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- Gobbo, Erik, 1990-
(författare)
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Gall induction in gall wasps (Cynipidae s. lat.) : Insights from comparative genomics
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Cynipidae are a family of wasps (Hymenoptera), whose larval stages develop inside plant galls, that is, abnormal plant structures formed in response to the presence of foreign organisms. Most cynipids are gall inducers and are often capable of notable levels of host manipulation. Others are inquilines, meaning they are dependent on other species for the initiation of the gall. Their larvae then develop inside the gall, often killing the original inducer and modifying the gall in the process. The biochemical mechanism of gall induction is still shrouded in mystery. In this thesis, various approaches are implemented to try to shed some light on the process. In Paper I, we used shotgun sequencing to investigate the bacterial association of larvae of different species inhabiting the bedeguar gall on roses, and showed that neither the inquiline nor the gall inducer inhabiting this gall are associated with symbiotic bacteria that are likely to be involved in gall induction, despite earlier speculations to that effect. In Paper II, I used comparative genomic analysis of a recently evolved gall inducer in the genus Synergus and three related inquilines to identify candidate genes involved in gall initiation. Specifically, I used a new method relying on genome-wide analyses to control for confounding factors, implemented in the software Bayescode. Then, I used Gene Onthology (GO) analysis to show that the candidate genes are associated with specific functions, such as “egg follicle development” and “neural development”. In paper III, we used genomic and transcriptomic data to infer the phylogeny of the family. The analysis confirmed that the phytophagous Cynipidae fall into two distinct lineages, as suggested by a recent phylogenomic analysis based on ultraconserved elements. We propose that these families be recognized as Cynipidae s. str. (oak gallers and relatives) and Diplolepididae (rose gallers and relatives). Finally, in paper IV, I applied the same methods as in Paper II to genomes of the Cynipidae s. str. to identify candidate genes associated with gall secondary structures. I inferred that these genes are often associated with GO terms relative to egg development and cell movement. In conclusion, the data presented here can provide a useful starting point for future research on cynipids.
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| 2. |
- Gobbo, Erik, 1990-, et al.
(författare)
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Shotgun sequencing of hymenopteran inhabitants of rose galls reveals a surprising lack of bacteria
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In recent years, our knowledge of the microbiomes associated with insects has increased rapidly thanks to new sequencing methods, but the taxonomic and biological diversity of the studied insect species is still limited. Insects inhabiting galls represent a particularly interesting ecological guild that has not yet had its microbiome fully characterized, although it is well known that many gall insects are infected by Wolbachia. Here, we use shotgun sequencing to characterize the microbiome of the larvae of four hymenopteran species inhabiting bedeguar galls on roses: the gall inducer (Diplolepis rosae, Cynipidae), a phytophagous inquiline (Periclistus brandtii, Cynipidae), and two parasitoids (Torymus bedeguaris, Torymidae, and Orthopelma mediator, Ichneumonidae). Analyses with Metaphlan2 detected the presence of Wolbachia in two of the larvae (one of three Diplolepis larvae, and one of two Torymus larvae); three other bacteria detected by Metaphlan2 in high abundance could be shown to be false positives. An annotation screen of the assembled genomes gave similar results. Almost all contigs that were likely to be of bacterial origin matched Wolbachia; the few remaining ones were likely false positives. Matching the assemblies to proteomes of candidate symbionts showed that the two infected larvae contained a substantial portion of the Wolbachia genome while the other Diplolepis and Torymus larvae only contained small sections of it. Our results suggest that the bedeguar gall is largely devoid of bacteria except for Wolbachia. This could potentially be related to previous reports that galls induced by cynipids produce antibiotics. Our results fail to support the much-discussed hypothesis that symbiotic bacteria are involved in gall induction in cynipids.
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| 3. |
- Hearn, Jack, et al.
(författare)
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Phylogenomic analysis of protein-coding genes resolves complex gall wasp relationships
- 2024
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Ingår i: Systematic Entomology. - 0307-6970 .- 1365-3113. ; 49:1, s. 110-137
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Tidskriftsartikel (refereegranskat)abstract
- Gall wasps (Hymenoptera: Cynipidae) comprise 13 distinct tribes whose interrelationships remain incompletely understood. Recent analyses of ultra-conserved elements (UCEs) represent the first attempt at resolving these relationships using phylogenomics. Here, we present the first analysis based on protein-coding sequences from genome and transcriptome assemblies. Unlike UCEs, these data allow more sophisticated substitution models, which can potentially resolve issues with long-branch attraction. We include data for 37 cynipoid species, including two tribes missing in the UCE analysis: Aylacini (s. str.) and Qwaqwaiini. Our results confirm the UCE result that Cynipidae are not monophyletic. Specifically, the Paraulacini and Diplolepidini + Pediaspidini fall outside a core clade (Cynipidae s. str.), which is more closely related to the insect-parasitic Figitidae, and this result is robust to the exclusion of long-branch taxa that could mislead the analysis. Given this, we here divide the Cynipidae into three families: the Paraulacidae stat. prom., Diplolepididae stat. prom. and Cynipidae (s. str.). Our results suggest that the Eschatocerini are the sister group of the remaining Cynipidae (s. str.). Within the Cynipidae (s. str.), the Aylacini (s. str.) are more closely related to oak gall wasps (Cynipini) and some of their inquilines (Ceroptresini) than to other herb gallers (Aulacideini and Phanacidini), and the Qwaqwaiini likely form a clade together with Synergini (s. str.) and Rhoophilini. Several alternative scenarios for the evolution of cynipid life histories are compatible with the relationships suggested by our analysis, but all are complex and require multiple shifts among parasitoids, inquilines and gall inducers.
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