Genomic changes following the reversal of a Y chromosome to an autosome in Drosophila pseudoobscura

Abstract

Robertsonian translocations resulting in fusions between sex chromosomes and autosomes shape karyotype evolution by creating new sex chromosomes from autosomes. These translocations can also reverse sex chromosomes back into autosomes, which is especially intriguing given the dramatic differences between autosomes and sex chromosomes. To study the genomic events following a Y chromosome reversal, we investigated an autosome-Y translocation in Drosophila pseudoobscura. The ancestral Y chromosome fused to a small autosome (the dot chromosome) approximately 10-15 Mya. We used single molecule real-time sequencing reads to assemble the D. pseudoobscura dot chromosome, including this Y-to-dot translocation. We find that the intervening sequence between the ancestral Y and the rest of the dot chromosome is only ∼78 Kb and is not repeat-dense, suggesting that the centromere now falls outside, rather than between, the fused chromosomes. The Y-to-dot region is 100 times smaller than the D. melanogaster Y chromosome, owing to changes in repeat landscape. However, we do not find a consistent reduction in intron sizes across the Y-to-dot region. Instead, deletions in intergenic regions and possibly a small ancestral Y chromosome size may explain the compact size of the Y-to-dot translocation.

Keywords: Dot chromosome; Robertsonian translocation; SMRT sequencing; Y chromosome.

Figure 1

The structure and gene orientation of the dot‐Y chromosome in D. pseudoobscura. The lines correspond to the coverage of all reads, reads >5 Kb, and reads >10 Kb across the entire dot‐Y chromosome. The Y‐to‐dot, conserved‐dot and telomeric regions are delineated by gray dotted lines. All 5 Y‐to‐dot genes, the duplicated gene between the Y‐to‐dot and conserved dot, 3 conserved‐dot genes (the most proximal and distal to the centromere) and their orientations are indicated with green lines. The coordinates of the D. persimilis BAC (36E‐15) are indicated with a black line. [Color figure can be viewed at wileyonlinelibrary.com]

Figure 2

Repeat landscape across D. pseudoobscura dot‐Y chromosome. The density of repeat types as categorized by RepeatMasker— RNA transposons (Class I), including LTR retrotransposons and LINEs, DNA transposons (Class II) including subclass I and subclass II, and simple tandem repeats —are plotted across the dot‐Y chromosome. See materials and methods for details. [Color figure can be viewed at wileyonlinelibrary.com]

Figure 3

Evolution of Y chromosome size in the obscura group. The phylogeny is modified from Gao et al. (2007). The relative size of the ancestral Y chromosome compared to the ancestral X chromosomal arm (i.e. Muller A) in spreads of mitotic chromosomes (Fig S4; Gao et al. 2004; Larracuente et al. 2010). The ancestral obscura group Y chromosome may have been small.

Figure 4

Intron size comparisons. A) Boxplots show intron size differences across the D. pseudoobscura genome. Intron sizes for the dot‐Y chromosome regions are based on our PacBio assembly and annotations; autosomal introns are based on the r3.03 reference genome assembly and annotations (Flybase). Only introns from the first isoforms of each gene were used. For all dot‐Y genes, we only plot those with orthologs in D. melanogaster (Blastx; e < 0.01). Asterisks (*) indicate significantly different means (pairwise MWU; P < 0.05). B) Comparisons of individual orthologous intron pairs between the D. melanogaster Y chromosome (circles) and the D. pseudoobscura Y‐to‐dot translocation (triangles). Introns in the D. melanogaster r6.03 reference Y chromosome with gaps (indicated by Ns; and therefore are minimum intron sizes) are in red and those without gaps are in black. Orthologous introns between the species pair are connected with a line. [Color figure can be viewed at wileyonlinelibrary.com]

Figure 5

Nucleotide diversity across the genome in D. pseudoobscura and D. miranda. The dot chromosome, including Y‐to‐dot and conserved‐dot regions, have lower pairwise nucleotide diversity than representative autosomes (those chromosome arms not involved in sex‐autosome translocation; i.e. Muller B and E) and the X chromosome (i.e. Muller A and D). Asterisks (*) indicate significantly different means (Kruskal‐Wallis; pair‐wise Bonferroni; P < 0.05)