Positive Selection and Horizontal Gene Transfer in the Genome of a Male-Killing Wolbachia

Abstract

Wolbachia are a genus of widespread bacterial endosymbionts in which some strains can hijack or manipulate arthropod host reproduction. Male killing is one such manipulation in which these maternally transmitted bacteria benefit surviving daughters in part by removing competition with the sons for scarce resources. Despite previous findings of interesting genome features of microbial sex ratio distorters, the population genomics of male-killers remain largely uncharacterized. Here, we uncover several unique features of the genome and population genomics of four Arizonan populations of a male-killing Wolbachia strain, wInn, that infects mushroom-feeding Drosophila innubila. We first compared the wInn genome with other closely related Wolbachia genomes of Drosophila hosts in terms of genome content and confirm that the wInn genome is largely similar in overall gene content to the wMel strain infecting D. melanogaster. However, it also contains many unique genes and repetitive genetic elements that indicate lateral gene transfers between wInn and non-Drosophila eukaryotes. We also find that, in line with literature precedent, genes in the Wolbachia prophage and Octomom regions are under positive selection. Of all the genes under positive selection, many also show evidence of recent horizontal transfer among Wolbachia symbiont genomes. These dynamics of selection and horizontal gene transfer across the genomes of several Wolbachia strains and diverse host species may be important underlying factors in Wolbachia's success as a male-killer of divergent host species.

Keywords: Wolbachia; evolutionary genomics; male killing.

Fig. 1.

(A) Schematic of the wInn genome. Circles correspond to the following: 1) GC content of the wInn genome in 10 kb windows, between 30% and 40%. Darker colors have higher GC content. 2) Locations of genes thought to interact with hosts, specifically prophage orthologous to WO-A and WO-B genes in wMel (blue), Type IV secretion pumps (green), and Octomom genes (yellow). 3) Loci of nonphage genes. 4) Loci of repetitive content, with short simple repeats and interspersed satellites (SSR and IS, black), and hAT or LINE TE insertions (red). (B) Phylogeny of Wolbachia genomes closely related to wInn for reference, as a subset of supplementary figure 1, Supplementary Material online. Bootstrap support of each branch is shown on the nodes (of 100 bootstraps). A description of each Wolbachia genome and the species they infect is given in supplementary table 1, Supplementary Material online. (C) The overlap of genes between wInn, wMel, and wRi. (D) Synteny between wMel and wInn, with single large inversion shown in blue, whereas consistent synteny groups are shown in gray.

Fig. 2.

Selection on genes of the wInn branch versus evolution on the wRi/wHa branches. Functional categories of interest (DNA metabolism genes, prophage genes, and Octomom genes) are highlighted by different shapes and colors. Dashed lines show dN/dS=1 for both axes, whereas the dotted line shows where dN/dS is equal on the axes. Genes of interest, either due to putative involvement in Wolbachia pathogenicity, or due to high dN/dS in wInn exclusively are named and labeled with a black outline to distinguish them.

Fig. 3.

Comparison of dS between pairs of Wolbachia suggesting horizontal transfer of genes. Point colors show the gene ontology categories (GO category) for Octomom genes and Prophage WO-B genes. Point shape indicates evidence of excessive divergence (and possible horizontal transfer) in either wInn, wHa, or both. Dashed lines show the mean plus the variance of dS for each axis as a rough cutoff for elevated synonymous divergence.

Fig. 4.

Principal component analysis of genetic variation in wInn. (A) Map of locations samples were taken from in this survey, adapted from Hill and Unckless (2020a). Phoenix and Tucson are shown as points of reference. (B) Total polymorphism and (C) silent polymorphism in wInn samples, colored and shaped by location of collection, Chiricahuas (CH, red circles), Huachucas (HU, orange squares), Prescott (PR, blue triangles), and Santa Ritas (SR, green diamonds).

Fig. 5.

Prophage abundance genes (prophage coverage/total Wolbachia coverage) compared with the Wolbachia titer (total Wolbachia coverage/host autosomal coverage) and Octomom copies compared with Wolbachia titer (total Wolbachia coverage/host autosomal coverage). A LOESS smoothed regression was added to the data for each plot to assist in visualizing the change in gene copy number with titer, showing the fitted curve of the average Octomom copy per 2-fold Wolbachia titer.