The mosaic genome structure of the Wolbachia w Ri strain infecting Drosophila simulans

Abstract

The obligate intracellular bacterium Wolbachia pipientis infects around 20% of all insect species. It is maternally inherited and induces reproductive alterations of insect populations by male killing, feminization, parthenogenesis, or cytoplasmic incompatibility. Here, we present the 1,445,873-bp genome of W. pipientis strain wRi that induces very strong cytoplasmic incompatibility in its natural host Drosophila simulans. A comparison with the previously sequenced genome of W. pipientis strain wMel from Drosophila melanogaster identified 35 breakpoints associated with mobile elements and repeated sequences that are stable in Drosophila lines transinfected with wRi. Additionally, 450 genes with orthologs in wRi and wMel were sequenced from the W. pipientis strain wUni, responsible for the induction of parthenogenesis in the parasitoid wasp Muscidifurax uniraptor. The comparison of these A-group Wolbachia strains uncovered the most highly recombining intracellular bacterial genomes known to date. This was manifested in a 500-fold variation in sequence divergences at synonymous sites, with different genes and gene segments supporting different strain relationships. The substitution-frequency profile resembled that of Neisseria meningitidis, which is characterized by rampant intraspecies recombination, rather than that of Rickettsia, where genes mostly diverge by nucleotide substitutions. The data further revealed diversification of ankyrin repeat genes by short tandem duplications and provided examples of horizontal gene transfer across A-and B-group strains that infect D. simulans. These results suggest that the transmission dynamics of Wolbachia and the opportunity for coinfections have created a freely recombining intracellular bacterial community with mosaic genomes.horizontal transfer ͉ recombination ͉ ankyrin repeat gene ͉ genome evolution ͉ insect symbiosis Wolbachia pipientis are intracellular ␣-proteobacteria of the order Rickettsiales that infect insects as well as isopods, spiders, scorpions, mites, and filarial nematodes (1, 2). These bacteria represent a single species, with strains classified into supergroups, of which the most abundant are supergroups A and B.

Genome comparisons indicate recent transfer ofwRi‐likeWolbachiabetween sister speciesDrosophila suzukiiandD. subpulchrella

“…As a control, we performed the same search using the complete reference genomes for w Ri (Klasson et al., 2009), w Au (Sutton, Harris, Parkhill, & Sinkins, 2014), w Mel (Wu et al., 2004), w Ha, and w No (Ellegaard et al., 2013). …”

“…As reported in Hamm et al. (2014), the MLST sequences from w Spc and w Suz were identical both to each other and to those of the w Ri reference genome from D. simulans (Klasson et al., 2009). …”

“…The trimmed Illumina reads from D. suzukii and D. subpulchrella were aligned to the w Ri reference (Klasson et al., 2009) with bwa v. 0.7.12 (Li & Durbin, 2009). As a control, we also aligned Illumina reads from Riv84 (Iturbe‐Ormaetxe et al., 2010), the D. simulans line used to make the w Ri reference.…”

“…Rohrscheib et al., 2016; Chrostek & Teixeira, 2017) were extracted from the w Mel reference (Richardson et al., 2012; Wu et al., 2004). Using BLAST, we identified orthologs in the w Ri reference (Klasson et al., 2009) and the draft assemblies for w Suz and w Spc.…”

“…Sequences homologous to loci putatively involved in CI in other Wolbachia strains (Beckmann & Fallon, 2013; Beckmann et al., 2017; LePage et al., 2017) were extracted from w Ri (Klasson et al., 2009) and the draft assemblies for w Suz and w Spc. Differences among these three genomes at these loci were assessed by aligning the w Suz and w Spc reads to the w Ri reference and calculating the percentage of reads with the non‐ w Ri base.…”