Satellite DNA-mediated diversification of a sex-ratio meiotic drive gene family in Drosophila

Abstract

Sex chromosomes are susceptible to the evolution of selfish meiotic drive elements that bias transmission and distort progeny sex ratios. Conflict between such sex-ratio drivers and the rest of the genome can trigger evolutionary arms races resulting in genetically suppressed 'cryptic' drive systems. The Winters cryptic sex-ratio drive system of Drosophila simulans comprises a driver, Distorter on the X (Dox) and an autosomal suppressor, Not much yang, a retroduplicate of Dox that suppresses via production of endogenous small interfering RNAs (esiRNAs). Here we report that over 22 Dox-like (Dxl) sequences originated, amplified and diversified over the ~250,000-year history of the three closely related species, D. simulans, D. mauritiana and D. sechellia. The Dxl sequences encode a rapidly evolving family of protamines. Dxl copy numbers amplified by ectopic exchange among euchromatic islands of satellite DNAs on the X chromosome and separately spawned four esiRNA-producing suppressors on the autosomes. Our results reveal the genomic consequences of evolutionary arms races and highlight complex interactions among different classes of selfish DNAs.

Extended Data Fig. 1 |. Schematic alignment of inserted sat359 islands in X:9.4–10.4 Mb, color-coded by putative sequence homology.

Segments of the same color aligned vertically are high-confidence nucleotide alignments, whereas segments of different color do not share sequence homology regardless of vertical alignment in the figure. One insertion into a sat359 island, the transposase-like sequence inserted into the D. sechellia Dxl-2 location, does not share sequence homology with any of the other loci, and has been omitted from this figure.

Extended Data Fig. 2 |. Alignment of the putative source material for Dxl genes found at approximate coordinates X:17.1 and X:17.2 Mb.

Segments of the same color aligned vertically are high-confidence nucleotide alignments. At X:17.2, the three D. simulans clade species all have remnants of an insertion (total span = ~3 kb) that interrupts the CG8664 gene. This sequence, along with some of CG8664 and additional material, is alignable with insertion at the second position, X:17.1 Mb. Putative homology of the inserted sequence at both locations, along with CG8664, are color-coded and the span of present-day Dxl homology is indicated.

Extended Data Fig. 3.. Chromosomal distribution of sat359 islands in X:9.4–10.4 Mb region with all identified inserted sequence, including Dxl genes, in D. simulans, D. mauritiana, and D. sechellia.

Tick marks indicate locations of conserved sat359 islands, blue dots indicate protein-coding genes of interest in the region, and the different colored squares represent the homologies of sequences inserted into sat359 islands (green=Dxl; purple=Ptpmeg2 fragment; brown=mkg-p retrotransposition; red=transposase-like sequence; yellow=cubn fragment; pink=CARPB intron fragments).

Extended Data Fig. 4.

Evidence for transfer of Dxl material via a circular DNA. Intermediate molecule. Dxl-12mau (green) is flanked by sat359 repeats 835 (blue arrows) and by CARPB intronic sequence (boxes labelled A and B). These flanking sequence match sequences present in Dxl-10mau and Dxl-14mau, but 836 the order of the two CARPB segments A and B differs from Dxl-12mau. The re-ordering of homologous sequences, as well as their intervening sequence, is 837 consistent with a transfer of material via circular DNA intermediate.

Figure 1.

Physical distribution of known Dxl genes in D. simulans, D. mauritiana, and D. sechellia. A schematic of the polytene X chromosome (top) shows location of the Dxl-containing region (Dmel r6 X:9400000–10400000). Tick marks show locations of sat359 islands conserved in all three D. simulans clade species and in the outgroup D. melanogaster; the single gray tick mark distal to Ur-Dox is a sat359 island found in the D. simulans clade species but not in D. melanogaster; the green squares show sat359 islands with a Dxl insertion; and the blue dots show protein-coding genes of interest. While Dxl insertions with the same name occupy orthologous sat359 islands in different species, the Dxl sequences are not necessarily orthologous due to the possibilities of independent, parallel insertion and ectopic exchange.

Figure 2.

Inferred stepwise historical origins of Dox. Color coding of sequence blocks indicates the putative sequence homology, and light blue arrows represent sat359 repeats.

Figure 3.

Dxl genes encode a rapidly evolving protamine. a. Dox gene structure, validated splice structure for functional transcript, and the inferred protamine-like, HMG-box, cytoplasmic, and transmembrane domains of the predicted 157-aa protein. b. Phylogeny of amino acid sequence positions 1–66 predicted for 24 Dxl genes aligned with known protamines, annotated with presence (filled circles) or absence (open circles) of “protamine-like” (blue) and “HMG-box” (red) domains. Dxl genes lacking intact ORFs are not included in the phylogeny.

Figure 4.

Structural and sequence evolution among Dxl gene copies. a. Schematic alignment of all known Dxl copies, organized by species, and color-coded by putative sequence homology. Internally duplicated segments are indicated by dashed fill. Dxl gene copies with RNA-seq evidence for expression are indicated by red font and those lacking an intact ORF are indicated by *. b. The average number of pairwise differences per bp among all Dxl copies is shown calculated in 20-bp windows across the region of Dxl homology. The blue box shows the alignment of sequences represented in panels a and b.

Figure 5.

Autosomal hpRNA suppressor loci in the D. simulans clade species. a. The three species have different, partially overlapping systems of Dxl genes and esiRNA-producing autosomal suppressors. D. simulans has Tmy and Nmy; D. mauritiana has Nmy and Tmyl; and D. sechellia has Tmyl and Emy. Structural features of the esiRNA-producing putative autosomal suppressors, Tmy and Tmyl (b), Nmy (c), and Emy (d). Each putative suppressor originated via the insertion of Dxl material into an autosomal location followed by internal duplication and inversion of sequence (gray arrows), allowing formation of hpRNA precursor molecules (red arrows). In D. sechellia, a ~7-kb region that includes Emy has been tandemly amplified four times (d).

Figure 6.

Species-specific small RNAs (≤22nt) map to Dxl-matching hairpin regions of each species’ autosomal suppressors. (a) Tmy and Nmy in D. simulans; (b) Tmyl and Nmy in D. mauritiana; and (c) Tmyl and Emy in D. sechellia. Reads per million reads mapped are shown (red = plus strand, blue = minus strand), with schematics of predicted hairpin arms shown for reference. Predicted hairpin stems are drawn to scale, hairpin loops are not.