| 1. |
- Baiao, Guilherme Costa, 1984-, et al.
(författare)
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Comparative Genomics Reveals Factors Associated with Phenotypic Expression of Wolbachia
- 2021
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 13:7
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Tidskriftsartikel (refereegranskat)abstract
- Wolbachia is a widespread, vertically transmitted bacterial endosymbiont known for manipulating arthropod reproduction. Its most common form of reproductive manipulation is cytoplasmic incompatibility (CI), observed when a modification in the male sperm leads to embryonic lethality unless a compatible rescue factor is present in the female egg. CI attracts scientific attention due to its implications for host speciation and in the use of Wolbachia for controlling vector-borne diseases. However, our understanding of CI is complicated by the complexity of the phenotype, whose expression depends on both symbiont and host factors. In the present study, we perform a comparative analysis of nine complete Wolbachia genomes with known CI properties in the same genetic host background, Drosophila simulans STC. We describe genetic differences between closely related strains and uncover evidence that phages and other mobile elements contribute to the rapid evolution of both genomes and phenotypes of Wolbachia. Additionally, we identify both known and novel genes associated with the modification and rescue functions of CI. We combine our observations with published phenotypic information and discuss how variability in cif genes, novel CI-associated genes, and Wolbachia titer might contribute to poorly understood aspects of CI such as strength and bidirectional incompatibility. We speculate that high titer CI strains could be better at invading new hosts already infected with a CI Wolbachia, due to a higher rescue potential, and suggest that titer might thus be a relevant parameter to consider for future strategies using CI Wolbachia in biological control.
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| 2. |
- Baiao, Guilherme Costa, et al.
(författare)
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Differential gene expression in semispecies and hybrids of Drosophila paulistorum
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Gene expression divergence is correlated with and can be either a cause or a consequence of species divergence. Studying gene expression differences between closely related species, and their hybrid offspring, can thus give us clues about genes and mechanisms associated with reproductive isolation (RI) between them and allow us to better understand early stages of speciation. In this study, we use RNA-Seq to investigate gene expression divergence between the Amazonian, Centro-American and Orinocan semispecies of Drosophila paulistorum, a species cluster in statu nascendi, and between inter-semispecies hybrids and their parents. We uncover a large number of genes with varying expression between semispecies, with the highest numbers in male abdomens. The differentially expressed genes are associated with a range of biological functions, but especially with broad, regulatory functions, that are governed by transcription, translation, post-translational modifications and induced by signal transduction. We found that the expression pattern of hybrids was much more similar to the maternal line and that very few genes have a different expression than both of their parents. When comparing the differentially expressed genes in semispecies and hybrids to gene affected by Wolbachia in D. paulistorum, we see a small overlap. However, especially in hybrids, some of the overlapping genes appear to be highly relevant. Our study provides insights about expression differences associated with RI in D. paulistorum, and the impact of Wolbachia on the divergence of semispecies and hybrid sterility.
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| 3. |
- Baião, Guilherme Costa, 1984-
(författare)
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Genomic and transcriptomic investigation of reproductive incompatibility in Drosophila
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Both nuclear and cytoplasmic elements can contribute to the emergence of reproductive incompatibilities that influence evolution and speciation. In the projects that compose this thesis, we use genomics and transcriptomics to study some of those elements in Drosophila.In the first study, we show that Wolbachia, an endosymbiotic bacterium known to cause reproductive alterations in its hosts, influences gene expression in D. paulistorum. Affected genes were associated with biological functions such as metabolism, immunity, reproduction, and chemical communication. Our results indicate that Wolbachia accentuates the differences in expression profiles between semispecies and suggest that the symbiont influences host pre-and postmating isolation. In the second paper, we uncover widespread persistent heteroplasmy in D. paulistorum. We reveal that D. paulistorum mitochondria are polyphyletic, with two divergent mitotypes, and that the heteroplasmy likely originated through introgression. One of the mitotypes shows biparental inheritance, non-responsiveness to host energy demands and rapid titer increase in the early embryo. We hypothesize that such selfish traits evolved in response to competition between mitotypes.In the third project, we show that differentially expressed genes between D. paulistorum semispecies are associated with a variety of biological processes, especially broad regulatory functions that occur via variability in transcription, translation and ubiquitination of post-translational modification. We reveal that the expression profile of F1 inter-semispecies hybrids is markedly similar to that of the maternal line, and that Wolbachia has a small but potentially significant interaction with genes that are differentially expressed in semispecies and F1 hybrids.Finally, we use comparative genomics to study the evolution of closely related Wolbachia strains with known reproductive phenotypes. We confirm previous observations that Wolbachia genomes are very dynamic and that phage-associated regions are particularly variable and likely involved in horizontal transfer of genes linked to reproductive phenotypes. An in-depth screen for genetic elements potentially involved in Wolbachia-induced cytoplasmic incompatibility recovers genes previously known to be involved in the phenotype and novel candidates.In conclusion, this thesis contributes to our understanding of genetic factors that affect Drosophila evolution, particularly those leading to reproductive incompatibility in D. paulistorum and associated with Wolbachia.
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| 4. |
- Baiao, Guilherme Costa, 1984-, et al.
(författare)
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Multiple introgressions shape mitochondrial evolutionary history in Drosophila paulistorum and the Drosophila willistoni group
- 2023
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier. - 1055-7903 .- 1095-9513. ; 180
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Tidskriftsartikel (refereegranskat)abstract
- Hybridization and the consequent introgression of genomic elements is an important source of genetic diversity for biological lineages. This is particularly evident in young clades in which hybrid incompatibilities are still incomplete and mixing between species is more likely to occur. Drosophila paulistorum, a representative of the Neotropical Drosophila willistoni subgroup, is a classic model of incipient speciation. The species is divided into six semispecies that show varying degrees of pre-and post-mating incompatibility with each other. In the present study, we investigate the mitochondrial evolutionary history of D. paulistorum and the willistoni subgroup. For that, we perform phylogenetic and comparative analyses of the complete mitochondrial genomes and draft nuclear assemblies of 25 Drosophila lines of the willistoni and saltans species groups. Our results show that the mitochondria of D. paulistorum are polyphyletic and form two non-sister clades that we name alpha and beta. Identi-fication and analyses of nuclear mitochondrial insertions further reveal that the willistoni subgroup has an alpha-like mitochondrial ancestor and strongly suggest that both the alpha and beta mitochondria of D. paulistorum were acquired through introgression from unknown fly lineages of the willistoni subgroup. We also uncover multiple mito-chondrial introgressions across D. paulistorum semispecies and generate novel insight into the evolution of the species.
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| 5. |
- Baiao, Guilherme Costa, et al.
(författare)
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Persistence of high-level heteroplasmy through biparental transmission of a selfish mitochondrion in Drosophila paulistorum
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Heteroplasmy, or the coexistence of multiple mitotypes in an individual, has during recent years been shown to be more common in animals than previously anticipated. However, cases of stable, high-titer heteroplasmy are still relatively rare, as are systems with consistent paternal mitochondrial inheritance. In this study, we sequenced and assembled the full mitochondrial genomes of 23 Neotropical Drosophila lines belonging to six species of the willistoni group and three of the saltans group and discovered that 40% the 13 sequenced Drosophila paulistorum lines, are persistently heteroplasmic. We further showed that the mitochondria of D. paulistorum are polyphyletic, forming two clades, a and b, and that mitochondria of the a2 clade are exclusively found in heteroplasmic flies. Genomic analysis indicates that a2 is a functional mitochondrion, with no signs of loss of function mutations. Even so, our results demonstrate that a2 displays unusual features, including lack of titer response to energetic demands, higher titer in males than females, and consistent biparental transmission due to rapid replication during early embryo development. Together these features indicate that a2 might be a selfish mitochondrion that persists due to efficient biparental transmission.Using the assembled genomes, we reconstructed the evolutionary history of mitochondria in the willistoni subgroup and identified signs of multiple mitochondrial losses, gains and introgressions. The data indicated an a-like mitochondrial ancestor in the willistoni subgroup, with the b mitochondrion likely being acquired through introgression from an unidentified donor. We hypothesize that the selfish characteristics of a2 might have emerged as a response to competition for inheritance with the introgressed b
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| 6. |
- Baiao, Guilherme Costa, et al.
(författare)
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Revision of the West Palaearctic species of Rhoptromeris Forster, 1869 (Hymenoptera: Figitidae: Eucoilinae)
- 2018
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Ingår i: Journal of Natural History. - : TAYLOR & FRANCIS LTD. - 0022-2933 .- 1464-5262. ; 52:17-18, s. 1201-1224
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Tidskriftsartikel (refereegranskat)abstract
- The West Palearctic species of Rhoptromeris are revised. A total of 11 species are recognised as valid in this region, including four newly described species: Rhoptromeris dichromata sp. nov., Rhoptromeris koponeni sp. nov., Rhoptromeris leptocornis sp. nov. and Rhoptromeris macaronesiensis sp. nov. Eucoila luteicornis Ionescu, 1959 is synonymised with Rhoptromeris heptoma (Hartig, 1840) syn. nov. A checklist of the Holarctic Rhoptromeris is presented and an identification key to the West Palearctic species is provided.www.zoobank.org/urn:lsid:zoobank.org:pub:8164332C-93E2-4E3F-A408-F5FF5DFB366E
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| 7. |
- Baiao, Guilherme Costa, et al.
(författare)
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The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation
- 2019
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Neotropical fruit fly Drosophila paulistorum (Diptera: Drosophilidae) is a species complex in statu nascendi comprising six reproductively isolated semispecies, each harboring mutualistic Wolbachia strains. Although wild type flies of each semispecies are isolated from the others by both pre- and postmating incompatibilities, mating between semispecies and successful offspring development can be achieved once flies are treated with antibiotics to reduce Wolbachia titer. Here we use RNA-seq to study the impact of Wolbachia on D. paulistorum and investigate the hypothesis that the symbiont may play a role in host speciation. For that goal, we analyze samples of heads and abdomens of both sexes of the Amazonian, Centro American and Orinocan semispecies of D. paulistorum.Results: We identify between 175 and 1192 differentially expressed genes associated with a variety of biological processes that respond either globally or according to tissue, sex or condition in the three semispecies. Some of the functions associated with differentially expressed genes are known to be affected by Wolbachia in other species, such as metabolism and immunity, whereas others represent putative novel phenotypes involving muscular functions, pheromone signaling, and visual perception.Conclusions: Our results show that Wolbachia affect a large number of biological functions in D. paulistorum, particularly when present in high titer. We suggest that the significant metabolic impact of the infection on the host may cause several of the other putative and observed phenotypes. We also speculate that the observed differential expression of genes associated with chemical communication and reproduction may be associated with the emergence of pre- and postmating barriers between semispecies, which supports a role for Wolbachia in the speciation of D. paulistorum.
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| 8. |
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| 9. |
- Janice, Jessin, et al.
(författare)
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Comparative genomics of closely related Wolbachia strains infecting Drosophila
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Cytoplasmic incompatibility (CI) is the most common form of reproductive manipulation induced by the vertically inherited endosymbiont Wolbachia. The phenotype causes partial or complete sterility in crosses between infected males and non-infected females, thus benefiting infected females in the population and the spread of the bacteria. Because of these properties, CI-inducing Wolbachia has been implicated as a mean for biological pest control. Although CI has been known for several decades, the first CI-associated genes, cifA and cifB, were only recently discovered. In this study, we sequenced five complete Wolbachia genomes (wSan, wYak, wTei, wAu, wMa,) and performed comparative genomic analyses between these and four previously published complete Wolbachia genomes (wRi, wNo, wHa, wMel), that have all had their CI properties tested in the same genetic host background, Drosophila simulans STC. Using these genomes, we investigate what types of genes differ between closely related Wolbachia strains and compare the sequences from some of the strains in their natural host vs. after transfer to D. simulans STC. We find that phage-associated and hypothetical genes are likely to vary more between genomes and that very few mutations have occurred when strains were transferred to D. simulans. Furthermore, we investigate the evolution of the known CI genes and take advantage of the highly similar genomes of some strains as well as their complex CI properties to identify further genes associated with both mod and resc functions of CI.
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