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

Abstract

Wolbachia endosymbionts may be acquired by horizontal transfer, by introgression through hybridization between closely related species, or by cladogenic retention during speciation. All three modes of acquisition have been demonstrated, but their relative frequency is largely unknown. Drosophila suzukii and its sister species D. subpulchrella harbor Wolbachia, denoted wSuz and wSpc, very closely related to wRi, identified in California populations of D. simulans. However, these variants differ in their induced phenotypes: wRi causes significant cytoplasmic incompatibility (CI) in D. simulans, but CI has not been detected in D. suzukii or D. subpulchrella. Our draft genomes of wSuz and wSpc contain full‐length copies of 703 of the 734 single‐copy genes found in wRi. Over these coding sequences, wSuz and wSpc differ by only 0.004% (i.e., 28 of 704,883 bp); they are sisters relative to wRi, from which each differs by 0.014%–0.015%. Using published data from D. melanogaster, Nasonia wasps and Nomada bees to calibrate relative rates of Wolbachia versus host nuclear divergence, we conclude that wSuz and wSpc are too similar—by at least a factor of 100—to be plausible candidates for cladogenic transmission. These three wRi‐like Wolbachia, which differ in CI phenotype in their native hosts, have different numbers of orthologs of genes postulated to contribute to CI; and the CI loci differ at several nucleotides that may account for the CI difference. We discuss the general problem of distinguishing alternative modes of Wolbachia acquisition, focusing on the difficulties posed by limited knowledge of variation in absolute and relative rates of molecular evolution for host nuclear genomes, mitochondria, and Wolbachia.

Evolutionary Genetics of Cytoplasmic Incompatibility Genes cifA and cifB in Prophage WO of Wolbachia

“…The split WOSuziC sequenced was concatenated to allow for a more robust phylogenetic reconstruction ( fig. 4 ), but it is in fact disrupted by a transposase ( Conner et al. 2017 ).…”

WolbachiaAcquisition byDrosophila yakuba-Clade Hosts and Transfer of Incompatibility Loci Between Distantly RelatedWolbachia

“…To assess the quality of these three draft assemblies, we used BUSCO v.3.0.0 to search for homologs of the near-universal, singlecopy genes in the BUSCO proteobacteria database (Simão et al 2015). For comparison, we followed Conner et al (2017) and performed the same search on the reference genomes for wMel (Wu et al 2004), wRi (Klasson et al 2009), wAu (Sutton et al 2014), and wHa and wNo (Ellegaard et al 2013) (Table S3).…”

“…Such cladogenic acquisition seems to be the rule for the obligate Wolbachia found in filarial nematodes (Bandi et al 1998); and there are also examples in at least two insect clades, Nasonia wasps (Raychoudhury et al 2009) and Nomada bees (Gerth and Bleidorn 2016). In contrast, infections can be relatively young and acquired through introgressive or horizontal transfer (Raychoudhury et al 2009;Schuler et al 2016;Conner et al 2017;Turelli et al 2018). Comparisons of host nuclear and mitochondrial genomes with the associated Wolbachia genomes enable discrimination among cladogenic, introgressive, and horizontal acquisition (Raychoudhury et al 2009;Turelli et al 2018; see Supplemental Material, Figure S1).…”

“…Distinguishing acquisition via introgression vs. horizontal or paternal transmission requires estimating phylogenies and relative divergence times of mitochondrial DNA (mtDNA) and Wolbachia (Raychoudhury et al 2009;Conner et al 2017;Turelli et al 2018). To convert sequence divergence to divergence-time estimates requires understanding relative rates of divergence for mtDNA, nuclear genomes, and Wolbachia.…”

A putative antimicrobial peptide from Hymenoptera in the megaplasmid pSCL4 of Streptomyces clavuligerus ATCC 27064 reveals a singular case of horizontal gene transfer with potential applications

“…Despite this observation, several studies have reported animals as acceptors in this process. Genomic sections of the endosymbiotic bacteria Wolbachia pipientis have been found in fruit flies and wasps (Conner et al, 2017;Dunning Hotopp et al, 2007). Anecdotally, HGT in the opposite direction was also observed because genomic regions of the mosquito Aedes aegypti were detected in W. pipientis.…”