Partial Amniote Sex Chromosomal Linkage Homologies Shared on Snake W Sex Chromosomes Support the Ancestral Super-Sex Chromosome Evolution in Amniotes

Abstract

Squamate reptile chromosome 2 (SR2) is thought to be an important remnant of an ancestral amniote super-sex chromosome, but a recent study showed that the Siamese cobra W sex chromosome is also a part of this larger ancestral chromosome. To confirm the existence of an ancestral amniote super-sex chromosome and understand the mechanisms of amniote sex chromosome evolution, chromosome maps of two snake species [Russell's viper: Daboia russelii (DRU) and the common tiger snake: Notechis scutatus (NSC)] were constructed using bacterial artificial chromosomes (BACs) derived from chicken and zebra finch libraries containing amniote sex chromosomal linkages. Sixteen BACs were mapped on the W sex chromosome of DRU and/or NSC, suggesting that these BACs contained a common genomic region shared with the W sex chromosome of these snakes. Two of the sixteen BACs were co-localized to DRU2 and NSC2, corresponding to SR2. Prediction of genomic content from all BACs mapped on snake W sex chromosomes revealed a large proportion of long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE) retrotransposons. These results led us to predict that amplification of LINE and SINE may have occurred on snake W chromosomes during evolution. Genome compartmentalization, such as transposon amplification, might be the key factor influencing chromosome structure and differentiation. Multiple sequence alignments of all BACs mapped on snake W sex chromosomes did not reveal common sequences. Our findings indicate that the SR2 and snake W sex chromosomes may have been part of a larger ancestral amniote super-sex chromosome, and support the view of sex chromosome evolution as a colorful myriad of situations and trajectories in which many diverse processes are in action.

Keywords: BAC; chromosome map; retrotransposon; snake; super-sex chromosome.

FIGURE 1

Gray images of DAPI-stained karyotypes of Russell’s viper (Daboia russelii) (A) and the common tiger snake (Notechis scutatus) (B). Scale bar represents 10 μm.

FIGURE 2

Chromosomal locations of chicken and zebra finch BACs in Russell’s viper (Daboia russelii) and the common tiger snake (Notechis scutatus). Russell’s viper, GGA5 BAC [Texas Red-labeled CH261-122F8 (red)] was localized to chromosome 1 (DRU1) (A) and GGAZ BAC [Texas Red-labeled TGMCBA-270I9 (red)] was localized to W sex chromosome (DRUW) (C). Common tiger snake, GGA1 BAC [Texas Red-labeled CH261-125F1 (red) and fluorescein isothiocyanate-labeled TGMCBA-167P13 (green)] were localized to chromosome 2 (NSC2) and W sex chromosome (NSCW), respectively (B) and GGAZ BAC [Texas Red-labeled TGMCBA-270I9 (red)] was localized to W sex chromosome (NSCW) (D). Arrows indicate hybridization signals. Scale bar represents 10 μm.

FIGURE 3

Comparative chromosome maps of chromosomes among the Siamese cobra (Naja kaouthia, NKA), Russell’s viper (Daboia russelii, DRU), and the common tiger snake (Notechis scutatus, NSC). Maps were constructed with 47 BACs and linkage maps of chicken (Gallus gallus, GGA), Japanese four-striped rat snake (Elaphe quadrivirgata, EQU), and chromosomes sharing homologies with sex chromosome of several other amniotes. Chromosome numbers indicate chicken (GGA), humans (Homo sapiens, HSA), tammar wallaby (Macropus eugenii, MEU), duck-billed platypus (Ornithorhynchus anatinus, OAN), green anole (Anolis carolinensis, ACA), bearded dragon lizard (Pogona vitticeps, PVI), sand lizard (Lacerta agilis, LAG), Hokou gecko (Gekko hokouensis, GHO), Komodo dragon (Varanus komodoensis, VKO), marsh turtle (Siebenrockiella crassicollis, SCR), wood turtle (Glyptemys insculpta, GIN), Mexican musk turtle (Staurotypus triporcatus, STR), giant musk turtle (Staurotypus salvinii, SSA), spiny softshell turtle (Apalone spinifera, ASP), and Chinese softshell turtle (Pelodiscus sinensis, PSI), showing partial homologies with Siamese cobra, green iguana (Iguana iguana), common garden lizard (Calotes versicolor), and water monitor lizard (Varanus salvator macromaculatus) chromosomes. Partial sex chromosomal linkage homologies are shown in the same color. Chromosomal locations of genes in the amniotes were obtained from comparative gene mapping (chromosome mapping via a cytogenetic technique) and whole genome sequencing as the following sources: GGA from Matsuda et al. (2005), HSA and MEU from Grützner et al. (2004), OAN from Veyrunes et al. (2008), ACA from Alföldi et al. (2011), PVI from Ezaz et al. (2013), LAG from Srikulnath et al. (2014), GHO from Kawai et al. (2009), VKO from Lind et al. (2019), EQU from Matsubara et al. (2006), SCR from Kawagoshi et al. (2012), GIN and STR from Montiel et al. (2016), SSA from Kawagoshi et al. (2014), ASP from Badenhorst et al. (2013), and PSI from Kawagoshi et al. (2009).

FIGURE 4

Boxplots showing average of repeat percentages between BACs mapped on autosomes of snake (blue) and BACs mapped on snake W sex chromosomes (red) of three snake species: the Siamese cobra (Naja kaouthia, NKA), Russell’s viper (Daboia russelii, DRU), and the common tiger snake (Notechis scutatus, NSC). No significant differences were detected in short interspersed nuclear elements (SINEs) (p = 0.6043) and DNA transposons (p = 0.9614). Significant differences were detected in long terminal repeat (LTR) elements (p = 0.0253), long interspersed nuclear elements (LINEs) (p = 0.0037), and total interspersed repeats (p = 0.0018). Data are shown as mean ± standard deviation. The box includes 50% of the data, and the whiskers reach the highest and lowest values within 95% of the distribution. Open circles represent single values outside 95% of the distribution. Degrees of statistical significance were represented as * for p ≤ 0.05, and ** for p ≤ 0.01.

FIGURE 5

Karyotype evolution of representative amniotes. A multi-karyotype view is shown for the reference chicken (Gallus gallus) genome. Reference chromosomes of the chicken share genomic sequences with common tiger snake (Notechis scutatus), human (Homo sapiens), central bearded dragon (Pogona vitticeps), Chinese softshell turtle (Pelodiscus sinensis), green anole lizard (Anolis carolinensis), painted turtle (Chrysemys picta), and zebra finch (Taeniopygia guttata) distinguished with different colors for homologs. Black arrows highlight homology with the chicken Z chromosome. The common tiger snake karyotype schematic shows the 50 longest scaffolds.