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

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 >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 (>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.,Fragment C sequence from the SB genomeSequence is obtained from scaffold01957 of the SB genome (Si_gnG). Translocation of fragment C in the Sb genome suggests two historical overlapping inversions.fragment_C_scaffold01957.faSingle homolog of fragment C in the S. geminata genomeBlastn output shows that fragment C has only one homologous sequence with high identity in the S. geminata draft genome (unpublished).fragment_C_scaffold01957_mega_sgem_t3p.txtPseudo SB sequenceThe SB sequence used to construct supplementary figure 1. Sequences of scaffold06568, scaffold05266, and scaffold01957 from the SB genome (Si_gnG), together with a 1 Mb NNN gap, are concatenated as the pseudo SB sequence. See README file for the scaffold order and orientation.pseudo_SBigB.faPseudo Sb sequenceThe Sb sequence used to construct supplementary figure 1. Sequences of contigs 000181F-2, 000396F, 000181F-1, 000102F-a, 000151F, and 000058F from the Sb genome (Sinv_littleb_tw_t2p), together with a 1 Mb NNN gap, are concatenated as the pseudo Sb sequence. See README file for the contig order and orientation.pseudo_Slittleb.faComparison of the pseudo SB and pseudo Sb sequencesThe comparison file used to construct supplementary figure 1. The blastn results comparing the pseudo SB and pseudo Sb sequences.pseudo_Slittleb_mega_pseudo_SBigB_outfmt6.txtBAC locations on the SB chromosomeBlastn result of the end sequences of six BAC clones in the SB genome (Si_gnG). BAC clones (SW_Ba): 073A18, 073A22, 073E03, 073E17, 073G23, and 145M22. README file summarizes the scaffolds and cytogenetic locations of the BACs in the SB chromosome.SW_Ba_BACs_mega_gng.txtEnd sequences for 6 S. invicta BAC clonesEnd sequencing of the BAC clones with T7P and SP6 primers. Sequence ends were trimmed for high quality using DNA Baser (v4.36.0). BAC clones (SW_Ba) are: 073A18, 073A22, 073E03, 073E17, 073G23, and 145M24.SW_Ba_BACs.faSequences of 6 contigs in the Sb supergeneSequences of the 6 Sb contigs used for the comparison between the SB and Sb supergenes in supplementary figure 1. Contigs were assembled with Pacbio reads using Falcon assembler (v0.5.0) and Quiver for polishing.Sinv_littleb_tw_t2p.faS. geminata contig 000043F sequenceThis contig contains the fragment C homolog in the S. geminata draft genome (unpublished).Sgem_tw_t3p_000043F.fa25 Kb insertionA slice of 25 Kb DNA sequence from Sinv_littleb_tw_t2p_000058F contig.slice_sc000058F_lbt2p_25kinsert.fastaBlast result of BAC_145M24 in the S. invicta Sb genomeA BLASTN search to query the ~93 kb SB sequence bounded by the two end sequences of BAC_145M24 against a preliminary PacBio assembly of the Sb genomeSi_gnF.scaffold01957_G12_mega_littleb_t2.txt,