Multiple large inversions and breakpoint rewiring of gene expression in the evolution of the fire ant social supergene

Abstract

Supergenes consist of co-adapted loci that segregate together and are associated with adaptive traits. In the fire ant Solenopsis invicta, two 'social' supergene variants regulate differences in colony queen number and other traits. Suppressed recombination in this system is maintained, in part, by a greater than 9 Mb inversion, but the supergene is larger. Has the supergene in S. invicta undergone multiple large inversions? The initial gene content of the inverted allele of a supergene would be the same as that of the wild-type allele. So, how did the inversion increase in frequency? To address these questions, we cloned one extreme breakpoint in the fire ant supergene. In doing so, we found a second large (greater than 800 Kb) rearrangement. Furthermore, we determined the temporal order of the two big inversions based on the translocation pattern of a third small fragment. Because the S. invicta supergene lacks evolutionary strata, our finding of multiple inversions may support an introgression model of the supergene. Finally, we showed that one of the inversions swapped the promoter of a breakpoint-adjacent gene, which might have conferred a selective advantage relative to the non-inverted allele. Our findings provide a rare example of gene alterations arising directly from an inversion event.

Keywords: Solenopsis invicta; fire ant; inversion; polygyne; social chromosome; supergene.

Figure 1.

The rearrangements on the fire ant social chromosomes. (a) Schematic diagram of the SB and Sb genomic structure around the supergene. Fragments A (yellow), B (red), and C (blue) comprise around three-quarters of the supergene in the SB chromosome. The rest of the supergene (dashed line) and the outside edges (grey boxes) are shown. Sb-specific sequences (brown boxes) in between or within fragments are shown. The simplified alignments between the SB and Sb fragments are shown with corresponding simple (same direction) or twisted (inversion) colour ribbons (see also the electronic supplementary material, figure S2). Informative scaffolds in the SB and Sb genomes are indicated as black lines. The positions of primers (P1 ∼ P12), PCR junctions (J1 ∼ J7) and cloned regions (C1 and C2) shown in c and S3 are indicated. Locations of BAC probes (A18 and M24) in SB are illustrated. (b) BAC-FISH identifies a breakpoint between the SB and Sb social chromosomes. The right panel shows a schematic interpretation of the hybridization patterns owing to the inversion of fragment B. Scale bars, 5 µm. (c) PCR amplifications of the SB- (J1 and J2) or Sb-specific junctions (J3 to J7) with three independent haploid Gp-9B and Gp-9b male samples.

Figure 2.

(a) Breakpoints are present at the 5′-untranslated region (UTR) of three protein-coding genes in Sb. Genes are depicted as boxes with light (UTR) or dark (exon) colours with linked lines. The direction of each gene is shown with 5′ and 3′ labels, accompanied by simple (same direction) or twisted (inverted) ribbons in between the SB and Sb gene pairs. Breakpoints (arrows) and their corresponding joins (red lines) with accumulation of transposons and other sequences (brown rectangles) in Sb are shown. The open arrows illustrate the directions of fragments B and C, as depicted in figure 1a. (b) Allele-specific expression of the three genes in SB/Sb worker antennae. Heat map shows the ratios of Sb-allele-specific reads over total reads for each SNP or indel within the UTR and coding region. Variants are oriented based on the gene direction in Sb, and their nucleotide positions to the coding DNA sequence are shown below. * or ** indicates unadjusted p < 0.05 or <0.01, binomial test; full data in the electronic supplementary material, table S5. (c) Expression levels of the three genes located at the breakpoints in antennae of workers of different genotypes. Gene expression levels are the counts per million mapped reads (cmp) averaged over four bioreplicates for each sample type. P-value scores were determined using edgeR and displayed if they passed a Bonferroni correction α = 0.0056 (nine comparisons). Error bars are standard deviations. Mono, monogyne; poly, polygyne. (d) Proposed scenario for the evolutionary history of the Sb social chromosome. (1) Joint inversion of fragments B and C from the ancestral SB chromosome (inversion 1), contributing to the largest genome rearrangement (greater than 9 Mb) between the SB and Sb social chromosomes. (2) Capture of fragment C (approx. 600 bp) by inversion 2, resulting in an additional 844 Kb rearrangement. (3) Accumulation of repeats, e.g. tandem repeats or transposons and other sequences (brown rectangles) throughout the supergene region of the Sb chromosome owing to the lack of recombination. The conceptual fragment δ is predicted to form a third inversion, together with the rearranged fragments A, B and C, comprise the supergene of the Sb social chromosome. The position and numbers of repeats are illustrative and are only depicted on the final line but may have appeared earlier.