Rhagoletis cingulata and Rhagoletis cerasi genome comparison

Wolbachia is a maternally inherited obligate endosymbiont that can induce
a wide spectrum of effects in its host, ranging from mutualism to
reproductive parasitism. At the genomic level, recombination within and
between strains, transposable elements, and horizontal transfer of strains
between host species make Wolbachia an evolutionarily dynamic bacterial
system. The invasive cherry fruit fly Rhagoletis cingulata arrived in
Europe from North America ~40 years ago, where it now co-occurs with the
native cherry pest R. cerasi. This shared distribution has been proposed
to have led to the horizontal transfer of different Wolbachia strains
between the two species. To better understand transmission dynamics, we
performed a comparative genome study of the strain wCin2 in native United
States and invasive European populations of R. cingulata with wCer2 in
European R. cerasi. Previous multilocus sequence genotyping (MLST) of six
genes implied that the source of wCer2 in R. cerasi was wCin2 from R.
cingulata. However, we report genomic evidence discounting the recent
horizontal transfer hypothesis for the origin of wCer2. Despite near
identical sequences for the MLST markers, substantial sequence differences
for other loci were found between wCer2 and wCin2, as well as structural
rearrangements, and differences in prophage, repetitive element, gene
content, and cytoplasmic incompatibility inducing genes. Our study
highlights the need for whole-genome sequencing rather than relying on
MLST markers for resolving Wolbachia strains and assessing their
evolutionary dynamics, and calls for additional studies of wCer2 to
determine its origin and history in R. cerasi.