A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridizing fire-bellied toads (Bombina bombinaandBombina variegata)

Abstract

Genomic analysis of hybrid zones offers unique insights into emerging reproductive isolation and the dynamics of introgression. Because hybrid genomes consist of blocks inherited from one or the other parental taxon, linkage information is essential. In most cases, the spectrum of local ancestry tracts can be efficiently uncovered from dense linkage maps. Here we report the development of such a map for the hybridising toads, Bombina bombina and B. variegata (Anura: Bombinatoridae). Faced with the challenge of a large (7-10 Gb), repetitive genome, we set out to identify a large number of Mendelian markers in the non-repetitive portion of the genome that report B. bombina vs. B. variegata ancestry with appropriately quantified statistical support. Bait sequences for targeted enrichment were selected from a draft genome assembly, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Validation of the resulting map with 4,755 markers underscored the large-scale synteny between Bombina and Xenopus tropicalis. By assessing the sex of late-stage F2 tadpoles from histological sections, we identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination.

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

“…3 and Supplementary Note 3 ). These species span the pipanuran clade, which comprises all extant frogs except for a small number of phylogenetically basal taxa, such as Bombina 40 and Ascaphus 50 .…”

“…At least some of these pipanuran elements have a deeper ancestry within amphibians. For example, the chromosomes of the discoglossid frog Bombina variegata ( n = 12), an outgroup to the pipanurans, show considerable conservation of synteny with X. tropicalis based on linkage mapping 40 . Compared with the pipanuran ancestral elements described here, the nine B. variegata chromosomes 2, 3, 4, 5, 6, 8, 9, 10, and 12 correspond to nine pipanuran elements A, B, C, F, G, H, I, E, and J, respectively, extending these syntenic elements to the last common ancestor of Bombina +pipanurans (which does not have a common name).…”

“…Based on cytological 36 , 37 and sequence comparisons 25 , 27 , 33 , 38 , 39 most frogs have n ~10–12 pairs of chromosomes. A recent meiotic map of the yellow-bellied toad Bombina variegata showed that its twelve chromosomes are simply related to the ten chromosomes of X. tropicalis 40 . The stability of the frog karyotype contrasts with the more dramatic variation seen across mammals 22 , 37 , 41 , 42 , which as a group is considerably younger than frogs.…”

“…Since frog karyotypes are so highly conserved, X. tropicalis can be used as a model for studying chromosome structure 40 , chromatin interaction, and recombination for the entire clade. Features that can be illuminated at the sequence level include the structure and organization of centromeres and the nature of the unusually long subtelomeres relative to mammals (frog subtelomeres are ~20 megabases, compared with the mammalian subtelomeres that are typically shorter than a megabase).…”

Sex chromosomes as supergenes of speciation: why amphibians defy the rules?

“…The non-recombining Y segment can thus be very short, to the point where high-throughput sequencing is required to reveal sex-linked polymorphisms (e.g. Bombina , [107]).…”