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Shropshire JD, Conner WR, Vanderpool D, Hoffmann AA, Turelli M, Cooper BS. Rapid host switching of Wolbachia and even more rapid turnover of their phages and incompatibility-causing loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.04.569981. [PMID: 38105949 PMCID: PMC10723362 DOI: 10.1101/2023.12.04.569981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
About half of all insect species carry maternally inherited Wolbachia alphaproteobacteria, making Wolbachia the most common endosymbionts known in nature. Often Wolbachia spread to high frequencies within populations due to cytoplasmic incompatibility (CI), a Wolbachia-induced sperm modification caused by prophage-associated genes (cifs) that kill embryos without Wolbachia. Several Wolbachia variants also block viruses, including wMel from Drosophila melanogaster when transinfected into the mosquito Aedes aegypti. CI enables the establishment and stable maintenance of pathogen-blocking wMel in natural Ae. aegypti populations. These transinfections are reducing dengue disease incidence on multiple continents. While it has long been known that closely related Wolbachia occupy distantly related hosts, the timing of Wolbachia host switching and molecular evolution has not been widely quantified. We provide a new, conservative calibration for Wolbachia chronograms based on examples of co-divergence of Wolbachia and their insect hosts. Synthesizing publicly available and new genomic data, we use our calibration to demonstrate that wMel-like variants separated by only about 370,000 years have naturally colonized holometabolous dipteran and hymenopteran insects that diverged approximately 350 million years ago. Data from Wolbachia variants closely related to those currently dominant in D. melanogaster and D. simulans illustrate that cifs are rapidly acquired and lost among Wolbachia genomes, on a time scale of 104-105 years. This turnover occurs with and without the Wovirus prophages that contain them, with closely related cifs found in distantly related phages and distantly related cifs found in closely related phages. We present evidence for purifying selection on CI rescue function and on particular Cif protein domains. Our results quantify the tempo and mode of rapid host switching and horizontal gene transfer that underlie the spread and diversity of Wolbachia sampled from diverse host species. The wMel variants we highlight from hosts in different climates may offer new options for broadening Wolbachia-based biocontrol of diseases and pests.
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Affiliation(s)
- J. Dylan Shropshire
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - William R. Conner
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Dan Vanderpool
- Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, Montana, USA
| | - Ary A. Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Michael Turelli
- Department of Evolution and Ecology, University of California, Davis, California, USA
| | - Brandon S. Cooper
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
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2
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Hague MTJ, Wheeler TB, Cooper BS. Comparative analysis of Wolbachia maternal transmission and localization in host ovaries. Commun Biol 2024; 7:727. [PMID: 38877196 PMCID: PMC11178894 DOI: 10.1038/s42003-024-06431-y] [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: 02/17/2024] [Accepted: 06/07/2024] [Indexed: 06/16/2024] Open
Abstract
Many insects and other animals carry microbial endosymbionts that influence their reproduction and fitness. These relationships only persist if endosymbionts are reliably transmitted from one host generation to the next. Wolbachia are maternally transmitted endosymbionts found in most insect species, but transmission rates can vary across environments. Maternal transmission of wMel Wolbachia depends on temperature in natural Drosophila melanogaster hosts and in transinfected Aedes aegypti, where wMel is used to block pathogens that cause human disease. In D. melanogaster, wMel transmission declines in the cold as Wolbachia become less abundant in host ovaries and at the posterior pole plasm (the site of germline formation) in mature oocytes. Here, we assess how temperature affects maternal transmission and underlying patterns of Wolbachia localization across 10 Wolbachia strains diverged up to 50 million years-including strains closely related to wMel-and their natural Drosophila hosts. Many Wolbachia maintain high transmission rates across temperatures, despite highly variable (and sometimes low) levels of Wolbachia in the ovaries and at the developing germline in late-stage oocytes. Identifying strains like closely related wMel-like Wolbachia with stable transmission across variable environmental conditions may improve the efficacy of Wolbachia-based biocontrol efforts as they expand into globally diverse environments.
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Affiliation(s)
| | - Timothy B Wheeler
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Brandon S Cooper
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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3
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Hague MT, Wheeler TB, Cooper BS. Comparative analysis of Wolbachia maternal transmission and localization in host ovaries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583170. [PMID: 38496649 PMCID: PMC10942406 DOI: 10.1101/2024.03.03.583170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Many insects and other animals carry microbial endosymbionts that influence their reproduction and fitness. These relationships only persist if endosymbionts are reliably transmitted from one host generation to the next. Wolbachia are maternally transmitted endosymbionts found in most insect species, but transmission rates can vary across environments. Maternal transmission of wMel Wolbachia depends on temperature in natural Drosophila melanogaster hosts and in transinfected Aedes aegypti, where wMel is used to block pathogens that cause human disease. In D. melanogaster, wMel transmission declines in the cold as Wolbachia become less abundant in host ovaries and at the posterior pole plasm (the site of germline formation) in mature oocytes. Here, we assess how temperature affects maternal transmission and underlying patterns of Wolbachia localization across 10 Wolbachia strains diverged up to 50 million years-including strains closely related to wMel-and their natural Drosophila hosts. Many Wolbachia maintain high transmission rates across temperatures, despite highly variable (and sometimes low) levels of Wolbachia in the ovaries and at the developing germline in late-stage oocytes. Identifying strains like closely related wMel-like Wolbachia with stable transmission across variable environmental conditions may improve the efficacy of Wolbachia-based biocontrol efforts as they expand into globally diverse environments.
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Affiliation(s)
| | - Timothy B. Wheeler
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Brandon S. Cooper
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
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4
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Trouche B, Schrieke H, Duron O, Eren AM, Reveillaud J. Wolbachia populations across organs of individual Culex pipiens: highly conserved intra-individual core pangenome with inter-individual polymorphisms. ISME COMMUNICATIONS 2024; 4:ycae078. [PMID: 38915450 PMCID: PMC11195471 DOI: 10.1093/ismeco/ycae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 04/26/2024] [Accepted: 06/06/2024] [Indexed: 06/26/2024]
Abstract
Wolbachia is a maternally inherited intracellular bacterium that infects a wide range of arthropods including mosquitoes. The endosymbiont is widely used in biocontrol strategies due to its capacity to modulate arthropod reproduction and limit pathogen transmission. Wolbachia infections in Culex spp. are generally assumed to be monoclonal but the potential presence of genetically distinct Wolbachia subpopulations within and between individual organs has not been investigated using whole genome sequencing. Here we reconstructed Wolbachia genomes from ovary and midgut metagenomes of single naturally infected Culex pipiens mosquitoes from Southern France to investigate patterns of intra- and inter-individual differences across mosquito organs. Our analyses revealed a remarkable degree of intra-individual conservancy among Wolbachia genomes from distinct organs of the same mosquito both at the level of gene presence-absence signal and single-nucleotide polymorphisms (SNPs). Yet, we identified several synonymous and non-synonymous substitutions between individuals, demonstrating the presence of some level of genomic heterogeneity among Wolbachia that infect the same C. pipiens field population. Overall, the absence of genetic heterogeneity within Wolbachia populations in a single individual confirms the presence of a dominant Wolbachia that is maintained under strong purifying forces of evolution.
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Affiliation(s)
- Blandine Trouche
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
| | - Hans Schrieke
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
| | - Olivier Duron
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
| | - A Murat Eren
- Marine Biological Laboratory, Woods Hole, MA 02543, United States
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, 26129 Oldenburg, Germany
| | - Julie Reveillaud
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
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5
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Adonyeva NV, Efimov VM, Gruntenko NE. The Effect of Genotype Combinations of Wolbachia and Its Drosophila melanogaster Host on Fertility, Developmental Rate and Heat Stress Resistance of Flies. INSECTS 2023; 14:928. [PMID: 38132601 PMCID: PMC10743879 DOI: 10.3390/insects14120928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
The best-known effect of the intracellular bacterium Wolbachia is its mostly negative influence on the reproduction of the host. However, there is evidence of a positive influence of Wolbachia on the host's resistance to stress, pathogens, and viruses. Here, we analyzed the effects of two Wolbachia strains belonging to wMel and wMelCS genotypes on D. melanogaster traits, such as fertility, survival under acute heat stress, and developmental rate. We found that D. melanogaster lines under study differ significantly in the above-mentioned characteristics, both when the natural infection was preserved, and when it was eliminated. One of Wolbachia strains, wMel, did not affect any of the studied traits. Another strain, wMelPlus, had a significant effect on the development time. Moreover, this effect is observed not only in the line in which it was discovered but also in the one it was transferred to. When transferred to a new line, wMelPlus also caused changes in survival under heat stress. Thus, it could be concluded that Wolbachia-Drosophila interaction depends on the genotypes of both the host and the symbiont, but some Wolbachia effects could depend not on the genotypes, but on the fact of recent transfer of the symbiont.
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Affiliation(s)
- Natalya V. Adonyeva
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia; (N.V.A.); (V.M.E.)
| | - Vadim M. Efimov
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia; (N.V.A.); (V.M.E.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nataly E. Gruntenko
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia; (N.V.A.); (V.M.E.)
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6
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Strunov A, Kirchner S, Schindelar J, Kruckenhauser L, Haring E, Kapun M. Historic Museum Samples Provide Evidence for a Recent Replacement of Wolbachia Types in European Drosophila melanogaster. Mol Biol Evol 2023; 40:msad258. [PMID: 37995370 PMCID: PMC10701101 DOI: 10.1093/molbev/msad258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/23/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
Wolbachia is one of the most common bacterial endosymbionts, which is frequently found in numerous arthropods and nematode taxa. Wolbachia infections can have a strong influence on the evolutionary dynamics of their hosts since these bacteria are reproductive manipulators that affect the fitness and life history of their host species for their own benefit. Host-symbiont interactions with Wolbachia are perhaps best studied in the model organism Drosophila melanogaster, which is naturally infected with at least 5 different variants among which wMel and wMelCS are the most frequent ones. Comparisons of infection types between natural flies and long-term lab stocks have previously indicated that wMelCS represents the ancestral type, which was only very recently replaced by the nowadays dominant wMel in most natural populations. In this study, we took advantage of recently sequenced museum specimens of D. melanogaster that have been collected 90 to 200 yr ago in Northern Europe to test this hypothesis. Our comparison to contemporary Wolbachia samples provides compelling support for the replacement hypothesis. Our analyses show that sequencing data from historic museum specimens and their bycatch are an emerging and unprecedented resource to address fundamental questions about evolutionary dynamics in host-symbiont interactions. However, we also identified contamination with DNA from crickets that resulted in co-contamination with cricket-specific Wolbachia in several samples. These results underpin the need for rigorous quality assessments of museomic data sets to account for contamination as a source of error that may strongly influence biological interpretations if it remains undetected.
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Affiliation(s)
- Anton Strunov
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Sandra Kirchner
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
| | - Julia Schindelar
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
| | - Luise Kruckenhauser
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
- Department for Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Elisabeth Haring
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
- Department for Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Martin Kapun
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
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7
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Adams GJ, O'Brien PA. The unified theory of sleep: Eukaryotes endosymbiotic relationship with mitochondria and REM the push-back response for awakening. Neurobiol Sleep Circadian Rhythms 2023; 15:100100. [PMID: 37484687 PMCID: PMC10362302 DOI: 10.1016/j.nbscr.2023.100100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/25/2023] Open
Abstract
The Unified Theory suggests that sleep is a process that developed in eukaryotic animals from a relationship with an endosymbiotic bacterium. Over evolutionary time the bacterium evolved into the modern mitochondrion that continues to exert an effect on sleep patterns, e.g. the bacterium Wolbachia establishes an endosymbiotic relationship with Drosophila and many other species of insects and is able to change the host's behaviour by making it sleep. The hypothesis is supported by other host-parasite relationships, e.g., Trypanosoma brucei which causes day-time sleepiness and night-time insomnia in humans and cattle. For eukaryotes such as Monocercomonoids that don't contain mitochondria we find no evidence of them sleeping. Mitochondria produce the neurotransmitter gamma aminobutyric acid (GABA), and ornithine a precursor of the neurotransmitter GABA, together with substances such as 3,4dihydroxy phenylalanine (DOPA) a precursor for the neurotransmitter dopamine: These substances have been shown to affect the sleep/wake cycles in animals such as Drosophilia and Hydra. Eukaryote animals have traded the very positive side of having mitochondria providing aerobic respiration for them with the negative side of having to sleep. NREM (Quiet sleep) is the process endosymbionts have imposed upon their host eukaryotes and REM (Active sleep) is the push-back adaptation of eukaryotes with brains, returning to wakefulness.
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Affiliation(s)
| | - Philip A. O'Brien
- College of Science, Health, Engineering and Education, Murdoch University, WA, Australia
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8
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Medina P, Russell SL, Corbett-Detig R. Deep data mining reveals variable abundance and distribution of microbial reproductive manipulators within and among diverse host species. PLoS One 2023; 18:e0288261. [PMID: 37432953 DOI: 10.1371/journal.pone.0288261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
Bacterial symbionts that manipulate the reproduction of their hosts are important factors in invertebrate ecology and evolution, and are being leveraged for host biological control. Infection prevalence restricts which biological control strategies are possible and is thought to be strongly influenced by the density of symbiont infection within hosts, termed titer. Current methods to estimate infection prevalence and symbiont titers are low-throughput, biased towards sampling infected species, and rarely measure titer. Here we develop a data mining approach to estimate symbiont infection frequencies within host species and titers within host tissues. We applied this approach to screen ~32,000 publicly available sequence samples from the most common symbiont host taxa, discovering 2,083 arthropod and 119 nematode infected samples. From these data, we estimated that Wolbachia infects approximately 44% of all arthropod and 34% of all nematode species, while other reproductive manipulators only infect 1-8% of arthropod and nematode species. Although relative titers within hosts were highly variable within and between arthropod species, a combination of arthropod host species and Wolbachia strain explained approximately 36% of variation in Wolbachia titer across the dataset. To explore potential mechanisms for host control of symbiont titer, we leveraged population genomic data from the model system Drosophila melanogaster. In this host, we found a number of SNPs associated with titer in candidate genes potentially relevant to host interactions with Wolbachia. Our study demonstrates that data mining is a powerful tool to detect bacterial infections and quantify infection intensities, thus opening an array of previously inaccessible data for further analysis in host-symbiont evolution.
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Affiliation(s)
- Paloma Medina
- Genomics Institute, Department of Biomolecular Engineering UC Santa Cruz, Santa Cruz, CA, United States of America
| | - Shelbi L Russell
- Genomics Institute, Department of Biomolecular Engineering UC Santa Cruz, Santa Cruz, CA, United States of America
| | - Russell Corbett-Detig
- Genomics Institute, Department of Biomolecular Engineering UC Santa Cruz, Santa Cruz, CA, United States of America
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9
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Lollar MJ, Biewer-Heisler TJ, Danen CE, Pool JE. Hybrid breakdown in male reproduction between recently diverged Drosophila melanogaster populations has a complex and variable genetic architecture. Evolution 2023; 77:1550-1563. [PMID: 37071601 PMCID: PMC10309968 DOI: 10.1093/evolut/qpad060] [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: 10/25/2022] [Revised: 03/15/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
Secondary contact between formerly isolated populations may result in hybrid breakdown, in which untested allelic combinations in hybrids are maladaptive and limit genetic exchange. Studying early-stage reproductive isolation may yield key insights into the genetic architectures and evolutionary forces underlying the first steps toward speciation. Here, we leverage the recent worldwide expansion of Drosophila melanogaster to test for hybrid breakdown between populations that diverged within the last 13,000 years. We found clear evidence for hybrid breakdown in male reproduction, but not female reproduction or viability, supporting the prediction that hybrid breakdown affects the heterogametic sex first. The frequency of non-reproducing F2 males varied among different crosses involving the same southern African and European populations, as did the qualitative effect of cross direction, implying a genetically variable basis of hybrid breakdown and a role for uniparentally inherited factors. The levels of breakdown observed in F2 males were not recapitulated in backcrossed individuals, consistent with the existence of incompatibilities with at least three partners. Thus, some of the very first steps toward reproductive isolation could involve incompatibilities with complex and variable genetic architectures. Collectively, our findings emphasize this system's potential for future studies on the genetic and organismal basis of early-stage reproductive isolation.
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Affiliation(s)
- Matthew J Lollar
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, United States
| | | | - Clarice E Danen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, United States
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10
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Frantz SI, Small CM, Cresko WA, Singh ND. Ovarian transcriptional response to Wolbachia infection in D. melanogaster in the context of between-genotype variation in gene expression. G3 (BETHESDA, MD.) 2023; 13:jkad047. [PMID: 36857313 PMCID: PMC10151400 DOI: 10.1093/g3journal/jkad047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 08/22/2022] [Accepted: 01/07/2023] [Indexed: 03/02/2023]
Abstract
Wolbachia is a maternally transmitted endosymbiotic bacteria that infects a wide variety of arthropod and nematode hosts. The effects of Wolbachia on host biology are far-reaching and include changes in host gene expression. However, previous work on the host transcriptional response has generally been investigated in the context of a single host genotype. Thus, the relative effect of Wolbachia infection versus vs. host genotype on gene expression is unknown. Here, we explicitly test the relative roles of Wolbachia infection and host genotype on host gene expression by comparing the ovarian transcriptomes of 4 strains of Drosophila melanogaster (D. melanogaster) infected and uninfected with Wolbachia. Our data suggest that infection explains a small amount of transcriptional variation, particularly in comparison to variation in gene expression among strains. However, infection specifically affects genes related to cell cycle, translation, and metabolism. We also find enrichment of cell division and recombination processes among genes with infection-associated differential expression. Broadly, the transcriptomic changes identified in this study provide novel understanding of the relative magnitude of the effect of Wolbachia infection on gene expression in the context of host genetic variation and also point to genes that are consistently differentially expressed in response to infection among multiple genotypes.
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Affiliation(s)
- Sophia I Frantz
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
| | - Clayton M Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, 97403USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, 97403USA
| | - Nadia D Singh
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
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11
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Dwivedi-Yu JA, Oppler ZJ, Mitchell MW, Song YS, Brisson D. A fast machine-learning-guided primer design pipeline for selective whole genome amplification. PLoS Comput Biol 2023; 19:e1010137. [PMID: 37068103 PMCID: PMC10138271 DOI: 10.1371/journal.pcbi.1010137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 04/27/2023] [Accepted: 03/23/2023] [Indexed: 04/18/2023] Open
Abstract
Addressing many of the major outstanding questions in the fields of microbial evolution and pathogenesis will require analyses of populations of microbial genomes. Although population genomic studies provide the analytical resolution to investigate evolutionary and mechanistic processes at fine spatial and temporal scales-precisely the scales at which these processes occur-microbial population genomic research is currently hindered by the practicalities of obtaining sufficient quantities of the relatively pure microbial genomic DNA necessary for next-generation sequencing. Here we present swga2.0, an optimized and parallelized pipeline to design selective whole genome amplification (SWGA) primer sets. Unlike previous methods, swga2.0 incorporates active and machine learning methods to evaluate the amplification efficacy of individual primers and primer sets. Additionally, swga2.0 optimizes primer set search and evaluation strategies, including parallelization at each stage of the pipeline, to dramatically decrease program runtime. Here we describe the swga2.0 pipeline, including the empirical data used to identify primer and primer set characteristics, that improve amplification performance. Additionally, we evaluate the novel swga2.0 pipeline by designing primer sets that successfully amplify Prevotella melaninogenica, an important component of the lung microbiome in cystic fibrosis patients, from samples dominated by human DNA.
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Affiliation(s)
- Jane A. Dwivedi-Yu
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
- Facebook AI Research, 1 Rathbone Square, London, England
| | - Zachary J. Oppler
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew W. Mitchell
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Coriell Institute for Medical Research, Camden, New Jersey, United States of America
| | - Yun S. Song
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
- Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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12
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Eugénio AT, Marialva MSP, Beldade P. Effects of Wolbachia on Transposable Element Expression Vary Between Drosophila melanogaster Host Genotypes. Genome Biol Evol 2023; 15:7059559. [PMID: 36929176 PMCID: PMC10025071 DOI: 10.1093/gbe/evad036] [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: 08/01/2022] [Revised: 02/13/2023] [Accepted: 02/19/2023] [Indexed: 03/18/2023] Open
Abstract
Transposable elements (TEs) are repetitive DNA sequences capable of changing position in host genomes, thereby causing mutations. TE insertions typically have deleterious effects but they can also be beneficial. Increasing evidence of the contribution of TEs to adaptive evolution further raises interest in understanding what factors impact TE activity. Based on previous studies associating the bacterial endosymbiont Wolbachia with changes in the abundance of piRNAs, a mechanism for TE repression, and to transposition of specific TEs, we hypothesized that Wolbachia infection would interfere with TE activity. We tested this hypothesis by studying the expression of 14 TEs in a panel of 25 Drosophila melanogaster host genotypes, naturally infected with Wolbachia and annotated for TE insertions. The host genotypes differed significantly in Wolbachia titers inside individual flies, with broad-sense heritability around 20%, and in the number of TE insertions, which depended greatly on TE identity. By removing Wolbachia from the target host genotypes, we generated a panel of 25 pairs of Wolbachia-positive and Wolbachia-negative lines in which we quantified transcription levels for our target TEs. We found variation in TE expression that was dependent on Wolbachia status, TE identity, and host genotype. Comparing between pairs of Wolbachia-positive and Wolbachia-negative flies, we found that Wolbachia removal affected TE expression in 21.1% of the TE-genotype combinations tested, with up to 2.3 times differences in the median level of transcript. Our data show that Wolbachia can impact TE activity in host genomes, underscoring the importance this endosymbiont can have in the generation of genetic novelty in hosts.
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Affiliation(s)
| | | | - Patrícia Beldade
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- cE3c (Center for Ecology, Evolution and Environmental Changes) and CHANGE (Global Change and Sustainability Institute), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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13
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Martinez J, Ross PA, Gu X, Ant TH, Murdochy SM, Tong L, da Silva Filipe A, Hoffmann AA, Sinkins SP. Genomic and Phenotypic Comparisons Reveal Distinct Variants of Wolbachia Strain wAlbB. Appl Environ Microbiol 2022; 88:e0141222. [PMID: 36318064 PMCID: PMC9680635 DOI: 10.1128/aem.01412-22] [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: 08/19/2022] [Accepted: 09/26/2022] [Indexed: 11/23/2022] Open
Abstract
The intracellular bacterium Wolbachia inhibits virus replication and is being harnessed around the world to fight mosquito-borne diseases through releases of mosquitoes carrying the symbiont. Wolbachia strains vary in their ability to invade mosquito populations and suppress viruses in part due to differences in their density within the insect and associated fitness costs. Using whole-genome sequencing, we demonstrate the existence of two variants in wAlbB, a Wolbachia strain being released in natural populations of Aedes aegypti mosquitoes. The two variants display striking differences in genome architecture and gene content. Differences in the presence/absence of 52 genes between variants include genes located in prophage regions and others potentially involved in controlling the symbiont's density. Importantly, we show that these genetic differences correlate with variation in wAlbB density and its tolerance to heat stress, suggesting that different wAlbB variants may be better suited for field deployment depending on local environmental conditions. Finally, we found that the wAlbB genome remained stable following its introduction in a Malaysian mosquito population. Our results highlight the need for further genomic and phenotypic characterization of Wolbachia strains in order to inform ongoing Wolbachia-based programs and improve the selection of optimal strains in future field interventions. IMPORTANCE Dengue is a viral disease transmitted by Aedes mosquitoes that threatens around half of the world population. Recent advances in dengue control involve the introduction of Wolbachia bacterial symbionts with antiviral properties into mosquito populations, which can lead to dramatic decreases in the incidence of the disease. In light of these promising results, there is a crucial need to better understand the factors affecting the success of such strategies, in particular the choice of Wolbachia strain for field releases and the potential for evolutionary changes. Here, we characterized two variants of a Wolbachia strain used for dengue control that differ at the genomic level and in their ability to replicate within the mosquito. We also found no evidence for the evolution of the symbiont within the 2 years following its deployment in Malaysia. Our results have implications for current and future Wolbachia-based health interventions.
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Affiliation(s)
- Julien Martinez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Perran A. Ross
- Pest and Environmental Adaptation Research Group, Bio21 Institute, the University of Melbourne, Parkville, VIC, Australia
| | - Xinyue Gu
- Pest and Environmental Adaptation Research Group, Bio21 Institute, the University of Melbourne, Parkville, VIC, Australia
| | - Thomas H. Ant
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Shivan M. Murdochy
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ary A. Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute, the University of Melbourne, Parkville, VIC, Australia
| | - Steven P. Sinkins
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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14
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Ryabinin AS, Shishkina OD, Ilinsky YY, Bykov RA. Rare Wolbachia genotypes in laboratory Drosophila melanogaster strains. Vavilovskii Zhurnal Genet Selektsii 2022; 26:553-559. [PMID: 36313820 PMCID: PMC9556306 DOI: 10.18699/vjgb-22-67] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 11/07/2022] Open
Abstract
Symbiotic bacteria of the genus Wolbachia are widespread in Drosophila melanogaster populations. Based on the polymorphism of the Wolbachia genome, the symbionts’ diversity in D. melanogaster is presented by two groups: MEL (wMel, wMel2, wMel3 and wMel4) and CS (wMelCS and wMelCS2). The wMel genotype is predominant in natural D. melanogaster populations and is distributed all over the world. The CS genotypes, on the other hand, are of particular interest because it is unclear how they are maintained in the fruit f ly populations since they should have been eliminated from them due to their low frequency and genetic drift or been replaced by the wMel genotype. However, this is not what is really observed, which means these genotypes are supported by selection. It is known that the wMelPlus strain of the wMelCS genotype can increase the lifespan of infected f lies at high temperatures. The same genotype also increases the intensity of dopamine metabolism in Drosophila compared to the MEL-group genotypes. In the present study, we searched for the rare Wolbachia wMelCS and wMelCS2 genotypes, as well as for new genotypes in wild-type D. melanogaster strains and in several mutant laboratory strains. The symbiont was found in all populations, in 200 out of 385 wild-type strains and in 83 out of 170 mutant strains. Wolbachia diversity in D. melanogaster wild-type strains was represented by the wMel, wMelCS and wMelCS2 genotypes. More than 90 % of the infected strains carried wMel; 9 %, wMelCS2; and only two strains were found to carry wMelCS. No new Wolbachia genotypes were found. The northernmost point reported for the wMelCS2 genotype was Izhevsk city (Udmurtia, Russia). For the f irst time the wMelCS2 genotype was detected in D. melanogaster from the Sakhalin Island, and wMelCS, in the f lies from Nalchik (the North Caucasus). A comparison of Wolbachia genetic diversity between the wild-type laboratory strains and previously obtained data on mutant laboratory strains demonstrated differences in the frequencies of rare CS genotypes, which were more prevalent in mutant strains, apparently due to the breeding history of these Drosophila strains
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Affiliation(s)
- A S Ryabinin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O D Shishkina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yu Yu Ilinsky
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - R A Bykov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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15
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Shastry V, Bell KL, Buerkle CA, Fordyce JA, Forister ML, Gompert Z, Lebeis SL, Lucas LK, Marion ZH, Nice CC. A continental-scale survey of Wolbachia infections in blue butterflies reveals evidence of interspecific transfer and invasion dynamics. G3 GENES|GENOMES|GENETICS 2022; 12:6670626. [PMID: 35976120 PMCID: PMC9526071 DOI: 10.1093/g3journal/jkac213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022]
Abstract
Infections by maternally inherited bacterial endosymbionts, especially Wolbachia, are common in insects and other invertebrates but infection dynamics across species ranges are largely under studied. Specifically, we lack a broad understanding of the origin of Wolbachia infections in novel hosts, and the historical and geographical dynamics of infections that are critical for identifying the factors governing their spread. We used Genotype-by-Sequencing data from previous population genomics studies for range-wide surveys of Wolbachia presence and genetic diversity in North American butterflies of the genus Lycaeides. As few as one sequence read identified by assembly to a Wolbachia reference genome provided high accuracy in detecting infections in host butterflies as determined by confirmatory PCR tests, and maximum accuracy was achieved with a threshold of only 5 sequence reads per host individual. Using this threshold, we detected Wolbachia in all but 2 of the 107 sampling localities spanning the continent, with infection frequencies within populations ranging from 0% to 100% of individuals, but with most localities having high infection frequencies (mean = 91% infection rate). Three major lineages of Wolbachia were identified as separate strains that appear to represent 3 separate invasions of Lycaeides butterflies by Wolbachia. Overall, we found extensive evidence for acquisition of Wolbachia through interspecific transfer between host lineages. Strain wLycC was confined to a single butterfly taxon, hybrid lineages derived from it, and closely adjacent populations in other taxa. While the other 2 strains were detected throughout the rest of the continent, strain wLycB almost always co-occurred with wLycA. Our demographic modeling suggests wLycB is a recent invasion. Within strain wLycA, the 2 most frequent haplotypes are confined almost exclusively to separate butterfly taxa with haplotype A1 observed largely in Lycaeides melissa and haplotype A2 observed most often in Lycaeides idas localities, consistent with either cladogenic mode of infection acquisition from a common ancestor or by hybridization and accompanying mutation. More than 1 major Wolbachia strain was observed in 15 localities. These results demonstrate the utility of using resequencing data from hosts to quantify Wolbachia genetic variation and infection frequency and provide evidence of multiple colonizations of novel hosts through hybridization between butterfly lineages and complex dynamics between Wolbachia strains.
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Affiliation(s)
- Vivaswat Shastry
- Committee on Genetics, Genomics and Systems Biology, University of Chicago , Chicago, IL 60637, USA
| | - Katherine L Bell
- Department of Biology, University of Nevada , Reno, NV 89557, USA
| | - C Alex Buerkle
- Department of Botany, University of Wyoming , Laramie, WY 82071, USA
| | - James A Fordyce
- Department of Ecology & Evolutionary Biology, University of Tennessee , Knoxville, TN 37996, USA
| | | | | | - Sarah L Lebeis
- Department of Microbiology & Molecular Genetics, Michigan State University , East Lansing, MI 48824, USA
| | - Lauren K Lucas
- Department of Biology, Utah State University , Logan, UT 84322, USA
| | - Zach H Marion
- Bio-Protection Research Centre, School of Biological Sciences, University of Canterbury , Christchurch, New Zealand
| | - Chris C Nice
- Department of Biology, Population and Conservation Biology, Texas State University , San Marcos, TX 78666, USA
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16
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Shropshire JD, Hamant E, Conner WR, Cooper BS. cifB-transcript levels largely explain cytoplasmic incompatibility variation across divergent Wolbachia. PNAS NEXUS 2022; 1:pgac099. [PMID: 35967981 PMCID: PMC9364212 DOI: 10.1093/pnasnexus/pgac099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/23/2022] [Indexed: 02/05/2023]
Abstract
Divergent hosts often associate with intracellular microbes that influence their fitness. Maternally transmitted Wolbachia bacteria are the most common of these endosymbionts, due largely to cytoplasmic incompatibility (CI) that kills uninfected embryos fertilized by Wolbachia-infected males. Closely related infections in females rescue CI, providing a relative fitness advantage that drives Wolbachia to high frequencies. One prophage-associated gene (cifA) governs rescue, and two contribute to CI (cifA and cifB), but CI strength ranges from very strong to very weak for unknown reasons. Here, we investigate CI-strength variation and its mechanistic underpinnings in a phylogenetic context across 20 million years (MY) of Wolbachia evolution in Drosophila hosts diverged up to 50 MY. These Wolbachia encode diverse Cif proteins (100% to 7.4% pairwise similarity), and AlphaFold structural analyses suggest that CifB sequence similarities do not predict structural similarities. We demonstrate that cifB-transcript levels in testes explain CI strength across all but two focal systems. Despite phylogenetic discordance among cifs and the bulk of the Wolbachia genome, closely related Wolbachia tend to cause similar CI strengths and transcribe cifB at similar levels. This indicates that other non-cif regions of the Wolbachia genome modulate cif-transcript levels. CI strength also increases with the length of the host's larval life stage, presumably due to prolonged cif action. Our findings reveal that cifB-transcript levels largely explain CI strength, while highlighting other covariates. Elucidating CI's mechanism contributes to our understanding of Wolbachia spread in natural systems and to improving the efficacy of CI-based biocontrol of arboviruses and agricultural pests globally.
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Affiliation(s)
| | - Emily Hamant
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - William R Conner
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Brandon S Cooper
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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17
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Strunov A, Lerch S, Blanckenhorn WU, Miller WJ, Kapun M. Complex effects of environment and Wolbachia infections on the life history of Drosophila melanogaster hosts. J Evol Biol 2022; 35:788-802. [PMID: 35532932 PMCID: PMC9321091 DOI: 10.1111/jeb.14016] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 12/29/2022]
Abstract
Wolbachia bacteria are common endosymbionts of many arthropods found in gonads and various somatic tissues. They manipulate host reproduction to enhance their transmission and confer complex effects on fitness-related traits. Some of these effects can serve to increase the survival and transmission efficiency of Wolbachia in the host population. The Wolbachia-Drosophila melanogaster system represents a powerful model to study the evolutionary dynamics of host-microbe interactions and infections. Over the past decades, there has been a replacement of the ancestral wMelCS Wolbachia variant by the more recent wMel variant in worldwide D. melanogaster populations, but the reasons remain unknown. To investigate how environmental change and genetic variation of the symbiont affect host developmental and adult life-history traits, we compared effects of both Wolbachia variants and uninfected controls in wild-caught D. melanogaster strains at three developmental temperatures. While Wolbachia did not influence any developmental life-history traits, we found that both lifespan and fecundity of host females were increased without apparent fitness trade-offs. Interestingly, wMelCS-infected flies were more fecund than uninfected and wMel-infected flies. By contrast, males infected with wMel died sooner, indicating sex-specific effects of infection that are specific to the Wolbachia variant. Our study uncovered complex temperature-specific effects of Wolbachia infections, which suggests that symbiont-host interactions in nature are strongly dependent on the genotypes of both partners and the thermal environment.
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Affiliation(s)
- Anton Strunov
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Sina Lerch
- Department of Cell and Developmental BiologyCenter for Anatomy and Cell BiologyMedical University of ViennaWienAustria
| | - Wolf U. Blanckenhorn
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Wolfgang J. Miller
- Department of Cell and Developmental BiologyCenter for Anatomy and Cell BiologyMedical University of ViennaWienAustria
| | - Martin Kapun
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
- Department of Cell and Developmental BiologyCenter for Anatomy and Cell BiologyMedical University of ViennaWienAustria
- Natural History Museum of ViennaWienAustria
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18
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Burdina EV, Gruntenko NE. Physiological Aspects of Wolbachia pipientis–Drosophila melanogaster Relationship. J EVOL BIOCHEM PHYS+ 2022. [DOI: 10.1134/s0022093022020016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Camus MF, Alexander-Lawrie B, Sharbrough J, Hurst GDD. Inheritance through the cytoplasm. Heredity (Edinb) 2022; 129:31-43. [PMID: 35525886 PMCID: PMC9273588 DOI: 10.1038/s41437-022-00540-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022] Open
Abstract
Most heritable information in eukaryotic cells is encoded in the nuclear genome, with inheritance patterns following classic Mendelian segregation. Genomes residing in the cytoplasm, however, prove to be a peculiar exception to this rule. Cytoplasmic genetic elements are generally maternally inherited, although there are several exceptions where these are paternally, biparentally or doubly-uniparentally inherited. In this review, we examine the diversity and peculiarities of cytoplasmically inherited genomes, and the broad evolutionary consequences that non-Mendelian inheritance brings. We first explore the origins of vertical transmission and uniparental inheritance, before detailing the vast diversity of cytoplasmic inheritance systems across Eukaryota. We then describe the evolution of genomic organisation across lineages, how this process has been shaped by interactions with the nuclear genome and population genetics dynamics. Finally, we discuss how both nuclear and cytoplasmic genomes have evolved to co-inhabit the same host cell via one of the longest symbiotic processes, and all the opportunities for intergenomic conflict that arise due to divergence in inheritance patterns. In sum, we cannot understand the evolution of eukaryotes without understanding hereditary symbiosis.
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Affiliation(s)
- M Florencia Camus
- Department of Genetics, Evolution and Environment, University College London, London, UK.
| | | | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, England
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20
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Palma F, Mangone I, Janowicz A, Moura A, Chiaverini A, Torresi M, Garofolo G, Criscuolo A, Brisse S, Di Pasquale A, Cammà C, Radomski N. In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes. BMC Genomics 2022; 23:235. [PMID: 35346021 PMCID: PMC8961897 DOI: 10.1186/s12864-022-08437-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/28/2022] [Indexed: 02/02/2023] Open
Abstract
Background Whole genome sequencing analyzed by core genome multi-locus sequence typing (cgMLST) is widely used in surveillance of the pathogenic bacteria Listeria monocytogenes. Given the heterogeneity of available bioinformatics tools to define cgMLST alleles, our aim was to identify parameters influencing the precision of cgMLST profiles. Methods We used three L. monocytogenes reference genomes from different phylogenetic lineages and assessed the impact of in vitro (i.e. tested genomes, successive platings, replicates of DNA extraction and sequencing) and in silico parameters (i.e. targeted depth of coverage, depth of coverage, breadth of coverage, assembly metrics, cgMLST workflows, cgMLST completeness) on cgMLST precision made of 1748 core loci. Six cgMLST workflows were tested, comprising assembly-based (BIGSdb, INNUENDO, GENPAT, SeqSphere and BioNumerics) and assembly-free (i.e. kmer-based MentaLiST) allele callers. Principal component analyses and generalized linear models were used to identify the most impactful parameters on cgMLST precision. Results The isolate’s genetic background, cgMLST workflows, cgMLST completeness, as well as depth and breadth of coverage were the parameters that impacted most on cgMLST precision (i.e. identical alleles against reference circular genomes). All workflows performed well at ≥40X of depth of coverage, with high loci detection (> 99.54% for all, except for BioNumerics with 97.78%) and showed consistent cluster definitions using the reference cut-off of ≤7 allele differences. Conclusions This highlights that bioinformatics workflows dedicated to cgMLST allele calling are largely robust when paired-end reads are of high quality and when the sequencing depth is ≥40X. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08437-4.
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21
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Gu X, Ross PA, Rodriguez-Andres J, Robinson KL, Yang Q, Lau MJ, Hoffmann AA. A wMel Wolbachia variant in Aedes aegypti from field-collected Drosophila melanogaster with increased phenotypic stability under heat stress. Environ Microbiol 2022; 24:2119-2135. [PMID: 35319146 PMCID: PMC9544352 DOI: 10.1111/1462-2920.15966] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/15/2022] [Accepted: 03/02/2022] [Indexed: 02/03/2023]
Abstract
Mosquito‐borne diseases remain a major cause of morbidity and mortality. Population replacement strategies involving the wMel strain of Wolbachia are being used widely to control mosquito‐borne diseases. However, these strategies may be influenced by temperature because wMel is vulnerable to heat. wMel infections in Drosophila melanogaster are genetically diverse, but few transinfections of wMel variants have been generated in Aedes aegypti. Here, we successfully transferred a wMel variant (termed wMelM) originating from a field‐collected D. melanogaster into Ae. aegypti. The new wMelM variant (clade I) is genetically distinct from the original wMel transinfection (clade III), and there are no genomic differences between wMelM in its original and transinfected host. We compared wMelM with wMel in its effects on host fitness, temperature tolerance, Wolbachia density, vector competence, cytoplasmic incompatibility and maternal transmission under heat stress in a controlled background. wMelM showed a higher heat tolerance than wMel, likely due to higher overall densities within the mosquito. Both wMel variants had minimal host fitness costs, complete cytoplasmic incompatibility and maternal transmission, and dengue virus blocking under laboratory conditions. Our results highlight phenotypic differences between Wolbachia variants and wMelM shows potential as an alternative strain in areas with strong seasonal temperature fluctuations.
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Affiliation(s)
- Xinyue Gu
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
| | - Perran A Ross
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
| | - Julio Rodriguez-Andres
- Peter Doherty Institute for Infection and Immunity and Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Vic, 3000, Australia
| | - Katie L Robinson
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
| | - Qiong Yang
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
| | - Meng-Jia Lau
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
| | - Ary A Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
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22
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Temperature effects on cellular host-microbe interactions explain continent-wide endosymbiont prevalence. Curr Biol 2022; 32:878-888.e8. [PMID: 34919808 PMCID: PMC8891084 DOI: 10.1016/j.cub.2021.11.065] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/09/2021] [Accepted: 11/26/2021] [Indexed: 01/03/2023]
Abstract
Endosymbioses influence host physiology, reproduction, and fitness, but these relationships require efficient microbe transmission between host generations to persist. Maternally transmitted Wolbachia are the most common known endosymbionts,1 but their frequencies vary widely within and among host populations for unknown reasons.2,3 Here, we integrate genomic, cellular, and phenotypic analyses with mathematical models to provide an unexpectedly simple explanation for global wMel Wolbachia prevalence in Drosophila melanogaster. Cooling temperatures decrease wMel cellular abundance at a key stage of host oogenesis, producing temperature-dependent variation in maternal transmission that plausibly explains latitudinal clines of wMel frequencies on multiple continents. wMel sampled from a temperate climate targets the germline more efficiently in the cold than a recently differentiated tropical variant (∼2,200 years ago), indicative of rapid wMel adaptation to climate. Genomic analyses identify a very narrow list of wMel alleles-most notably, a derived stop codon in the major Wolbachia surface protein WspB-that underlie thermal sensitivity of cellular Wolbachia abundance and covary with temperature globally. Decoupling temperate wMel and host genomes further reduces transmission in the cold, a pattern that is characteristic of host-microbe co-adaptation to a temperate climate. Complex interactions among Wolbachia, hosts, and the environment (GxGxE) mediate wMel cellular abundance and maternal transmission, implicating temperature as a key determinant of Wolbachia spread and equilibrium frequencies, in conjunction with Wolbachia effects on host fitness and reproduction.4,5 Our results motivate the strategic use of locally selected wMel variants for Wolbachia-based biocontrol efforts, which protect millions of individuals from arboviruses that cause human disease.6.
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23
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Dosage sensitivity and exon shuffling shape the landscape of polymorphic duplicates in Drosophila and humans. Nat Ecol Evol 2021; 6:273-287. [PMID: 34969986 DOI: 10.1038/s41559-021-01614-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022]
Abstract
Despite polymorphic duplicate genes' importance for the early stages of duplicate gene evolution, they are less studied than old gene duplicates. Two essential questions thus remain poorly addressed: how does dosage sensitivity, imposed by stoichiometry in protein complexes or by X chromosome dosage compensation, affect the emergence of complete duplicate genes? Do introns facilitate intergenic and intragenic chimaerism as predicted by the theory of exon shuffling? Here, we analysed new data for Drosophila and public data for humans, to characterize polymorphic duplicate genes with respect to dosage, exon-intron structures and allele frequencies. We found that complete duplicate genes are under dosage constraint induced by protein stoichiometry but potentially tolerated by X chromosome dosage compensation. We also found that in the intron-rich human genome, gene fusions and intragenic duplications extensively use intronic breakpoints generating in-frame proteins, in accordance with the theory of exon shuffling. Finally, we found that only a small proportion of complete or partial duplicates are at high frequencies, indicating the deleterious nature of dosage or gene structural changes. Altogether, we demonstrate how mechanistic factors including dosage sensitivity and exon-intron structure shape the short-term functional consequences of gene duplication.
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24
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Bubnell JE, Fernandez-Begne P, Ulbing CKS, Aquadro CF. Diverse wMel variants of Wolbachia pipientis differentially rescue fertility and cytological defects of the bag of marbles partial loss of function mutation in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2021; 11:6365939. [PMID: 34580706 PMCID: PMC8664471 DOI: 10.1093/g3journal/jkab312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022]
Abstract
In Drosophila melanogaster, the maternally inherited endosymbiont Wolbachia pipientis interacts with germline stem cell genes during oogenesis. One such gene, bag of marbles (bam) is the key switch for differentiation and also shows signals of adaptive evolution for protein diversification. These observations have led us to hypothesize that W. pipientis could be driving the adaptive evolution of bam for control of oogenesis. To test this hypothesis, we must understand the specificity of the genetic interaction between bam and W. pipientis. Previously, we documented that the W. pipientis variant, wMel, rescued the fertility of the bamBW hypomorphic mutant as a transheterozygote over a bam null. However, bamBW was generated more than 20 years ago in an uncontrolled genetic background and maintained over a balancer chromosome. Consequently, the chromosome carrying bamBW accumulated mutations that have prevented controlled experiments to further assess the interaction. Here, we used CRISPR/Cas9 to engineer the same single amino acid bam hypomorphic mutation (bamL255F) and a new bam null disruption mutation into the w1118 isogenic background. We assess the fertility of wildtype bam, bamL255F/bamnull hypomorphic, and bamL255F/bamL255F mutant females, each infected individually with 10 W. pipientis wMel variants representing three phylogenetic clades. Overall, we find that all of the W. pipientis variants tested here rescue bam hypomorphic fertility defects with wMelCS-like variants exhibiting the strongest rescue effects. In addition, these variants did not increase wildtype bam female fertility. Therefore, both bam and W. pipientis interact in genotype-specific ways to modulate female fertility, a critical fitness phenotype.
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Affiliation(s)
- Jaclyn E Bubnell
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Paula Fernandez-Begne
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Cynthia K S Ulbing
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Charles F Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
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25
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Dainty KR, Hawkey J, Judd LM, Pacidônio EC, Duyvestyn JM, Gonçalves DS, Lin SY, O'Donnell TB, O'Neill SL, Simmons CP, Holt KE, Flores HA. wMel Wolbachia genome remains stable after 7 years in Australian Aedes aegypti field populations. Microb Genom 2021; 7. [PMID: 34468309 PMCID: PMC8715424 DOI: 10.1099/mgen.0.000641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Infection of wMel Wolbachia in Aedes aegypti imparts two signature features that enable its application for biocontrol of dengue. First, the susceptibility of mosquitoes to viruses such as dengue and Zika is reduced. Second, a reproductive manipulation is caused that enables wMel introgression into wild-type mosquito populations. The long-term success of this method relies, in part, on evolution of the wMel genome not compromising the critical features that make it an attractive biocontrol tool. This study compared the wMel Wolbachia genome at the time of initial releases and 1-7 years post-release in Cairns, Australia. Our results show the wMel genome remains highly conserved up to 7 years post-release in gene sequence, content, synteny and structure. This work suggests the wMel genome is stable in its new mosquito host and, therefore, provides reassurance on the potential for wMel to deliver long-term public-health impacts.
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Affiliation(s)
- Kimberley R Dainty
- Institute of Vector-Borne Disease, Monash University, Melbourne, Victoria, Australia.,Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Etiene C Pacidônio
- Institute of Vector-Borne Disease, Monash University, Melbourne, Victoria, Australia.,World Mosquito Program, Monash University, Melbourne, Victoria, Australia
| | - Johanna M Duyvestyn
- Institute of Vector-Borne Disease, Monash University, Melbourne, Victoria, Australia.,World Mosquito Program, Monash University, Melbourne, Victoria, Australia
| | - Daniela S Gonçalves
- Institute of Vector-Borne Disease, Monash University, Melbourne, Victoria, Australia.,World Mosquito Program, Monash University, Melbourne, Victoria, Australia
| | - Silk Yu Lin
- Institute of Vector-Borne Disease, Monash University, Melbourne, Victoria, Australia.,World Mosquito Program, Monash University, Melbourne, Victoria, Australia
| | - Tanya B O'Donnell
- Institute of Vector-Borne Disease, Monash University, Melbourne, Victoria, Australia.,World Mosquito Program, Monash University, Melbourne, Victoria, Australia
| | - Scott L O'Neill
- Institute of Vector-Borne Disease, Monash University, Melbourne, Victoria, Australia.,World Mosquito Program, Monash University, Melbourne, Victoria, Australia
| | - Cameron P Simmons
- Institute of Vector-Borne Disease, Monash University, Melbourne, Victoria, Australia.,World Mosquito Program, Monash University, Melbourne, Victoria, Australia.,Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Heather A Flores
- Institute of Vector-Borne Disease, Monash University, Melbourne, Victoria, Australia.,World Mosquito Program, Monash University, Melbourne, Victoria, Australia
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26
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Arif S, Gerth M, Hone-Millard WG, Nunes MDS, Dapporto L, Shreeve TG. Evidence for multiple colonisations and Wolbachia infections shaping the genetic structure of the widespread butterfly Polyommatus icarus in the British Isles. Mol Ecol 2021; 30:5196-5213. [PMID: 34402109 DOI: 10.1111/mec.16126] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 12/24/2022]
Abstract
The paradigm of isolation in southern refugia during glacial periods followed by expansions during interglacials, producing limited genetic differentiation in northern areas, dominates European phylogeography. However, the existence of complex structured populations in formerly glaciated areas, and islands connected to mainland areas during glacial maxima, call for alternative explanations. We reconstructed the mtDNA phylogeography of the widespread Polyommatus Icarus butterfly with an emphasis on the formerly glaciated and connected British Isles. We found distinct geographical structuring of CO1 haplogroups, with an ancient lineage restricted to the marginal European areas, including Northern Scotland and Outer Hebrides. Population genomic analyses, using ddRADSeq genomic markers, also reveal substantial genetic structuring within Britain. However, there is negligble mito-nuclear concordance consistent with independent demographic histories of mitochondrial versus nuclear DNA. While mtDNA-Wolbachia associations in northern Britain could account for the geographic structuring of mtDNA across most of the British Isles, for nuclear DNA markers (derived from ddRADseq data) butterflies from France cluster between northern and southern British populations - an observation consistent with a scenario of multiple recolonisation. Taken together our results suggest that contemporary mtDNA structuring in the British Isles (and potentially elsewhere in Europe) largely results from Wolbachia infections, however, nuclear genomic structuring suggests a history of at least two distinct colonisations. This two-stage colonisation scenario has previously been put forth to explain genetic diversity and structuring in other British flora and fauna. Additionally, we also present preliminary evidence for potential Wolbachia-induced feminization in the Outer Hebrides.
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Affiliation(s)
- Saad Arif
- Centre for Functional Genomics, Oxford Brookes University, Oxford, UK.,Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Michael Gerth
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | | | - Maria D S Nunes
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Leonardo Dapporto
- ZEN Laboratory, Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Timothy G Shreeve
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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27
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Abstract
Recent field trials have demonstrated that dengue incidence can be substantially reduced by introgressing strains of the endosymbiotic bacterium Wolbachia into Aedes aegypti mosquito populations. This strategy relies on Wolbachia reducing the susceptibility of Ae. aegypti to disseminated infection by positive-sense RNA viruses like dengue. However, RNA viruses are well known to adapt to antiviral pressures. Here, we review the viral infection stages where selection for Wolbachia-resistant virus variants could occur. We also consider the genetic constraints imposed on viruses that alternate between vertebrate and invertebrate hosts, and the likely selection pressures to which dengue virus might adapt in order to be effectively transmitted by Ae. aegypti that carry Wolbachia. While there are hurdles to dengue viruses developing resistance to Wolbachia, we suggest that long-term surveillance for resistant viruses should be an integral component of Wolbachia-introgression biocontrol programs.
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Affiliation(s)
| | - Heather A. Flores
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, Australia
| | - Cameron P. Simmons
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, Australia
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Johanna E. Fraser
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
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28
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Duarte EH, Carvalho A, López-Madrigal S, Costa J, Teixeira L. Forward genetics in Wolbachia: Regulation of Wolbachia proliferation by the amplification and deletion of an addictive genomic island. PLoS Genet 2021; 17:e1009612. [PMID: 34143770 PMCID: PMC8244876 DOI: 10.1371/journal.pgen.1009612] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/30/2021] [Accepted: 05/18/2021] [Indexed: 01/08/2023] Open
Abstract
Wolbachia is one of the most prevalent bacterial endosymbionts, infecting approximately 40% of terrestrial arthropod species. Wolbachia is often a reproductive parasite but can also provide fitness benefits to its host, as, for example, protection against viral pathogens. This protective effect is currently being applied to fight arboviruses transmission by releasing Wolbachia-transinfected mosquitoes. Titre regulation is a crucial aspect of Wolbachia biology. Higher titres can lead to stronger phenotypes and fidelity of transmission but can have a higher cost to the host. Since Wolbachia is maternally transmitted, its fitness depends on host fitness, and, therefore, its cost to the host may be under selection. Understanding how Wolbachia titres are regulated and other aspects of Wolbachia biology has been hampered by the lack of genetic tools. Here we developed a forward genetic screen to identify new Wolbachia over-proliferative mutant variants. We characterized in detail two new mutants, wMelPop2 and wMelOctoless, and show that the amplification or loss of the Octomom genomic region lead to over-proliferation. These results confirm previous data and expand on the complex role of this genomic region in the control of Wolbachia proliferation. Both new mutants shorten the host lifespan and increase antiviral protection. Moreover, we show that Wolbachia proliferation rate in Drosophila melanogaster depends on the interaction between Octomom copy number, the host developmental stage, and temperature. Our analysis also suggests that the life shortening and antiviral protection phenotypes of Wolbachia are dependent on different, but related, properties of the endosymbiont; the rate of proliferation and the titres near the time of infection, respectively. We also demonstrate the feasibility of a novel and unbiased experimental approach to study Wolbachia biology, which could be further adapted to characterize other genetically intractable bacterial endosymbionts.
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Affiliation(s)
- Elves H. Duarte
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Faculdade de Ciências e Tecnologia, Universidade de Cabo Verde, Palmarejo, Cabo Verde
| | - Ana Carvalho
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - João Costa
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Luís Teixeira
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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29
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Manoj RRS, Latrofa MS, Epis S, Otranto D. Wolbachia: endosymbiont of onchocercid nematodes and their vectors. Parasit Vectors 2021; 14:245. [PMID: 33962669 PMCID: PMC8105934 DOI: 10.1186/s13071-021-04742-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022] Open
Abstract
Background Wolbachia is an obligate intracellular maternally transmitted, gram-negative bacterium which forms a spectrum of endosymbiotic relationships from parasitism to obligatory mutualism in a wide range of arthropods and onchocercid nematodes, respectively. In arthropods Wolbachia produces reproductive manipulations such as male killing, feminization, parthenogenesis and cytoplasmic incompatibility for its propagation and provides an additional fitness benefit for the host to protect against pathogens, whilst in onchocercid nematodes, apart from the mutual metabolic dependence, this bacterium is involved in moulting, embryogenesis, growth and survival of the host. Methods This review details the molecular data of Wolbachia and its effect on host biology, immunity, ecology and evolution, reproduction, endosymbiont-based treatment and control strategies exploited for filariasis. Relevant peer-reviewed scientic papers available in various authenticated scientific data bases were considered while writing the review. Conclusions The information presented provides an overview on Wolbachia biology and its use in the control and/or treatment of vectors, onchocercid nematodes and viral diseases of medical and veterinary importance. This offers the development of new approaches for the control of a variety of vector-borne diseases. Graphic Abstract ![]()
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Affiliation(s)
| | | | - Sara Epis
- Department of Biosciences and Pediatric CRC 'Romeo Ed Enrica Invernizzi', University of Milan, Milan, Italy
| | - Domenico Otranto
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy. .,Faculty of Veterinary Sciences, Bu-Ali Sina University, Hamedan, Iran.
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30
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Wolfe TM, Bruzzese DJ, Klasson L, Corretto E, Lečić S, Stauffer C, Feder JL, Schuler H. Comparative genome sequencing reveals insights into the dynamics of Wolbachia in native and invasive cherry fruit flies. Mol Ecol 2021; 30:6259-6272. [PMID: 33882628 PMCID: PMC9290052 DOI: 10.1111/mec.15923] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/21/2021] [Accepted: 04/06/2021] [Indexed: 12/13/2022]
Abstract
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 its 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.
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Affiliation(s)
- Thomas M Wolfe
- Department of Forest and Soil Sciences, Boku, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Daniel J Bruzzese
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Lisa Klasson
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Erika Corretto
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bozen-Bolzano, Italy
| | - Sonja Lečić
- Department of Evolutionary Biology, Ludwig-Maximilians University, Munich, Germany
| | - Christian Stauffer
- Department of Forest and Soil Sciences, Boku, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Hannes Schuler
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bozen-Bolzano, Italy.,Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bozen-Bolzano, Italy
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31
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Zhang W, Reeves GR, Tautz D. Testing Implications of the Omnigenic Model for the Genetic Analysis of Loci Identified through Genome-wide Association. Curr Biol 2021; 31:1092-1098.e6. [PMID: 33417882 DOI: 10.1016/j.cub.2020.12.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/19/2020] [Accepted: 12/15/2020] [Indexed: 10/22/2022]
Abstract
Organismal phenotypes usually have a quantitative distribution, and their genetic architecture can be studied by genome-wide association (GWA) mapping approaches. In most of such studies, it has become clear that many genes of moderate or small effects contribute to the phenotype.1-4 Hence, the attention has turned toward the loci falling below the GWA cut-off, which may contribute to the phenotype through modifier interactions with a set of core genes, as proposed in the omnigenic model.5 One can thus predict that both moderate effect GWA-derived candidate genes and randomly chosen genes should have a similar likelihood to affect a given phenotype when they are analyzed via gene disruption assays. We have tested this hypothesis by using an automated phenotyping system for Drosophila pupal phenotypes.6,7 We first identified candidate genes for pupal length in a GWA based on the Drosophila Genetic Reference Panel (DGRP)8,9 and showed that most of these candidate genes are indeed involved in the phenotype. We then randomly chose genes below a GWA significance threshold and found that three-quarters of them had also an effect on the trait with comparable effect sizes as the GWA candidate genes. We further tested the effects of these knockout lines on an independent behavioral pupal trait (pupation site choice) and found that a similar fraction had a significant effect as well. Our data thus confirm the implication that a large number of genes can influence independent quantitative traits.
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Affiliation(s)
- Wenyu Zhang
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany
| | - Guy R Reeves
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany.
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32
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Gerth M, Martinez-Montoya H, Ramirez P, Masson F, Griffin JS, Aramayo R, Siozios S, Lemaitre B, Mateos M, Hurst GDD. Rapid molecular evolution of Spiroplasma symbionts of Drosophila. Microb Genom 2021; 7:000503. [PMID: 33591248 PMCID: PMC8208695 DOI: 10.1099/mgen.0.000503] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/22/2021] [Indexed: 12/21/2022] Open
Abstract
Spiroplasma is a genus of Mollicutes whose members include plant pathogens, insect pathogens and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have documented a high genomic turnover in Spiroplasma symbionts and plant pathogens. These observations suggest that Spiroplasma evolves quickly in comparison to other insect symbionts. Here, we systematically assess evolutionary rates and patterns of Spiroplasma poulsonii, a natural symbiont of Drosophila. We analysed genomic evolution of sHy within flies, and sMel within in vitro culture over several years. We observed that S. poulsonii substitution rates are among the highest reported for any bacteria, and around two orders of magnitude higher compared with other inherited arthropod endosymbionts. The absence of mismatch repair loci mutS and mutL is conserved across Spiroplasma, and likely contributes to elevated substitution rates. Further, the closely related strains sMel and sHy (>99.5 % sequence identity in shared loci) show extensive structural genomic differences, which potentially indicates a higher degree of host adaptation in sHy, a protective symbiont of Drosophila hydei. Finally, comparison across diverse Spiroplasma lineages confirms previous reports of dynamic evolution of toxins, and identifies loci similar to the male-killing toxin Spaid in several Spiroplasma lineages and other endosymbionts. Overall, our results highlight the peculiar nature of Spiroplasma genome evolution, which may explain unusual features of its evolutionary ecology.
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Affiliation(s)
- Michael Gerth
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Present address: Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Humberto Martinez-Montoya
- Laboratorio de Genética y Genómica Comparativa, Unidad Académica Multidisciplinaria Reynosa Aztlán, Universidad Autónoma de Tamaulipas, Reynosa, Mexico
| | - Paulino Ramirez
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Florent Masson
- Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (École Polytechnique Fédérale de Lausanne), Lausanne, Switzerland
| | - Joanne S. Griffin
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Rodolfo Aramayo
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Stefanos Siozios
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Bruno Lemaitre
- Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (École Polytechnique Fédérale de Lausanne), Lausanne, Switzerland
| | - Mariana Mateos
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
| | - Gregory D. D. Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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33
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Sanaei E, Charlat S, Engelstädter J. Wolbachia
host shifts: routes, mechanisms, constraints and evolutionary consequences. Biol Rev Camb Philos Soc 2020; 96:433-453. [DOI: 10.1111/brv.12663] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Ehsan Sanaei
- School of Biological Sciences The University of Queensland Saint Lucia Brisbane QLD 4067 Australia
| | - Sylvain Charlat
- Laboratoire de Biométrie et Biologie Evolutive Université de Lyon, Université Lyon 1, CNRS, UMR 5558 43 boulevard du 11 novembre 1918 Villeurbanne F‐69622 France
| | - Jan Engelstädter
- School of Biological Sciences The University of Queensland Saint Lucia Brisbane QLD 4067 Australia
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34
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Large scale genome reconstructions illuminate Wolbachia evolution. Nat Commun 2020; 11:5235. [PMID: 33067437 PMCID: PMC7568565 DOI: 10.1038/s41467-020-19016-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/25/2020] [Indexed: 12/21/2022] Open
Abstract
Wolbachia is an iconic example of a successful intracellular bacterium. Despite its importance as a manipulator of invertebrate biology, its evolutionary dynamics have been poorly studied from a genomic viewpoint. To expand the number of Wolbachia genomes, we screen over 30,000 publicly available shotgun DNA sequencing samples from 500 hosts. By assembling over 1000 Wolbachia genomes, we provide a substantial increase in host representation. Our phylogenies based on both core-genome and gene content provide a robust reference for future studies, support new strains in model organisms, and reveal recent horizontal transfers amongst distantly related hosts. We find various instances of gene function gains and losses in different super-groups and in cytoplasmic incompatibility inducing strains. Our Wolbachia-host co-phylogenies indicate that horizontal transmission is widespread at the host intraspecific level and that there is no support for a general Wolbachia-mitochondrial synchronous divergence. By greatly expanding the number of assembled genomes for Wolbachia (a group of intracellular bacteria) and constructing robust phylogenies, this study finds strong rate heterogeneity among Wolbachiapopulations and no support for synchronous divergence between Wolbachia and host mitochondria.
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35
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Hague MTJ, Caldwell CN, Cooper BS. Pervasive Effects of Wolbachia on Host Temperature Preference. mBio 2020; 11:e01768-20. [PMID: 33024036 PMCID: PMC7542361 DOI: 10.1128/mbio.01768-20] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Heritable symbionts can modify a range of ecologically important host traits, including behavior. About half of all insect species are infected with maternally transmitted Wolbachia, a bacterial endosymbiont known to alter host reproduction, nutrient acquisition, and virus susceptibility. Here, we broadly test the hypothesis that Wolbachia modifies host behavior by assessing the effects of eight different Wolbachia strains on the temperature preference of six Drosophila melanogaster subgroup species. Four of the seven host genotypes infected with A-group Wolbachia strains (wRi in Drosophila simulans, wHa in D. simulans, wSh in Drosophila sechellia, and wTei in Drosophila teissieri) prefer significantly cooler temperatures relative to uninfected genotypes. Contrastingly, when infected with divergent B-group wMau, Drosophila mauritiana prefers a warmer temperature. For most strains, changes to host temperature preference do not alter Wolbachia titer. However, males infected with wSh and wTei tend to experience an increase in titer when shifted to a cooler temperature for 24 h, suggesting that Wolbachia-induced changes to host behavior may promote bacterial replication. Our results indicate that Wolbachia modifications to host temperature preference are likely widespread, which has important implications for insect thermoregulation and physiology. Understanding the fitness consequences of these Wolbachia effects is crucial for predicting evolutionary outcomes of host-symbiont interactions, including how Wolbachia spreads to become common.IMPORTANCE Microbes infect a diversity of species, influencing the performance and fitness of their hosts. Maternally transmitted Wolbachia bacteria infect most insects and other arthropods, making these bacteria some of the most common endosymbionts in nature. Despite their global prevalence, it remains mostly unknown how Wolbachia influence host physiology and behavior to proliferate. We demonstrate pervasive effects of Wolbachia on Drosophila temperature preference. Most hosts infected with A-group Wolbachia prefer cooler temperatures, whereas the one host species infected with divergent B-group Wolbachia prefers warmer temperatures, relative to uninfected genotypes. Changes to host temperature preference generally do not alter Wolbachia abundance in host tissues, but for some A-group strains, adult males have increased Wolbachia titer when shifted to a cooler temperature. This suggests that Wolbachia-induced changes to host behavior may promote bacterial replication. Our results help elucidate the impact of endosymbionts on their hosts amid the global Wolbachia pandemic.
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Affiliation(s)
- Michael T J Hague
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Chelsey N Caldwell
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Brandon S Cooper
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
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36
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Cross ST, Maertens BL, Dunham TJ, Rodgers CP, Brehm AL, Miller MR, Williams AM, Foy BD, Stenglein MD. Partitiviruses Infecting Drosophila melanogaster and Aedes aegypti Exhibit Efficient Biparental Vertical Transmission. J Virol 2020; 94:e01070-20. [PMID: 32759315 PMCID: PMC7527066 DOI: 10.1128/jvi.01070-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/22/2020] [Indexed: 12/26/2022] Open
Abstract
Partitiviruses are segmented, multipartite double-stranded RNA (dsRNA) viruses that until recently were only known to infect fungi, plants, and protozoans. Metagenomic surveys have revealed that partitivirus-like sequences are also commonly associated with arthropods. One arthropod-associated partitivirus, galbut virus, is common in wild populations of Drosophila melanogaster To begin to understand the processes that underlie this virus's high global prevalence, we established colonies of wild-caught infected flies. Infection remained at stably high levels over 3 years, with between 63 and 100% of individual flies infected. Galbut virus infects fly cells and replicates in tissues throughout infected adults, including reproductive tissues and the gut epithelium. We detected no evidence of horizontal transmission via ingestion, but vertical transmission from either infected females or infected males was ∼100% efficient. Vertical transmission of a related partitivirus, verdadero virus, that we discovered in a laboratory colony of Aedes aegypti mosquitoes was similarly efficient. This suggests that efficient biparental vertical transmission may be a feature of at least a subset of insect-infecting partitiviruses. To study the impact of galbut virus infection free from the confounding effect of other viruses, we generated an inbred line of flies with galbut virus as the only detectable virus infection. We were able to transmit infection experimentally via microinjection of homogenate from these galbut-only flies. This sets the stage for experiments to understand the biological impact and possible utility of partitiviruses infecting model organisms and disease vectors.IMPORTANCE Galbut virus is a recently discovered partitivirus that is extraordinarily common in wild populations of the model organism Drosophila melanogaster Like for most viruses discovered through metagenomics, most of the basic biological questions about this virus remain unanswered. We found that galbut virus, along with a closely related partitivirus found in Aedes aegypti mosquitoes, is transmitted from infected females or males to offspring with ∼100% efficiency and can be maintained in laboratory colonies over years. This efficient transmission mechanism likely underlies the successful spread of these viruses through insect populations. We created Drosophila lines that contained galbut virus as the only virus infection and showed that these flies can be used as a source for experimental infections. This provides insight into how arthropod-infecting partitiviruses may be maintained in nature and sets the stage for exploration of their biology and potential utility.
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Affiliation(s)
- Shaun T Cross
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Bernadette L Maertens
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Tillie J Dunham
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Case P Rodgers
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Ali L Brehm
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Megan R Miller
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Alissa M Williams
- Department of Biology, College of Natural Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Brian D Foy
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
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A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts. G3-GENES GENOMES GENETICS 2020; 10:3243-3260. [PMID: 32718933 PMCID: PMC7467002 DOI: 10.1534/g3.120.401534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Wolbachia is a genus containing obligate, intracellular endosymbionts with arthropod and nematode hosts. Numerous studies have identified differentially expressed transcripts in Wolbachia endosymbionts that potentially inform the biological interplay between these endosymbionts and their hosts, albeit with discordant results. Here, we re-analyze previously published Wolbachia RNA-Seq transcriptomics data sets using a single workflow consisting of the most up-to-date algorithms and techniques, with the aim of identifying trends or patterns in the pan-Wolbachia transcriptional response. We find that data from one of the early studies in filarial nematodes did not allow for robust conclusions about Wolbachia differential expression with these methods, suggesting the original interpretations should be reconsidered. Across datasets analyzed with this unified workflow, there is a general lack of global gene regulation with the exception of a weak transcriptional response resulting in the upregulation of ribosomal proteins in early larval stages. This weak response is observed across diverse Wolbachia strains from both nematode and insect hosts suggesting a potential pan-Wolbachia transcriptional response during host development that diverged more than 700 million years ago.
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38
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Kapun M, Barrón MG, Staubach F, Obbard DJ, Wiberg RAW, Vieira J, Goubert C, Rota-Stabelli O, Kankare M, Bogaerts-Márquez M, Haudry A, Waidele L, Kozeretska I, Pasyukova EG, Loeschcke V, Pascual M, Vieira CP, Serga S, Montchamp-Moreau C, Abbott J, Gibert P, Porcelli D, Posnien N, Sánchez-Gracia A, Grath S, Sucena É, Bergland AO, Guerreiro MPG, Onder BS, Argyridou E, Guio L, Schou MF, Deplancke B, Vieira C, Ritchie MG, Zwaan BJ, Tauber E, Orengo DJ, Puerma E, Aguadé M, Schmidt P, Parsch J, Betancourt AJ, Flatt T, González J. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses. Mol Biol Evol 2020; 37:2661-2678. [PMID: 32413142 PMCID: PMC7475034 DOI: 10.1093/molbev/msaa120] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.
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Affiliation(s)
- Martin Kapun
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
- Division of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Maite G Barrón
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Fabian Staubach
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Darren J Obbard
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - R Axel W Wiberg
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Jorge Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Clément Goubert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Omar Rota-Stabelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’ Adige, Italy
| | - Maaria Kankare
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - María Bogaerts-Márquez
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Annabelle Haudry
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Lena Waidele
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Iryna Kozeretska
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center of Ministry of Education and Science of Ukraine, Kyiv, Ukraine
| | - Elena G Pasyukova
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genome Variation, Institute of Molecular Genetics of RAS, Moscow, Russia
| | - Volker Loeschcke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
| | - Marta Pascual
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristina P Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Svitlana Serga
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Catherine Montchamp-Moreau
- The European Drosophila Population Genomics Consortium (DrosEU)
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Jessica Abbott
- The European Drosophila Population Genomics Consortium (DrosEU)
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Patricia Gibert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Damiano Porcelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Animal and Plant Sciences, Sheffield, United Kingdom
| | - Nico Posnien
- The European Drosophila Population Genomics Consortium (DrosEU)
- Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Universität Göttingen, Göttingen, Germany
| | - Alejandro Sánchez-Gracia
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Sonja Grath
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Élio Sucena
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Alan O Bergland
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Maria Pilar Garcia Guerreiro
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Banu Sebnem Onder
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Eliza Argyridou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Lain Guio
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Mads Fristrup Schou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Bart Deplancke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Bio-engineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Cristina Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Michael G Ritchie
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
| | - Bas J Zwaan
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Eran Tauber
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Dorcas J Orengo
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Eva Puerma
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Paul Schmidt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - John Parsch
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Andrea J Betancourt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Thomas Flatt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Josefa González
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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39
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Wang JB, Elya C, St Leger RJ. Genetic variation for resistance to the specific fly pathogen Entomophthora muscae. Sci Rep 2020; 10:14284. [PMID: 32868814 PMCID: PMC7459287 DOI: 10.1038/s41598-020-71262-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/10/2020] [Indexed: 11/09/2022] Open
Abstract
We found substantial variation in resistance to the fly-specific pathogen Entomophthora muscae 'Berkeley' (Entomophthoromycota), in 20 lines from the Drosophila melanogaster Genetic Reference Panel (DGRP). Resistance to E. muscae is positively (r = 0.55) correlated with resistance to the broad host range ascomycete entomopathogen Metarhizium anisopliae (Ma549), indicative of generalist (non-specific) defenses. Most of the lines showing above average resistance to Ma549 showed cross-resistance to E. muscae. However, lines that succumbed quickly to Ma549 exhibited the full range of resistance to E. muscae. This suggests fly populations differ in E. muscae-specific resistance mechanisms as well as generic defences effective against both Ma549 and E. muscae. We looked for trade-offs that could account for inter-line variation, but increases (decreases) in disease resistance to E. muscae are not consistently associated with increases (decreases) of resistance to oxidative stress, starvation stress and sleep indices. That these pathogens are dynamic agents of selection on hosts is reflected in this genetic variation for resistance in lines derived from wild populations.
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Affiliation(s)
- Jonathan B Wang
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Carolyn Elya
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Raymond J St Leger
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA.
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40
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Sex-Specific Wolbachia Infection Patterns in Populations of Polygraphus proximus Blandford (Coleoptera; Curculionidae: Scolytinae). INSECTS 2020; 11:insects11080547. [PMID: 32824858 PMCID: PMC7469224 DOI: 10.3390/insects11080547] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 12/02/2022]
Abstract
Simple Summary Wolbachia bacteria are the most common symbionts of insects. These bacteria are ordinarily transmitted via oocyte cytoplasm from mother to progeny, like mitochondria, and are sporadically transmitted from one species to another. The Wolbachia symbionts have evolved to be parasitic (feminization of genetic males, male-killing, parthenogenesis, and cytoplasmic incompatibility) or/and mutualistic (increasing lifespan and fecundity, providing vitamins and nutrients, defending against viruses and parasites). Here we have studied Wolbachia infection in populations of four-eyed fir bark beetle Polygraphusproximus, which is one of the most dangerous pests of Siberian fir forests. A high rate of the only wProx Wolbachia strain in P.proximus populations was found in a vastly studied territory. Surprisingly, females were more often harboring Wolbachia than males. Besides, a comparison of the Wolbachia density in individuals has revealed that females contain much more Wolbachia symbionts than males. We suppose that the difference in infection status, as well as the difference in Wolbachia load between males and females within a population, can be found in some other Wolbachia–host associations. Abstract Wolbachia symbionts are maternally inherited bacteria that are widely distributed among Arthropoda hosts. Wolbachia influence their host biology in diverse ways. They may induce reproductive abnormalities, protect hosts against pathogens and parasites, or benefit hosts through metabolic provisioning. The progeny of an infected female are ordinarily infected with Wolbachia; however, Wolbachia have no future in male host progeny because they cannot transmit the symbiont to the next generation. Here, we analyze native and invasive populations of the four-eyed fir bark beetle (Polygraphus proximus) for Wolbachia prevalence and symbiont genetic diversity. This species is a dangerous pest of Siberian fir (Abies sibirica) forests. The native range of P. proximus includes the territories of the Russian Far East, Japan, Korea, and Northeast China, whereas its invasive range includes West Siberia, with further expansion westward. Surprisingly, we revealed a difference in the patterns of Wolbachia prevalence for males and females. Infection rate and Wolbachia titers were higher in females than in males. ST-533, the only haplotype of Wolbachia supergroup B, was associated with a minimum of three out of the five described mitochondrial haplotypes.
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41
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Hague MTJ, Mavengere H, Matute DR, Cooper BS. Environmental and Genetic Contributions to Imperfect wMel-Like Wolbachia Transmission and Frequency Variation. Genetics 2020; 215:1117-1132. [PMID: 32546497 PMCID: PMC7404227 DOI: 10.1534/genetics.120.303330] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022] Open
Abstract
Maternally transmitted Wolbachia bacteria infect about half of all insect species. They usually show imperfect maternal transmission and often produce cytoplasmic incompatibility (CI). Irrespective of CI, Wolbachia frequencies tend to increase when rare only if they benefit host fitness. Several Wolbachia, including wMel that infects Drosophila melanogaster, cause weak or no CI and persist at intermediate frequencies. On the island of São Tomé off West Africa, the frequencies of wMel-like Wolbachia infecting Drosophila yakuba (wYak) and Drosophila santomea (wSan) fluctuate, and the contributions of imperfect maternal transmission, fitness effects, and CI to these fluctuations are unknown. We demonstrate spatial variation in wYak frequency and transmission on São Tomé. Concurrent field estimates of imperfect maternal transmission do not predict spatial variation in wYak frequencies, which are highest at high altitudes where maternal transmission is the most imperfect. Genomic and genetic analyses provide little support for D. yakuba effects on wYak transmission. Instead, rearing at cool temperatures reduces wYak titer and increases imperfect transmission to levels observed on São Tomé. Using mathematical models of Wolbachia frequency dynamics and equilibria, we infer that temporally variable imperfect transmission or spatially variable effects on host fitness and reproduction are required to explain wYak frequencies. In contrast, spatially stable wSan frequencies are plausibly explained by imperfect transmission, modest fitness effects, and weak CI. Our results provide insight into causes of wMel-like frequency variation in divergent hosts. Understanding this variation is crucial to explain Wolbachia spread and to improve wMel biocontrol of human disease in transinfected mosquito systems.
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Affiliation(s)
- Michael T J Hague
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
| | - Heidi Mavengere
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Daniel R Matute
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Brandon S Cooper
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
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42
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Keaney TA, Wong HWS, Dowling DK, Jones TM, Holman L. Sibling rivalry versus mother's curse: can kin competition facilitate a response to selection on male mitochondria? Proc Biol Sci 2020; 287:20200575. [PMID: 32605521 DOI: 10.1098/rspb.2020.0575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Assuming that fathers never transmit mitochondrial DNA (mtDNA) to their offspring, mitochondrial mutations that affect male fitness are invisible to direct selection on males, leading to an accumulation of male-harming alleles in the mitochondrial genome (mother's curse). However, male phenotypes encoded by mtDNA can still undergo adaptation via kin selection provided that males interact with females carrying related mtDNA, such as their sisters. Here, using experiments with Drosophila melanogaster carrying standardized nuclear DNA but distinct mitochondrial DNA, we test whether the mitochondrial haplotype carried by interacting pairs of larvae affects survival to adulthood, as well as the fitness of the adults. Although mtDNA had no detectable direct or indirect genetic effect on larva-to-adult survival, the fitness of male and female adults was significantly affected by their own mtDNA and the mtDNA carried by their social partner in the larval stage. Thus, mtDNA mutations that alter the effect of male larvae on nearby female larvae (which often carry the same mutation, due to kinship) could theoretically respond to kin selection. We discuss the implications of our findings for the evolution of mitochondria and other maternally inherited endosymbionts.
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Affiliation(s)
- Thomas A Keaney
- School of Biosciences, The University of Melbourne, Vic. 3010, Australia
| | - Heidi W S Wong
- School of Biosciences, The University of Melbourne, Vic. 3010, Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Vic. 3800, Australia
| | - Therésa M Jones
- School of Biosciences, The University of Melbourne, Vic. 3010, Australia
| | - Luke Holman
- School of Biosciences, The University of Melbourne, Vic. 3010, Australia
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43
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Gora NV, Serga SV, Maistrenko OM, Ślęzak-Parnikoza A, Parnikoza IY, Tarasiuk AN, Demydov SV, Kozeretska IA. Climate Factors and Wolbachia Infection Frequencies in Natural Populations of Drosophila melanogaster. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720030044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Mazzucco R, Nolte V, Vijayan T, Schlötterer C. Long-Term Dynamics Among Wolbachia Strains During Thermal Adaptation of Their Drosophila melanogaster Hosts. Front Genet 2020; 11:482. [PMID: 32477411 PMCID: PMC7241558 DOI: 10.3389/fgene.2020.00482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/17/2020] [Indexed: 11/13/2022] Open
Abstract
Climate change is a major evolutionary force triggering thermal adaptation in a broad range of species. While the consequences of global warming are being studied for an increasing number of species, limited attention has been given to the evolutionary dynamics of endosymbionts in response to climate change. Here, we address this question by studying the dynamics of Wolbachia, a well-studied endosymbiont of Drosophila melanogaster. D. melanogaster populations infected with 13 different Wolbachia strains were exposed to novel hot and cold laboratory environments for up to 180 generations. The short-term dynamics suggested a temperature-related fitness difference resulting in the increase of clade V strains in the cold environment only. Our long-term analysis now uncovers that clade V dominates in all replicates after generation 60 irrespective of temperature treatment. We propose that adaptation of the Drosophila host to either temperature or Drosophila C virus (DCV) infection are the cause of the replicated, temporally non-concordant Wolbachia dynamics. Our study provides an interesting case demonstrating that even simple, well-controlled experiments can result in complex, but repeatable evolutionary dynamics, thus providing a cautionary note on too simple interpretations on the impact of climate change.
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Affiliation(s)
- Rupert Mazzucco
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Wien, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Wien, Austria
| | - Thapasya Vijayan
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Wien, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Wien, Austria
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45
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Hundertmark A, Goodacre SL, Brookfield JFY. Alternative evolutionary outcomes following endosymbiont‐mediated selection on male mating preference alleles. J Evol Biol 2020; 33:653-667. [PMID: 32030839 PMCID: PMC7318244 DOI: 10.1111/jeb.13602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 01/20/2020] [Accepted: 01/23/2020] [Indexed: 11/16/2022]
Abstract
In many arthropods, intracellular bacteria, such as those of the genus Wolbachia, may spread through host populations as a result of cytoplasmic incompatibility (CI). Here, there is sterility or reduced fertility in crosses between infected males and uninfected females. As the bacterium is maternally inherited, the reduced fertility of uninfected females increases the frequency of the infection. If the transmission fidelity of the bacterium is less than 100%, the bacterium cannot invade from a low frequency, but if its frequency exceeds a threshold, it increases to a high, stable, equilibrium frequency. We explore the expected evolutionary dynamics of mutant alleles that cause their male bearers to avoid mating with uninfected females. For alleles which create this avoidance behaviour conditional upon the male being infected, there is a wide zone of parameter space that allows the preference allele to drive Wolbachia from the population when it would otherwise stably persist. There is also a wide zone of parameter space that allows a joint stable equilibrium for the Wolbachia and a polymorphism for the preference allele. When the male's avoidance of uninfected females is unconditional, the preference allele's effect on Wolbachia frequency is reduced, but there is a narrow range of values for the transmission rate and CI fertility that allow an unconditional preference allele to drive Wolbachia from the population, in a process driven by positive linkage disequilibrium between Wolbachia and the preference allele. The possibility of the evolution of preference could hamper attempts to manipulate wild populations through Wolbachia introductions.
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Affiliation(s)
- Antje Hundertmark
- School of Life Sciences University of Nottingham, University Park Nottingham UK
| | - Sara L. Goodacre
- School of Life Sciences University of Nottingham, University Park Nottingham UK
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46
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Individual, but not population asymmetries, are modulated by social environment and genotype in Drosophila melanogaster. Sci Rep 2020; 10:4480. [PMID: 32161330 PMCID: PMC7066193 DOI: 10.1038/s41598-020-61410-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 02/18/2020] [Indexed: 11/09/2022] Open
Abstract
Theory predicts that social interactions can induce an alignment of behavioral asymmetries between individuals (i.e., population-level lateralization), but evidence for this effect is mixed. To understand how interaction with other individuals affects behavioral asymmetries, we systematically manipulated the social environment of Drosophila melanogaster, testing individual flies and dyads (female-male, female-female and male-male pairs). In these social contexts we measured individual and population asymmetries in individual behaviors (circling asymmetry, wing use) and dyadic behaviors (relative position and orientation between two flies) in five different genotypes. We reasoned that if coordination between individuals drives alignment of behavioral asymmetries, greater alignment at the population-level should be observed in social contexts compared to solitary individuals. We observed that the presence of other individuals influenced the behavior and position of flies but had unexpected effects on individual and population asymmetries: individual-level asymmetries were strong and modulated by the social context but population-level asymmetries were mild or absent. Moreover, the strength of individual-level asymmetries differed between strains, but this was not the case for population-level asymmetries. These findings suggest that the degree of social interaction found in Drosophila is insufficient to drive population-level behavioral asymmetries.
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47
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Vaught RC, Voigt S, Dobler R, Clancy DJ, Reinhardt K, Dowling DK. Interactions between cytoplasmic and nuclear genomes confer sex-specific effects on lifespan in Drosophila melanogaster. J Evol Biol 2020; 33:694-713. [PMID: 32053259 DOI: 10.1111/jeb.13605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 12/19/2022]
Abstract
Genetic variation outside of the cell nucleus can affect the phenotype. The cytoplasm is home to the mitochondria, and in arthropods often hosts intracellular bacteria such as Wolbachia. Although numerous studies have implicated epistatic interactions between cytoplasmic and nuclear genetic variation as mediators of phenotypic expression, two questions remain. Firstly, it remains unclear whether outcomes of cyto-nuclear interactions will manifest differently across the sexes, as might be predicted given that cytoplasmic genomes are screened by natural selection only through females as a consequence of their maternal inheritance. Secondly, the relative contribution of mitochondrial genetic variation to other cytoplasmic sources of variation, such as Wolbachia infection, in shaping phenotypic outcomes of cyto-nuclear interactions remains unknown. Here, we address these questions, creating a fully crossed set of replicated cyto-nuclear populations derived from three geographically distinct populations of Drosophila melanogaster, measuring the lifespan of males and females from each population. We observed that cyto-nuclear interactions shape lifespan and that the outcomes of these interactions differ across the sexes. Yet, we found no evidence that placing the cytoplasms from one population alongside the nuclear background of others (generating putative cyto-nuclear mismatches) leads to decreased lifespan in either sex. Although it was difficult to partition mitochondrial from Wolbachia effects, our results suggest at least some of the cytoplasmic genotypic contribution to lifespan was directly mediated by an effect of sequence variation in the mtDNA. Future work should explore the degree to which cyto-nuclear interactions result in sex differences in the expression of other components of organismal life history.
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Affiliation(s)
- Rebecca C Vaught
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Susanne Voigt
- Faculty of Biology, Applied Zoology, TU Dresden, Dresden, Germany
| | - Ralph Dobler
- Faculty of Biology, Applied Zoology, TU Dresden, Dresden, Germany
| | - David J Clancy
- Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster, UK
| | - Klaus Reinhardt
- Faculty of Biology, Applied Zoology, TU Dresden, Dresden, Germany
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
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Martin SH, Singh KS, Gordon IJ, Omufwoko KS, Collins S, Warren IA, Munby H, Brattström O, Traut W, Martins DJ, Smith DAS, Jiggins CD, Bass C, ffrench-Constant RH. Whole-chromosome hitchhiking driven by a male-killing endosymbiont. PLoS Biol 2020; 18:e3000610. [PMID: 32108180 PMCID: PMC7046192 DOI: 10.1371/journal.pbio.3000610] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/23/2020] [Indexed: 12/30/2022] Open
Abstract
Neo-sex chromosomes are found in many taxa, but the forces driving their emergence and spread are poorly understood. The female-specific neo-W chromosome of the African monarch (or queen) butterfly Danaus chrysippus presents an intriguing case study because it is restricted to a single 'contact zone' population, involves a putative colour patterning supergene, and co-occurs with infection by the male-killing endosymbiont Spiroplasma. We investigated the origin and evolution of this system using whole genome sequencing. We first identify the 'BC supergene', a broad region of suppressed recombination across nearly half a chromosome, which links two colour patterning loci. Association analysis suggests that the genes yellow and arrow in this region control the forewing colour pattern differences between D. chrysippus subspecies. We then show that the same chromosome has recently formed a neo-W that has spread through the contact zone within approximately 2,200 years. We also assembled the genome of the male-killing Spiroplasma, and find that it shows perfect genealogical congruence with the neo-W, suggesting that the neo-W has hitchhiked to high frequency as the male-killer has spread through the population. The complete absence of female crossing-over in the Lepidoptera causes whole-chromosome hitchhiking of a single neo-W haplotype, carrying a single allele of the BC supergene and dragging multiple non-synonymous mutations to high frequency. This has created a population of infected females that all carry the same recessive colour patterning allele, making the phenotypes of each successive generation highly dependent on uninfected male immigrants. Our findings show how hitchhiking can occur between the physically unlinked genomes of host and endosymbiont, with dramatic consequences.
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Affiliation(s)
- Simon H. Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Kumar Saurabh Singh
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, United Kingdom
| | - Ian J. Gordon
- Center of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, Huye, Rwanda
| | - Kennedy Saitoti Omufwoko
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States of America
- Mpala Research Centre, Nanyuki, Kenya
| | - Steve Collins
- African Butterfly Research Institute, Nairobi, Kenya
| | - Ian A. Warren
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Hannah Munby
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Oskar Brattström
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Walther Traut
- Institut für Biologie, Universität Lübeck, Lübeck, Germany
| | - Dino J. Martins
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States of America
- Mpala Research Centre, Nanyuki, Kenya
| | | | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, United Kingdom
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49
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Zhang W, Reeves GR, Tautz D. Identification of a genetic network for an ecologically relevant behavioural phenotype in Drosophila melanogaster. Mol Ecol 2019; 29:502-518. [PMID: 31867742 DOI: 10.1111/mec.15341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 11/28/2022]
Abstract
Pupation site choice of Drosophila third-instar larvae is critical for the survival of individuals, as pupae are exposed to various biotic and abiotic dangers while immobilized during the 3-4 days of metamorphosis. This singular behavioural choice is sensitive to both environmental and genetic factors. Here, we developed a high-throughput phenotyping approach to assay the variation in pupation height in Drosophila melanogaster, while controlling for possibly confounding factors. We find substantial variation of mean pupation height among sampled natural stocks and we show that the Drosophila Genetic Reference Panel (DGRP) reflects this variation. Using the DGRP stocks for genome-wide association (GWA) mapping, 16 loci involved in determining pupation height could be resolved. The candidate genes in these loci are enriched for high expression in the larval central nervous system. A genetic network could be constructed from the candidate loci, which places scribble (scrib) at the centre, plus other genes known to be involved in nervous system development, such as Epidermal growth factor receptor (Egfr) and p53. Using gene disruption lines, we could functionally validate several of the initially identified loci, as well as additional loci predicted from network analysis. Our study shows that the combination of high-throughput phenotyping with a genetic analysis of variation captured from the wild can be used to approach the genetic dissection of an environmentally relevant behavioural phenotype.
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Affiliation(s)
- Wenyu Zhang
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Guy Richard Reeves
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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50
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Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nat Metab 2019; 1:1226-1242. [PMID: 32694676 DOI: 10.1038/s42255-019-0147-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 11/07/2019] [Indexed: 01/04/2023]
Abstract
The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear allelic imbalances, thus implying that mitochondrial haplotypes are reflected in the nuclear genome. However, no major fitness effects are associated with mitonuclear imbalance, suggesting that such imbalances reflect population structure at the mitochondrial level rather than genomic incompatibilities. Although mitochondrial haplotypes have no direct impact on mitochondrial respiration, some haplotypes are associated with stress- and metabolism-related phenotypes, including food intake in males. Finally, through reciprocal swapping of mitochondrial genomes, we demonstrate that a mitochondrial haplotype associated with high food intake can rescue a low food intake phenotype. Together, our findings provide new insight into population structure at the mitochondrial level and point to the importance of incorporating mitochondrial haplotypes in genotype-phenotype relationship studies.
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Affiliation(s)
- Roel P J Bevers
- Laboratory of Systems Biology and Genetics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Genomics England, London, UK
| | - Maria Litovchenko
- Laboratory of Systems Biology and Genetics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Adamandia Kapopoulou
- Laboratory of Systems Biology and Genetics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Virginie S Braman
- Laboratory of Systems Biology and Genetics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matthew R Robinson
- Complex Trait Genetics Group, Université de Lausanne, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Brian Hollis
- Laboratory of Systems Biology and Genetics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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