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Jacobs J, Nakamoto A, Mastoras M, Loucks H, Mirchandani C, Karim L, Penunuri G, Wanket C, Russell SL. Complete de novo assembly of Wolbachia endosymbiont of Drosophila willistoni using long-read genome sequencing. Sci Rep 2024; 14:17770. [PMID: 39090271 PMCID: PMC11294445 DOI: 10.1038/s41598-024-68716-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024] Open
Abstract
Wolbachia is an obligate intracellular α-proteobacterium, which commonly infects arthropods and filarial nematodes. Different strains of Wolbachia are capable of a wide range of regulatory manipulations in their diverse hosts, including the modulation of host cellular differentiation to influence host reproduction. The genetic basis for the majority of these phenotypes is unknown. The wWil strain from the neotropical fruit fly, Drosophila willistoni, exhibits a remarkably high affinity for host germline-derived cells relative to the somatic cells. This trait could be leveraged for understanding how Wolbachia influences the host germline and for controlling host populations in the field. To further the use of this strain in biological and biomedical research, we sequenced the genome of the wWil strain isolated from host cell culture cells. Here, we present the first high quality Nanopore assembly of wWil, the Wolbachia endosymbiont of D. willistoni. Our assembly resulted in a circular genome of 1.27 Mb with a BUSCO completeness score of 99.7%. Consistent with other insect-associated Wolbachia strains, comparative genomic analysis revealed that wWil has a highly mosaic genome relative to the closely related wMel and wAu strains from Drosophila melanogaster and Drosophila simulans, respectively.
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Affiliation(s)
- Jodie Jacobs
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Anne Nakamoto
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Mira Mastoras
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Hailey Loucks
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Cade Mirchandani
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Lily Karim
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Gabriel Penunuri
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Ciara Wanket
- Genomics Institute, University of California, Santa Cruz, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Shelbi L Russell
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA.
- Genomics Institute, University of California, Santa Cruz, CA, USA.
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Jacobs J, Nakamoto A, Mastoras M, Loucks H, Mirchandani C, Karim L, Penunuri G, Wanket C, Russell SL. Complete de novo assembly of Wolbachia endosymbiont of Drosophila willistoni using long-read genome sequencing. RESEARCH SQUARE 2024:rs.3.rs-4510571. [PMID: 38946980 PMCID: PMC11213192 DOI: 10.21203/rs.3.rs-4510571/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Wolbachia is an obligate intracellular α-proteobacterium which commonly infects arthropods and filarial nematodes. Different strains of Wolbachia are capable of a wide range of regulatory manipulations in many hosts and modulate host cellular differentiation to influence host reproduction. The genetic basis for the majority of these phenotypes is unknown. The wWil strain from the neotropical fruit fly, Drosophila willistoni, exhibits a remarkably high affinity for host germline-derived cells relative to the soma. This trait could be leveraged for understanding how Wolbachia influences the host germline and for controlling host populations in the field. To further the use of this strain in biological and biomedical research, we sequenced the genome of the wWil strain isolated from host cell culture cells. Here, we present the first high quality nanopore assembly of wWil, the Wolbachia endosymbiont of D. willistoni. Our assembly resulted in a circular genome of 1.27 Mb with a BUSCO completeness score of 99.7%. Consistent with other insect-associated Wolbachia strains, comparative genomic analysis revealed that wWil has a highly mosaic genome relative to the closely related wMel strain from Drosophila melanogaster.
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Affiliation(s)
- Jodie Jacobs
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Anne Nakamoto
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Mira Mastoras
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Hailey Loucks
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Lily Karim
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Gabriel Penunuri
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Ciara Wanket
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz
| | - Shelbi L Russell
- Department of Biomolecular Engineering, University of California Santa Cruz
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Bourne ME, Gloder G, Weldegergis BT, Slingerland M, Ceribelli A, Crauwels S, Lievens B, Jacquemyn H, Dicke M, Poelman EH. Parasitism causes changes in caterpillar odours and associated bacterial communities with consequences for host-location by a hyperparasitoid. PLoS Pathog 2023; 19:e1011262. [PMID: 36947551 PMCID: PMC10069771 DOI: 10.1371/journal.ppat.1011262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 04/03/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023] Open
Abstract
Microorganisms living in and on macroorganisms may produce microbial volatile compounds (mVOCs) that characterise organismal odours. The mVOCs might thereby provide a reliable cue to carnivorous enemies in locating their host or prey. Parasitism by parasitoid wasps might alter the microbiome of their caterpillar host, affecting organismal odours and interactions with insects of higher trophic levels such as hyperparasitoids. Hyperparasitoids parasitise larvae or pupae of parasitoids, which are often concealed or inconspicuous. Odours of parasitised caterpillars aid them to locate their host, but the origin of these odours and its relationship to the caterpillar microbiome are unknown. Here, we analysed the odours and microbiome of the large cabbage white caterpillar Pieris brassicae in relation to parasitism by its endoparasitoid Cotesia glomerata. We identified how bacterial presence in and on the caterpillars is correlated with caterpillar odours and tested the attractiveness of parasitised and unparasitised caterpillars to the hyperparasitoid Baryscapus galactopus. We manipulated the presence of the external microbiome and the transient internal microbiome of caterpillars to identify the microbial origin of odours. We found that parasitism by C. glomerata led to the production of five characteristic volatile products and significantly affected the internal and external microbiome of the caterpillar, which were both found to have a significant correlation with caterpillar odours. The preference of the hyperparasitoid was correlated with the presence of the external microbiome. Likely, the changes in external microbiome and body odour after parasitism were driven by the resident internal microbiome of caterpillars, where the bacterium Wolbachia sp. was only present after parasitism. Micro-injection of Wolbachia in unparasitised caterpillars increased hyperparasitoid attraction to the caterpillars compared to untreated caterpillars, while no differences were found compared to parasitised caterpillars. In conclusion, our results indicate that host-parasite interactions can affect multi-trophic interactions and hyperparasitoid olfaction through alterations of the microbiome.
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Affiliation(s)
- Mitchel E Bourne
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Gabriele Gloder
- CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department M2S, KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Berhane T Weldegergis
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Marijn Slingerland
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Andrea Ceribelli
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Sam Crauwels
- CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department M2S, KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Bart Lievens
- CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department M2S, KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Hans Jacquemyn
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
- Laboratory of Plant Conservation and Population Biology, Biology Department, KU Leuven, Leuven, Belgium
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Erik H Poelman
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
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Bauer DuMont VL, White SL, Zinshteyn D, Aquadro CF. Molecular population genetics of Sex-lethal ( Sxl) in the Drosophila melanogaster species group: a locus that genetically interacts with Wolbachia pipientis in Drosophila melanogaster. G3 GENES|GENOMES|GENETICS 2021; 11:6296609. [PMID: 34849818 PMCID: PMC8496275 DOI: 10.1093/g3journal/jkab197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022]
Abstract
Abstract
Sex-lethal (Sxl) is the sex determination switch in Drosophila, and also plays a critical role in germ-line stem cell daughter differentiation in Drosophila melanogaster. Three female-sterile alleles at Sxl in D. melanogaster were previously shown to genetically interact to varying degrees with the maternally inherited endosymbiont Wolbachia pipientis. Given this genetic interaction and W. pipientis’ ability to manipulate reproduction in Drosophila, we carried out a careful study of both the population genetics (within four Drosophila species) and molecular evolutionary analysis (across 20 Drosophila species) of Sxl. Consistent with earlier studies, we find that selective constraint has played a prominent role in Sxl’s molecular evolution within Drosophila, but we also observe patterns that suggest both episodic bursts of protein evolution and recent positive selection at Sxl. The episodic nature of Sxl’s protein evolution is discussed in light of its genetic interaction with W. pipientis.
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Affiliation(s)
| | - Simone L White
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Daniel Zinshteyn
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Charles F Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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Reliance of Wolbachia on High Rates of Host Proteolysis Revealed by a Genome-Wide RNAi Screen of Drosophila Cells. Genetics 2017; 205:1473-1488. [PMID: 28159754 DOI: 10.1534/genetics.116.198903] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/27/2017] [Indexed: 11/18/2022] Open
Abstract
Wolbachia are gram-negative, obligate, intracellular bacteria carried by a majority of insect species worldwide. Here we use a Wolbachia-infected Drosophila cell line and genome-wide RNA interference (RNAi) screening to identify host factors that influence Wolbachia titer. By screening an RNAi library targeting 15,699 transcribed host genes, we identified 36 candidate genes that dramatically reduced Wolbachia titer and 41 that increased Wolbachia titer. Host gene knockdowns that reduced Wolbachia titer spanned a broad array of biological pathways including genes that influenced mitochondrial function and lipid metabolism. In addition, knockdown of seven genes in the host ubiquitin and proteolysis pathways significantly reduced Wolbachia titer. To test the in vivo relevance of these results, we found that drug and mutant inhibition of proteolysis reduced levels of Wolbachia in the Drosophila oocyte. The presence of Wolbachia in either cell lines or oocytes dramatically alters the distribution and abundance of ubiquitinated proteins. Functional studies revealed that maintenance of Wolbachia titer relies on an intact host Endoplasmic Reticulum (ER)-associated protein degradation pathway (ERAD). Accordingly, electron microscopy studies demonstrated that Wolbachia is intimately associated with the host ER and dramatically alters the morphology of this organelle. Given Wolbachia lack essential amino acid biosynthetic pathways, the reliance of Wolbachia on high rates of host proteolysis via ubiquitination and the ERAD pathways may be a key mechanism for provisioning Wolbachia with amino acids. In addition, the reliance of Wolbachia on the ERAD pathway and disruption of ER morphology suggests a previously unsuspected mechanism for Wolbachia's potent ability to prevent RNA virus replication.
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Wallau GL, da Rosa MT, De Ré FC, Loreto ELS. Wolbachia from Drosophila incompta: just a hitchhiker shared by Drosophila in the New and Old World? INSECT MOLECULAR BIOLOGY 2016; 25:487-499. [PMID: 27122079 DOI: 10.1111/imb.12237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Wolbachia are intracellular endosymbionts that infect arthropods and filarial nematodes, occasionally causing a wide variety of modifications in host biology, such as male-killing and cytoplasmic incompatibility (CI), amongst others. This study assembled draft genomes for Wolbachia infecting Drosophila incompta, a species that uses flowers as exclusive breeding and feeding sites, in two distinct Brazilian populations. The absence of four genes involved in CI from this genome, together with literature reports of low frequencies of infected flies in wild populations that contain high mitogenome polymorphism, suggests that this bacterium does not induce CI in D. incompta. Phylogenomic analysis placed Wolbachia infecting D. incompta as closely related to the wMel strain which received such name since it was originally detected in Drosophila melanogaster. In addition, phylogenetic analysis using the Wolbachia surface protein gene and five genes used for multilocus sequence typing of Wolbachia found infecting Drosophila and other arthropod species of Old and New World displayed a complex evolutionary scenario involving recent horizontal transfer bursts in all major clades of Wolbachia pipens belonging to the supergroup A in both geographical regions.
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Affiliation(s)
- G L Wallau
- PPG Biodiversade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
- Departamento de Entomologia, Centro de Pesquisas Aggeu Magalhães - FIOCRUZ-CPqAM, Recife, PE, Brazil
| | - M T da Rosa
- PPG Biodiversade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - F C De Ré
- PPG Biodiversade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - E L S Loreto
- PPG Biodiversade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
- Departamento Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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Richardson KM, Schiffer M, Griffin PC, Lee SF, Hoffmann AA. Tropical Drosophila pandora carry Wolbachia infections causing cytoplasmic incompatibility or male killing. Evolution 2016; 70:1791-802. [PMID: 27282489 PMCID: PMC4980230 DOI: 10.1111/evo.12981] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 06/01/2016] [Indexed: 01/14/2023]
Abstract
Wolbachia infections have been described in several Drosophila species, but relatively few have been assessed for phenotypic effects. Cytoplasmic incompatibility (CI) is the most common phenotypic effect that has been detected, while some infections cause male killing or feminization, and many Wolbachia infections have few host effects. Here, we describe two new infections in a recently described species, Drosophila pandora, one of which causes near-complete CI and near-perfect maternal transmission (the "CI" strain). The other infection is a male killer (the "MK" strain), which we confirm by observing reinitiation of male production following tetracycline treatment. No incompatibility was detected in crosses between CI strain males and MK strain females, and rare MK males do not cause CI. Molecular analyses indicate that the CI and MK infections are distantly related and the CI infection is closely related to the wRi infection of Drosophila simulans. Two population surveys indicate that all individuals are infected with Wolbachia, but the MK infection is uncommon. Given patterns of incompatibility among the strains, the infection dynamics is expected to be governed by the relative fitness of the females, suggesting that the CI infection should have a higher fitness. This was evidenced by changes in infection frequencies and sex ratios in population cages initiated at different starting frequencies of the infections.
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Affiliation(s)
- Kelly M Richardson
- School of BioSciences, Bio21 Institute, The University of Melbourne, Victoria, 3010, Australia
| | - Michele Schiffer
- School of BioSciences, Bio21 Institute, The University of Melbourne, Victoria, 3010, Australia
| | - Philippa C Griffin
- School of BioSciences, Bio21 Institute, The University of Melbourne, Victoria, 3010, Australia
| | - Siu F Lee
- School of BioSciences, Bio21 Institute, The University of Melbourne, Victoria, 3010, Australia
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Victoria, 3010, Australia.
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Iwase S, Tani S, Saeki Y, Tuda M, Haran J, Skuhrovec J, Takagi M. Dynamics of infection with Wolbachia in Hypera postica (Coleoptera: Curculionidae) during invasion and establishment. Biol Invasions 2015. [DOI: 10.1007/s10530-015-0985-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Hamm CA, Begun DJ, Vo A, Smith CCR, Saelao P, Shaver AO, Jaenike J, Turelli M. Wolbachia do not live by reproductive manipulation alone: infection polymorphism in Drosophila suzukii and D. subpulchrella. Mol Ecol 2014; 23:4871-85. [PMID: 25156506 DOI: 10.1111/mec.12901] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/09/2014] [Accepted: 08/15/2014] [Indexed: 01/30/2023]
Abstract
Drosophila suzukii recently invaded North America and Europe. Populations in Hawaii, California, New York and Nova Scotia are polymorphic for Wolbachia, typically with <20% infection frequency. The Wolbachia in D. suzukii, denoted wSuz, is closely related to wRi, the variant prevalent in continental populations of D. simulans. wSuz is also nearly identical to Wolbachia found in D. subpulchrella, plausibly D. suzukii's sister species. This suggests vertical Wolbachia transmission through cladogenesis ('cladogenic transmission'). The widespread occurrence of 7-20% infection frequencies indicates a stable polymorphism. wSuz is imperfectly maternally transmitted, with wild infected females producing on average 5-10% uninfected progeny. As expected from its low frequency, wSuz produces no cytoplasmic incompatibility (CI), that is, no increased embryo mortality when infected males mate with uninfected females, and no appreciable sex-ratio distortion. The persistence of wSuz despite imperfect maternal transmission suggests positive fitness effects. Assuming a balance between selection and imperfect transmission, we expect a fitness advantage on the order of 20%. Unexpectedly, Wolbachia-infected females produce fewer progeny than do uninfected females. We do not yet understand the maintenance of wSuz in D. suzukii. The absence of detectable CI in D. suzukii and D. subpulchrella makes it unlikely that CI-based mechanisms could be used to control this species without transinfection using novel Wolbachia. Contrary to their reputation as horizontally transmitted reproductive parasites, many Wolbachia infections are acquired through introgression or cladogenesis and many cause no appreciable reproductive manipulation. Such infections, likely to be mutualistic, may be central to understanding the pervasiveness of Wolbachia among arthropods.
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Affiliation(s)
- Christopher A Hamm
- Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA, 95616, USA
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