Genome analyses of four Wolbachia strains and associated mitochondria of Rhagoletis cerasi expose cumulative modularity of cytoplasmic incompatibility factors and cytoplasmic hitchhiking across host populations

Mitochondrial genomes of four slug moths (Lepidoptera, Limacodidae): Genome description and phylogenetic implications

The family Limacodidae belongs to the superfamily Zygaenoidea, which includes 1672 species commonly referred to as slug moths. Limacodidae larvae are major pests for many economically important plant species and can cause human dermatitis. At present, the structure of the mitochondrial genome (mitogenome), phylogenetic position, and adaptive evolution of slug moths are poorly understood. Herein, the mitogenomes of Parasa lepida, Phlossa conjuncta, Thosea sinensis, and Setora sinensis were sequenced and compared with other available mitogenome sequences to better characterize the mitogenomic diversity and evolution of this moth family. The mitogenomes of P. lepida, P. conjuncta, T. sinensis, and S. sinensis were confirmed to be circular in structure with lengths of 15,575 bp, 15,553 bp, 15,535 bp, and 15,529 bp, respectively. The Limacodidae mitogenomes exhibited similar nucleotide composition, codon usage, RNA structure, and control region patterns, indicating the conservation of the mitogenome in the family Limacodidae. A sliding window, Ka/Ks, and genetic distance analyses revealed that the atp8 and nad6 genes exhibited the highest levels of variability and the most rapid evolutionary rates among the 13 protein-coding genes (PCGs) encoded in these Limacodidae mitogenomes, suggesting that they may offer value as candidate DNA markers. The phylogenetic analysis recovered the overall relationship as Tortricoidea + (Sesiidae + (Zygaenoidea + (Cossoidea/+Choreutoidea + (others)))). Within Zygaenoidea, Limacodidae was recovered as monophyletic, and the phylogenetic relationships were recovered as (Phaudidae + Zyganidae) + Limacodidae in all six phylogenetic trees. The analysis indicated that P. lepida, P. conjuncta, T. sinensis, and S. sinensis are members of the Limacodidae.

Two sympatric lineages of Australian Cnestus solidus share Ambrosiella symbionts but not Wolbachia

Sympatric lineages of inbreeding species provide an excellent opportunity to investigate species divergence patterns and processes. Many ambrosia beetle lineages (Curculionidae: Scolytinae) reproduce by predominant inbreeding through sib mating in nests excavated in woody plant parts wherein they cultivate symbiotic ambrosia fungi as their sole source of nutrition. The Xyleborini ambrosia beetle species Cnestus solidus and Cnestus pseudosolidus are sympatrically distributed across eastern Australia and have overlapping morphological variation. Using multilocus sequencing analysis of individuals collected from 19 sites spanning their sympatric distribution, we assessed their phylogenetic relationships, taxonomic status and microbial symbionts. We found no genetic differentiation between individuals morphologically identified as C. solidus and C. pseudosolidus confirming previous suggestions that C. pseudosolidus is synonymous to C. solidus. However, within C. solidus we unexpectedly discovered the sympatric coexistence of two morphologically indistinguishable but genetically distinct lineages with small nuclear yet large mitochondrial divergence. At all sites except one, individuals of both lineages carried the same primary fungal symbiont, a new Ambrosiella species, indicating that fungal symbiont differentiation may not be involved in lineage divergence. One strain of the maternally inherited bacterial endosymbiont Wolbachia was found at high prevalence in individuals of the more common lineage but not in the other, suggesting that it may influence host fitness. Our data suggest that the two Australian Cnestus lineages diverged allopatrically, and one lineage then acquired Wolbachia. Predominant inbreeding and Wolbachia infection may have reinforced reproductive barriers between these two lineages after their secondary contact contributing to their current sympatric distribution.

Substantial rearrangements, single nucleotide frameshift deletion and low diversity in mitogenome of Wolbachia-infected strepsipteran endoparasitoid in comparison to its tephritid hosts

Insect mitogenome organisation is highly conserved, yet, some insects, especially with parasitic life cycles, have rearranged mitogenomes. Furthermore, intraspecific mitochondrial diversity can be reduced by fitness-affecting bacterial endosymbionts like Wolbachia due to their maternal coinheritance with mitochondria. We have sequenced mitogenomes of the Wolbachia-infected endoparasitoid Dipterophagus daci (Strepsiptera: Halictophagidae) and four of its 22 known tephritid fruit fly host species using total genomic extracts of parasitised flies collected across > 700 km in Australia. This halictophagid mitogenome revealed extensive rearrangements relative to the four fly mitogenomes which exhibited the ancestral insect mitogenome pattern. Compared to the only four available other strepsipteran mitogenomes, the D. daci mitogenome had additional transpositions of one rRNA and two tRNA genes, and a single nucleotide frameshift deletion in nad5 requiring translational frameshifting or, alternatively, resulting in a large protein truncation. Dipterophagus daci displays an almost completely endoparasitic life cycle when compared to Strepsiptera that have maintained the ancestral state of free-living adults. Our results support the hypothesis that the transition to extreme endoparasitism evolved together with increased levels of mitogenome changes. Furthermore, intraspecific mitogenome diversity was substantially smaller in D. daci than the parasitised flies suggesting Wolbachia reduced mitochondrial diversity because of a role in D. daci fitness.

Host-endoparasitoid-endosymbiont relationships: concealed Strepsiptera provide new twist to Wolbachia in Australian tephritid fruit flies

Wolbachia are widespread endosymbionts that affect arthropod reproduction and fitness. Mostly maternally inherited, Wolbachia are occasionally transferred horizontally. Previously, two Wolbachia strains were reported at low prevalence and titres across seven Australian tephritid species, possibly indicative of frequent horizontal transfer. Here, we performed whole-genome sequencing of field-caught Wolbachia-positive flies. Unexpectedly, we found complete mitogenomes of an endoparasitic strepsipteran, Dipterophagus daci, suggesting that Wolbachia in the flies are linked to concealed parasitization. We performed the first genetic characterization of D. daci and detected D. daci in Wolbachia-positive flies not visibly parasitized, and most but not all Wolbachia-negative flies were D. daci-negative, presumably reflecting polymorphism for the Wolbachia infections in D. daci. We dissected D. daci from stylopized flies and confirmed that Wolbachia infects D. daci, but also found Wolbachia in stylopized fly tissues, likely somatic, horizontally transferred, non-heritable infections. Furthermore, no Wolbachia cif and wmk genes were detected and very low mitogenomic variation in D. daci across its distribution. Therefore, Wolbachia may influence host fitness without reproductive manipulation. Our study of 13 tephritid species highlights that concealed early stages of strepsipteran parasitization led to the previous incorrect assignment of Wolbachia co-infections to tephritid species, obscuring ecological studies of this common endosymbiont and its horizontal transmission by parasitoids.