolis patterns here are less informative in this regard as the sequencing method employed is not directly comparable to the other 3 genomes.