Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly

Abstract

The guppy Y Chromosome has been a paradigmatic model for studying the genetics of sex-linked traits and Y Chromosome-driven evolution for more than a century. Despite strong efforts, knowledge on genomic organization and molecular differentiation of the sex chromosome pair remains unsatisfactory and partly contradictory with respect to regions of reduced recombination. Especially the border between pseudoautosomal and male-specific regions of the Y has not been defined so far. To circumvent the problems in assigning the repeat-rich differentiated hemizygous or heterozygous sequences of the sex chromosome pair, we sequenced a YY male generated by a cross of a sex-reversed Maculatus strain XY female to a normal XY male from the inbred Guanapo population. High-molecular-weight genomic DNA from the YY male was sequenced on the Pacific Biosciences platform, and both Y haplotypes were reconstructed by Trio binning. By mapping of male specific SNPs and RADseq sequences, we identify a single male specific-region of ∼5 Mb length at the distal end of the Y (MSY). Sequence divergence between X and Y in the segment is on average five times higher than in the proximal part in agreement with reduced recombination. The MSY is enriched for repeats and transposons but does not differ in the content of coding genes from the X, indicating that genic degeneration has not progressed to a measurable degree.

Figure 1.

Adult male guppy phenotypes. (A) Male of the Maculatus strain, genotype X_macY_mac. (B) Male of the Guanapo strain, genotype X_GuaY_Gua. (C) F₁ male with sex chromosome constitution Y_guaY_mac. Note that both the characteristic Maculatus black spot on the dorsal fin (arrowhead) and Guanapo black spot on the anterior trunk (arrow), as well as the Guanapo tail pattern (star), are expressed in the Y_guaY_mac male.

Figure 2.

Alignment of Y_gua and Y_mac to published XY male Chromosome 12 (LR880656) and female LG12 (NC024342). Roman numbers specify positions of XY contigs on LR880656; for details see Supplemental Table S1. Positions of additional unplaced scaffolds of the XY assembly are indicated under Y_gua: 1, 00013F_0; 2, 000200F_0; 3, 000250F_0; 4, 000181F_0; and 5, 000149F_0.

Figure 3.

Alignment of Y_gua and Y_mac haplotypes to Xiphophorus Chromosome 8. A 3.5 Mb inversion distinguishes X. hellerii and X. maculatus. The position of the long contig Gua_tig00000294 that spans the inversion of X. maculatus Chr 8 is indicated at the top. The position of a short proximal sequence of the guppy Y also conforms to X. hellerii Chr 8, whereas it is translocated to the chromosome end in X. maculatus. Y_gua and Y_mac conform to one another and to X. hellerii Chr 8, with most divergence seen from 23 Mb to the end of guppy Y haplotypes.

Figure 4.

Alignment of reconstructed X Chromosomes to Y_gua and Y_mac haplotypes. Y_gua and Y_mac assembled as described in Supplemental Table S2 are aligned to X_gua and a virtual X_mac. Both X Chromosomes were rescaffolded from the female Guanapo contigs using Y_gua and Y_mac as templates.

Figure 5.

Sequence divergence between Y haplotypes and the reconstructed X_gua. (A) Sequence difference calculated as the number of SNPs and indels in 10 kb sliding windows along the Y Chromosomes. (B) Y_gua and Y_mac are aligned to the X. Male-specific RAD-tags from Caroni swamp guppies (blue bars) and from four different guppy strains (red bars) were mapped on the aligned Y_gua (top) and Y_mac (bottom) sequences. The four strains represent a broader range of geographic origins, from East Trinidad to West Venezuela. About 70% of these RAD-tags (red bars) had best hits (e-40) within the distal 16% of the Y (>24 Mb). Both Y haplotypes are aligned to the reconstructed X_gua (middle). The green dotted line indicates the congruent MSY identified by sequence divergence and RAD-tags from the Trinidad populations of guppy.

Figure 6.

Overview of the data flow and methods for genome assembly and comparisons with published results.