Homologous Sex Chromosomes in Three Deeply Divergent Anuran Species
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ORIGINAL ARTICLE doi:10.1111/evo.12151 HOMOLOGOUS SEX CHROMOSOMES IN THREE DEEPLY DIVERGENT ANURAN SPECIES Alan Brelsford,1,2 Matthias Stock,¨ 1,3 Caroline Betto-Colliard,1 Sylvain Dubey,1 Christophe Dufresnes,1 Hel´ ene` Jourdan-Pineau,1 Nicolas Rodrigues,1 Romain Savary,1 Roberto Sermier,1 and Nicolas Perrin1 1Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland 2E-mail: [email protected] 3Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Muggelseedamm¨ 310, D-12587, Berlin, Germany Received February 6, 2013 Accepted April 15, 2013 Data Archived: Dryad doi:10.5061/dryad.5nt3g; GenBank KF017619-KF017623, KF053415-KF053429; NCBI SRA SRP021099 Comparative genomic studies are revealing that, in sharp contrast with the strong stability found in birds and mammals, sex determination mechanisms are surprisingly labile in cold-blooded vertebrates, with frequent transitions between different pairs of sex chromosomes. It was recently suggested that, in context of this high turnover, some chromosome pairs might be more likely than others to be co-opted as sex chromosomes. Empirical support, however, is still very limited. Here we show that sex-linked markers from three highly divergent groups of anurans map to Xenopus tropicalis scaffold 1, a large part of which is homologous to the avian sex chromosome. Accordingly, the bird sex determination gene DMRT1, known to play a key role in sex differentiation across many animal lineages, is sex linked in all three groups. Our data provide strong support for the idea that some chromosome pairs are more likely than others to be co-opted as sex chromosomes because they harbor key genes from the sex determination pathway. KEY WORDS: Amphibian, Bufo siculus, convergent evolution, conserved synteny, DMRT1, Hyla arborea, Rana temporaria,sex chromosome turnover.. Sex chromosomes have been a focus of evolutionary biology for Two recent reviews have suggested that some chromosomes a long time, but until recently, most research has focused on might be more likely than others to carry the master sex de- organisms with well-differentiated sex chromosomes, such as fruit termination gene, through conservation of an ancestral system flies, mammals, and birds (Bachtrog et al. 2011). In contrast, sex of sex determination or the reuse of a small set of genes that chromosomes are much less differentiated in most amphibians, can capture the top position in the pathway (Graves and Peichel reptiles, and fishes. Cold-blooded vertebrates also differ from 2010, O’Meally et al. 2012). Thus far, few empirical examples are mammals and birds in displaying a relatively high rate of transition available to support this hypothesis: among amniotes, the same in sex determination systems. The sex-determining locus is often chromosome is sex linked in birds, monotremes, and one lizard found on nonhomologous chromosomes in closely related species, species, and another chromosome is sex linked in both a turtle or even within single species (Charlesworth and Mank 2010). and a lizard species (O’Meally et al. 2012). However, neither the This diversity is at first surprising, given the strong conservation snake nor the therian sex chromosomes are known to be sex linked of elements of the sex determination pathway across animals in any other amniote (O’Meally et al. 2012). In fish, eight differ- (Raymond et al. 1998), but may be explained by mutations causing ent chromosomes are sex linked among the 16 cases reviewed different genes to take over the top position in a conserved sex by Graves and Peichel (2010). In insects, no homology is evi- determining cascade (Wilkins 1995; Schartl 2004; Volff et al. dent between the sex chromosomes of Diptera, Lepidoptera, and 2007; Graves 2013). Coleoptera (Pease and Hahn 2012). C 2013 The Author(s). 1 Evolution ALAN BRELSFORD ET AL. Another aspect of homology in sex determination pertains H. arborea (Niculita-Hirzel et al. 2008), is located on the same to the master sex-determining gene itself, rather than the chro- scaffold as DMRT1 in X. tropicalis (scaffold 1, assembly 7.1, mosome on which it occurs (e.g., Woram et al. 2003; Yano http://xenbase.org). Here, we use a largely novel set of gene- et al. 2013). The transcription factor DMRT1 is a prime exam- associated molecular markers to address three questions: (1) Is ple of a gene involved in sex determination in deeply divergent the rate of chromosomal rearrangement sufficiently low in anu- taxa (Brunner et al. 2001; Matson and Zarkower 2012; Gamble rans that synteny is preserved between X. tropicalis and distantly and Zarkower 2012). DMRT1 orthologs play key roles in male related species? (2) If so, can we find homologies between sex differentiation in Drosophila (doublesex)andCaenorhabditis el- chromosomes of deeply divergent taxa? (3) If so, is the candidate egans (mab3; Raymond et al. 1998). DMRT1 is a strong candidate sex determination gene DMRT1 involved in these homologies? for the major sex-determining gene in birds (Smith et al. 2009). Its paralogs in medaka fish (Oryzias latipes) and African clawed frogs (Xenopus laevis) act as dominant determiners of maleness Methods and femaleness, respectively (Matsuda et al. 2002; Nanda et al. SAMPLES 2002; Yoshimoto et al. 2008). DMRT1 is also associated with Hyla arborea full-sib groups and parental DNA samples were polygenic sex determination in zebrafish (Bradley et al. 2011) sampled from Ciˇ ziˇ ci,´ Croatia (six families, 20–30 offspring per and has recently been shown to be important for the mainte- family), Progar, Serbia (one family, 30 offspring), and Gefira, nance of the adult male gonadal phenotype in mice (Matson et al. Greece (one family, 30 offspring). Hyla intermedia families were 2011). collected from Piazzogna, Switzerland (two families, 20 offspring To date, little evidence exists for comparisons of sex chro- per family; Stock¨ et al. 2011a). For RNA sequencing, a single male mosomes across amphibians. A sex-determining gene (DM-W) H. arborea was collected at Lavigny, Switzerland. has been identified only in X. laevis (Yoshimoto et al. 2008), The Bufo family used in this study resulted from a backcross and this gene, a partial duplication of DMRT1, is found only between a wild-caught Bufo balearicus female and a F -male in a few closely related polyploid species (Bewick et al. 2011). 1 resulting from a previous cross between a male Bufo siculus and A single chromosome is associated with sex in four species of a female B. balearicus (Colliard et al. 2010). Offspring from this the Hyla arborea group, based on several anonymous microsatel- backcross (n = 48) were previously characterized with sex-linked lites and two markers associated with the gene MED15 (Stock¨ microsatellite markers (Stock¨ et al. 2013). By design, females had et al. 2011a, in press). In Rana rugosa, four genes have been two balearicus X chromosomes, and males one balearicus Xand mapped to the sex chromosome by fluorescence in situ hybridiza- one siculus Y chromosome. tion (Miura et al. 1998; Uno et al. 2008). Finally, a series of Rana temporaria families originated from four wild popula- allozyme linkage studies on 17 species or populations of ranid tions, at Bex, Lavigny, Meitreile, and Retaud, Switzerland. Seven frogs (reviewed by Miura 2007) show that sex is associated with mating pairs were caught during spring 2011. One clutch was ob- five different chromosomes (out of 13), depending on species or tained from each couple, and offspring were raised until metamor- population. The recent completion of the first high-quality draft phosis. A total of 424 offspring (40 tadpoles and 9–41 froglets per assembly of an amphibian genome (Xenopus tropicalis; Hellsten family) were characterized with 10 microsatellite markers from et al. 2010; Wells et al. 2011) presents a highly useful tool for linkage group 2 (Rodrigues et al. in press), previously shown to sex chromosome comparisons (e.g., Macha´ et al. 2012), although be sex-linked in Fennoscandian populations (Cano et al. 2011). DM-W is absent in this species (Yoshimoto et al. 2008; Bewick et al. 2011) and little information is available on its sex chromo- some (Olmstead et al. 2010). Provided that synteny is sufficiently MARKER DESIGN conserved across anurans, sex linkage of orthologous genomic re- In each species group, we identified or developed six to 16 gene- gions may be identified even if different genes are sampled in each based markers with orthologs on X. tropicalis scaffold 1, which species. is 216 Mbp in length (Table 1). Markers were developed for three Previous work on Bufo, Hyla,andRana has suggested strong genes (DMRT1, FGA,andSMARCB1) in all groups, whereas synteny between representative karyotypes of these three anu- other genes were tested in a single group. Details of marker de- ran families (Miura 1995). More recently, several anonymous sign, primers, and PCR conditions are presented in Supplementary sex-linked microsatellite markers have been identified within the Materials and Methods. Briefly, we sequenced and assembled the Bufo viridis, H. arborea,andRana temporaria species groups transcriptome of a single H. arborea individual, from which we (Berset-Brandli¨ et al. 2006; Berset-Brandli¨ et al. 2008; Matsuba identified SNPs and microsatellite repeats. We used the transcrip- et al. 2008; Cano et al. 2011; Stock¨ et al. 2011a,b, 2013). The only tome sequence and public Rana and Xenopus sequences to design characterized sex-linked gene in any of these species, MED15 in intron-crossing