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Li C, Li CQ, Chen ZB, Liu BQ, Sun X, Wei KH, Li CY, Luan JB. Wolbachia symbionts control sex in a parasitoid wasp using a horizontally acquired gene. Curr Biol 2024; 34:2359-2372.e9. [PMID: 38692276 DOI: 10.1016/j.cub.2024.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/26/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024]
Abstract
Host reproduction can be manipulated by bacterial symbionts in various ways. Parthenogenesis induction is the most effective type of reproduction manipulation by symbionts for their transmission. Insect sex is determined by regulation of doublesex (dsx) splicing through transformer2 (tra2) and transformer (tra) interaction. Although parthenogenesis induction by symbionts has been studied since the 1970s, its underlying molecular mechanism is unknown. Here we identify a Wolbachia parthenogenesis-induction feminization factor gene (piff) that targets sex-determining genes and causes female-producing parthenogenesis in the haplodiploid parasitoid Encarsia formosa. We found that Wolbachia elimination repressed expression of female-specific dsx and enhanced expression of male-specific dsx, which led to the production of wasp haploid male offspring. Furthermore, we found that E. formosa tra is truncated and non-functional, and Wolbachia has a functional tra homolog, termed piff, with an insect origin. Wolbachia PIFF can colocalize and interact with wasp TRA2. Moreover, Wolbachia piff has coordinated expression with tra2 and dsx of E. formosa. Our results demonstrate the bacterial symbiont Wolbachia has acquired an insect gene to manipulate the host sex determination cascade and induce parthenogenesis in wasps. This study reveals insect-to-bacteria horizontal gene transfer drives the evolution of animal sex determination systems, elucidating a striking mechanism of insect-microbe symbiosis.
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Affiliation(s)
- Ce Li
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Chu-Qiao Li
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhan-Bo Chen
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Bing-Qi Liu
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiang Sun
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Kai-Heng Wei
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Chen-Yi Li
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Jun-Bo Luan
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
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2
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Fricke LC, Lindsey ARI. Identification of Parthenogenesis-Inducing Effector Proteins in Wolbachia. Genome Biol Evol 2024; 16:evae036. [PMID: 38530785 PMCID: PMC11019157 DOI: 10.1093/gbe/evae036] [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: 12/13/2023] [Revised: 02/12/2024] [Accepted: 02/18/2024] [Indexed: 03/28/2024] Open
Abstract
Bacteria in the genus Wolbachia have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing females. This so-called "parthenogenesis induction" phenotype can be found in a number of Wolbachia strains that infect arthropods with haplodiploid sex determination systems, including parasitoid wasps. Despite the discovery of microbe-mediated parthenogenesis more than 30 yr ago, the underlying genetic mechanisms have remained elusive. We used a suite of genomic, computational, and molecular tools to identify and characterize two proteins that are uniquely found in parthenogenesis-inducing Wolbachia and have strong signatures of host-associated bacterial effector proteins. These putative parthenogenesis-inducing proteins have structural homology to eukaryotic protein domains including nucleoporins, the key insect sex determining factor Transformer, and a eukaryotic-like serine-threonine kinase with leucine-rich repeats. Furthermore, these proteins significantly impact eukaryotic cell biology in the model Saccharomyces cerevisiae. We suggest that these proteins are parthenogenesis-inducing factors and our results indicate that this would be made possible by a novel mechanism of bacterial-host interaction.
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Affiliation(s)
- Laura C Fricke
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
| | - Amelia R I Lindsey
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
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3
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Kaur R, McGarry A, Shropshire JD, Leigh BA, Bordenstein SR. Prophage proteins alter long noncoding RNA and DNA of developing sperm to induce a paternal-effect lethality. Science 2024; 383:1111-1117. [PMID: 38452081 PMCID: PMC11187695 DOI: 10.1126/science.adk9469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024]
Abstract
The extent to which prophage proteins interact with eukaryotic macromolecules is largely unknown. In this work, we show that cytoplasmic incompatibility factor A (CifA) and B (CifB) proteins, encoded by prophage WO of the endosymbiont Wolbachia, alter long noncoding RNA (lncRNA) and DNA during Drosophila sperm development to establish a paternal-effect embryonic lethality known as cytoplasmic incompatibility (CI). CifA is a ribonuclease (RNase) that depletes a spermatocyte lncRNA important for the histone-to-protamine transition of spermiogenesis. Both CifA and CifB are deoxyribonucleases (DNases) that elevate DNA damage in late spermiogenesis. lncRNA knockdown enhances CI, and mutagenesis links lncRNA depletion and subsequent sperm chromatin integrity changes to embryonic DNA damage and CI. Hence, prophage proteins interact with eukaryotic macromolecules during gametogenesis to create a symbiosis that is fundamental to insect evolution and vector control.
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Affiliation(s)
- Rupinder Kaur
- Pennsylvania State University, Departments of Biology and Entomology, University Park, PA 16802, USA
- One Health Microbiome Center, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, USA
| | - Angelina McGarry
- Pennsylvania State University, Departments of Biology and Entomology, University Park, PA 16802, USA
- One Health Microbiome Center, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - J. Dylan Shropshire
- Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, USA
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Brittany A. Leigh
- Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, USA
| | - Seth R. Bordenstein
- Pennsylvania State University, Departments of Biology and Entomology, University Park, PA 16802, USA
- One Health Microbiome Center, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, USA
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4
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Fricke LC, Lindsey ARI. Identification of parthenogenesis-inducing effector proteins in Wolbachia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569668. [PMID: 38076953 PMCID: PMC10705499 DOI: 10.1101/2023.12.01.569668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Bacteria in the genus Wolbachia have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing females. This so-called "parthenogenesis-induction" phenotype can be found in a number of Wolbachia strains that infect arthropods with haplodiploid sex determination systems, including parasitoid wasps. Despite the discovery of microbe-mediated parthenogenesis more than 30 years ago, the underlying genetic mechanisms have remained elusive. We used a suite of genomic, computational, and molecular tools to identify and characterize two proteins that are uniquely found in parthenogenesis-inducing Wolbachia and have strong signatures of host-associated bacterial effector proteins. These putative parthenogenesis-inducing proteins have structural homology to eukaryotic protein domains including nucleoporins, the key insect sex-determining factor Transformer, and a eukaryotic-like serine-threonine kinase with leucine rich repeats. Furthermore, these proteins significantly impact eukaryotic cell biology in the model, Saccharomyces cerevisiae. We suggest these proteins are parthenogenesis-inducing factors and our results indicate this would be made possible by a novel mechanism of bacterial-host interaction.
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Affiliation(s)
- Laura C Fricke
- Department of Entomology, University of Minnesota, St. Paul, Minnesota, 55108
| | - Amelia RI Lindsey
- Department of Entomology, University of Minnesota, St. Paul, Minnesota, 55108
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Muro T, Hikida H, Fujii T, Kiuchi T, Katsuma S. Two Complete Genomes of Male-Killing Wolbachia Infecting Ostrinia Moth Species Illuminate Their Evolutionary Dynamics and Association with Hosts. MICROBIAL ECOLOGY 2023; 86:1740-1754. [PMID: 36810610 PMCID: PMC10497655 DOI: 10.1007/s00248-023-02198-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Wolbachia is an extremely widespread intracellular symbiont which causes reproductive manipulation on various arthropod hosts. Male progenies are killed in Wolbachia-infected lineages of the Japanese Ostrinia moth population. While the mechanism of male killing and the evolutionary interaction between host and symbiont are significant concerns for this system, the absence of Wolbachia genomic information has limited approaches to these issues. We determined the complete genome sequences of wFur and wSca, the male-killing Wolbachia of Ostrinia furnacalis and Ostrinia scapulalis. The two genomes shared an extremely high degree of homology, with over 95% of the predicted protein sequences being identical. A comparison of these two genomes revealed nearly minimal genome evolution, with a strong emphasis on the frequent genome rearrangements and the rapid evolution of ankyrin repeat-containing proteins. Additionally, we determined the mitochondrial genomes of both species' infected lineages and performed phylogenetic analyses to deduce the evolutionary dynamics of Wolbachia infection in the Ostrinia clade. According to the inferred phylogenetic relationship, two possible scenarios were proposed: (1) Wolbachia infection was established in the Ostrinia clade prior to the speciation of related species such as O. furnacalis and O. scapulalis, or (2) Wolbachia infection in these species was introgressively transferred from a currently unidentified relative. Simultaneously, the relatively high homology of mitochondrial genomes suggested recent Wolbachia introgression between infected Ostrinia species. The findings of this study collectively shed light on the host-symbiont interaction from an evolutionary standpoint.
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Affiliation(s)
- Tomohiro Muro
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Hiroyuki Hikida
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Takeshi Fujii
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka, Japan
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan.
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Sharma AK, Som A. Assigning new supergroups V and W to the Wolbachia diversity. Bioinformation 2023; 19:336-340. [PMID: 37808371 PMCID: PMC10557451 DOI: 10.6026/97320630019336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 10/10/2023] Open
Abstract
Wolbachia are endosymbiotic and alphaproteobacteria that belong to the order Rickettsiales. They are known to infect half of the insect population and cause host manipulation, and have been categorized into 19 monophyletic lineages called supergroups. Recently, two strains, wCfeJ and wCfeT were isolated from cat fleas (Ctenocephalides felis), but their supergroup relationships were not assigned. In this article, we have attempted to classify these two novel strains and establish their evolutionary lineage (i.e., supergroup designation). For this we performed 16S rRNA similarity analysis and reconstructed 16S rRNA phylogeny of 52 Wolbachia strains (including two novel strains) belong to 19 supergroups. We also performed average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) studies to measure genomic similarity between the two novel genomes. The results revealed that 16S rRNA similarity between the two novel strains is 97.94%, which is below the threshold value of 98.6% and phylogeny shows that they are placed at the two different positions (i.e., showing distinct evolutionary lineages). Further, genomic similarity analysis revealed that the novel genomes have ANI and dDDH values 79% and 22.4% respectively, which were below the threshold value of ANI (95%) and dDDH (70%). These results suggested that the novel strains neither shared a species boundary between them nor with any other previously identified supergroups, which designate them as two new supergroups, namely supergroup V (strain wCfeJ) and supergroup W (strain wCfeT).
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Affiliation(s)
- Amresh Kumar Sharma
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj - 211002, India
| | - Anup Som
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj - 211002, India
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Infection Dynamics of Cotransmitted Reproductive Symbionts Are Mediated by Sex, Tissue, and Development. Appl Environ Microbiol 2022; 88:e0052922. [PMID: 35730939 PMCID: PMC9275221 DOI: 10.1128/aem.00529-22] [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] [Indexed: 12/25/2022] Open
Abstract
One of the most prevalent intracellular infections on earth is with Wolbachia, a bacterium in the Rickettsiales that infects a range of insects, crustaceans, chelicerates, and nematodes. Wolbachia is maternally transmitted to offspring and has profound effects on the reproduction and physiology of its hosts, which can result in reproductive isolation, altered vectorial capacity, mitochondrial sweeps, and even host speciation. Some populations stably harbor multiple Wolbachia strains, which can further contribute to reproductive isolation and altered host physiology. However, almost nothing is known about the requirements for multiple intracellular microbes to be stably maintained across generations while they likely compete for space and resources. Here, we use a coinfection of two Wolbachia strains (“wHa” and “wNo”) in Drosophila simulans to define the infection and transmission dynamics of an evolutionarily stable double infection. We find that a combination of sex, tissue, and host development contributes to the infection dynamics of the two microbes and that these infections exhibit a degree of niche partitioning across host tissues. wHa is present at a significantly higher titer than wNo in most tissues and developmental stages, but wNo is uniquely dominant in ovaries. Unexpectedly, the ratio of wHa to wNo in embryos does not reflect those observed in the ovaries, indicative of strain-specific transmission dynamics. Understanding how Wolbachia strains interact to establish and maintain stable infections has important implications for the development and effective implementation of Wolbachia-based vector biocontrol strategies, as well as more broadly defining how cooperation and conflict shape intracellular communities. IMPORTANCEWolbachia is a maternally transmitted intracellular bacterium that manipulates the reproduction and physiology of arthropods, resulting in drastic effects on the fitness, evolution, and even speciation of its hosts. Some hosts naturally harbor multiple strains of Wolbachia that are stably transmitted across generations, but almost nothing is known about the factors that limit or promote these coinfections, which can have profound effects on the host’s biology and evolution and are under consideration as an insect-management tool. Here, we define the infection dynamics of a known stably transmitted double infection in Drosophila simulans with an eye toward understanding the patterns of infection that might facilitate compatibility between the two microbes. We find that a combination of sex, tissue, and development all contributes to infection dynamics of the coinfection.
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Xiao Z, Tao X, Xu X, Zhu C, Nian X, Han D, Wang D, He Y. A Comparative Study on the Biological Characteristics of Parthenogenetic and Bisexual Restored Trichogramma pretiosum Lines. JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:2355-2360. [PMID: 34617112 DOI: 10.1093/jee/toab194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Indexed: 06/13/2023]
Abstract
In order to investigate the effect of Wolbachia on fitness of their hosts, the biological characteristics of a primarily parthenogenetic line and a bisexual restored line (obtained by antibiotic treatment) of Trichogramma pretiosum were compared in the laboratory. Results indicated that both the mean longevity and fecundity of parthenogenetic line (14.2 d and 165 eggs/female) were significantly higher than those in bisexual restored line (8.4 d and 124.2 eggs/female). Both lines of T. pretiosum had the highest daily fecundity (23.3 eggs/female for parthenogenetic line and 19.8 eggs/female for bisexual restored line) on the first day during their reproduction period, and their survival rate and daily fecundity decreased gradually with age; however, the survival rate and daily fecundity of the parthenogenetic line were always higher than those of bisexual restored line, during the entire experimental period. There was no significant difference in emergence rate and deformity rate between the two T. pretiosum lines. The life-table parameter results indicated that net reproduction rate (R0) and mean generation time (T) in parthenogenetic line (133 and 16.8) were significantly higher than those in bisexual restored line (61.7 and 15.5); intrinsic rate of natural increase (rm) and finite rate of increase (λ) in parthenogenetic line (0.29 and 1.34) were higher than those in bisexual restored line (0.26 and 1.3). Based on these results, it can be confirmed that the removal of Wolbachia in the parthenogenetic line had an adverse effect on fitness of T. pretiosum.
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Affiliation(s)
- Zhuangting Xiao
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou 510642, Guangdong Province, China
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, Guangdong Province, China
| | - Xiaobing Tao
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou 510642, Guangdong Province, China
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, Guangdong Province, China
| | - Xin Xu
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
- The Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming 650224, Yunnan Province, China
| | - Congying Zhu
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou 510642, Guangdong Province, China
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, Guangdong Province, China
| | - Xiaoge Nian
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou 510642, Guangdong Province, China
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, Guangdong Province, China
| | - Dongliang Han
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou 510642, Guangdong Province, China
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, Guangdong Province, China
| | - Desen Wang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou 510642, Guangdong Province, China
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, Guangdong Province, China
| | - Yurong He
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou 510642, Guangdong Province, China
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, Guangdong Province, China
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Morrow JL, Schneider DI, Klasson L, Janitz C, Miller WJ, Riegler M. Parallel Sequencing of Wolbachia wCer2 from Donor and Novel Hosts Reveals Multiple Incompatibility Factors and Genome Stability after Host Transfers. Genome Biol Evol 2021; 12:720-735. [PMID: 32163151 PMCID: PMC7259677 DOI: 10.1093/gbe/evaa050] [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] [Accepted: 03/10/2020] [Indexed: 12/11/2022] Open
Abstract
The application of Wolbachia in insect pest and vector control requires the establishment of genotypically stable host associations. The cytoplasmic incompatibility (CI) inducing Wolbachia strain wCer2 naturally occurs in the cherry fruit fly Rhagoletis cerasi as co-infection with other strains and was transferred to other fruit fly species by embryonic microinjections. We obtained wCer2 genome data from its native and three novel hosts, Drosophila simulans, Drosophila melanogaster, and Ceratitis capitata and assessed its genome stability, characteristics, and CI factor (cif) genes. De novo assembly was successful from Wolbachia cell-enriched singly infected D. simulans embryos, with minimal host and other bacterial genome traces. The low yield of Wolbachia sequence reads from total genomic extracts of one multiply infected R. cerasi pupa and one singly infected C. capitata adult limited de novo assemblies but was sufficient for comparative analyses. Across hosts wCer2 was stable in genome synteny and content. Polymorphic nucleotide sites were found in wCer2 of each host; however, only one nucleotide was different between R. cerasi and C. capitata, and none between replicated D. simulans lines. The wCer2 genome is highly similar to wAu (D. simulans), wMel (D. melanogaster), and wRec (Drosophila recens). In contrast to wMel and wRec (each with one cif gene pair) and wAu (without any cif genes), wCer2 has three pairs of Type I cif genes, and one Type V cifB gene without a cifA complement. This may explain previously reported CI patterns of wCer2, including incomplete rescue of its own CI modification in three novel host species.
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Affiliation(s)
- Jennifer L Morrow
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Daniela I Schneider
- Division of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Austria.,Department of Epidemiology of Microbial Diseases, Yale University, New Haven, Connecticut
| | - Lisa Klasson
- Molecular Evolution, Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Caroline Janitz
- Next Generation Sequencing Facility, Western Sydney University, Penrith, NSW, Australia
| | - Wolfgang J Miller
- Division of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Austria
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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10
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Kaur R, Shropshire JD, Cross KL, Leigh B, Mansueto AJ, Stewart V, Bordenstein SR, Bordenstein SR. Living in the endosymbiotic world of Wolbachia: A centennial review. Cell Host Microbe 2021. [PMID: 33945798 DOI: 10.20944/preprints202103.0338.v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The most widespread intracellular bacteria in the animal kingdom are maternally inherited endosymbionts of the genus Wolbachia. Their prevalence in arthropods and nematodes worldwide and stunning arsenal of parasitic and mutualistic adaptations make these bacteria a biological archetype for basic studies of symbiosis and applied outcomes for curbing human and agricultural diseases. Here, we conduct a summative, centennial analysis of living in the Wolbachia world. We synthesize literature on Wolbachia's host range, phylogenetic diversity, genomics, cell biology, and applications to filarial, arboviral, and agricultural diseases. We also review the mobilome of Wolbachia including phage WO and its essentiality to hallmark reproductive phenotypes in arthropods. Finally, the Wolbachia system is an exemplar for discovery-based science education using biodiversity, biotechnology, and bioinformatics lessons. As we approach a century of Wolbachia research, the interdisciplinary science of this symbiosis stands as a model for consolidating and teaching the integrative rules of endosymbiotic life.
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Affiliation(s)
- Rupinder Kaur
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA.
| | - J Dylan Shropshire
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Karissa L Cross
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Brittany Leigh
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Alexander J Mansueto
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Victoria Stewart
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Sarah R Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37235, USA.
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11
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Kaur R, Shropshire JD, Cross KL, Leigh B, Mansueto AJ, Stewart V, Bordenstein SR, Bordenstein SR. Living in the endosymbiotic world of Wolbachia: A centennial review. Cell Host Microbe 2021; 29:879-893. [PMID: 33945798 PMCID: PMC8192442 DOI: 10.1016/j.chom.2021.03.006] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/28/2021] [Accepted: 03/08/2021] [Indexed: 02/08/2023]
Abstract
The most widespread intracellular bacteria in the animal kingdom are maternally inherited endosymbionts of the genus Wolbachia. Their prevalence in arthropods and nematodes worldwide and stunning arsenal of parasitic and mutualistic adaptations make these bacteria a biological archetype for basic studies of symbiosis and applied outcomes for curbing human and agricultural diseases. Here, we conduct a summative, centennial analysis of living in the Wolbachia world. We synthesize literature on Wolbachia's host range, phylogenetic diversity, genomics, cell biology, and applications to filarial, arboviral, and agricultural diseases. We also review the mobilome of Wolbachia including phage WO and its essentiality to hallmark reproductive phenotypes in arthropods. Finally, the Wolbachia system is an exemplar for discovery-based science education using biodiversity, biotechnology, and bioinformatics lessons. As we approach a century of Wolbachia research, the interdisciplinary science of this symbiosis stands as a model for consolidating and teaching the integrative rules of endosymbiotic life.
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Affiliation(s)
- Rupinder Kaur
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA.
| | - J Dylan Shropshire
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Karissa L Cross
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Brittany Leigh
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Alexander J Mansueto
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Victoria Stewart
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Sarah R Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN 37235, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37235, USA.
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12
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Ferguson KB, Visser S, Dalíková M, Provazníková I, Urbaneja A, Pérez‐Hedo M, Marec F, Werren JH, Zwaan BJ, Pannebakker BA, Verhulst EC. Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest. INSECT MOLECULAR BIOLOGY 2021; 30:188-209. [PMID: 33305885 PMCID: PMC8048687 DOI: 10.1111/imb.12688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 11/25/2020] [Accepted: 12/07/2020] [Indexed: 05/14/2023]
Abstract
Nesidiocoris tenuis (Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. From the family Miridae, it is an economically important insect yet very little is known in terms of genetic information and no genomic or transcriptomic studies have been published. Here, we use a linked-read sequencing strategy on a single female N. tenuis. From this, we assembled the 355 Mbp genome and delivered an ab initio, homology-based and evidence-based annotation. Along the way, the bacterial "contamination" was removed from the assembly. In addition, bacterial lateral gene transfer (LGT) candidates were detected in the N. tenuis genome. The complete gene set is composed of 24 688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis, Halyomorpha halys and Acyrthosiphon pisum). We visualized the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n = 32. Additional analyses include the localization of 18S rDNA and unique satellite probes as well as pooled sequencing to assess nucleotide diversity and neutrality of the commercial population. This is one of the first mirid genomes to be released and the first of a mirid biological control agent.
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Affiliation(s)
- K. B. Ferguson
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - S. Visser
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - M. Dalíková
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - I. Provazníková
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
- European Molecular Biology LaboratoryHeidelbergGermany
| | - A. Urbaneja
- Centro de Protección Vegetal y BiotecnologíaInstituto Valenciano de Investigaciones Agrarias (IVIA)MoncadaSpain
| | - M. Pérez‐Hedo
- Centro de Protección Vegetal y BiotecnologíaInstituto Valenciano de Investigaciones Agrarias (IVIA)MoncadaSpain
| | - F. Marec
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
| | - J. H. Werren
- Department of BiologyUniversity of RochesterRochesterNew YorkUSA
| | - B. J. Zwaan
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - B. A. Pannebakker
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - E. C. Verhulst
- Laboratory of EntomologyWageningen UniversityWageningenThe Netherlands
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13
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Olafson PU, Aksoy S, Attardo GM, Buckmeier G, Chen X, Coates CJ, Davis M, Dykema J, Emrich SJ, Friedrich M, Holmes CJ, Ioannidis P, Jansen EN, Jennings EC, Lawson D, Martinson EO, Maslen GL, Meisel RP, Murphy TD, Nayduch D, Nelson DR, Oyen KJ, Raszick TJ, Ribeiro JMC, Robertson HM, Rosendale AJ, Sackton TB, Saelao P, Swiger SL, Sze SH, Tarone AM, Taylor DB, Warren WC, Waterhouse RM, Weirauch MT, Werren JH, Wilson RK, Zdobnov EM, Benoit JB. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control. BMC Biol 2021; 19:41. [PMID: 33750380 PMCID: PMC7944917 DOI: 10.1186/s12915-021-00975-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/03/2021] [Indexed: 01/01/2023] Open
Abstract
Background The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. Results This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways. Conclusions The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-00975-9.
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Affiliation(s)
- Pia U Olafson
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA.
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Geoffrey M Attardo
- Department of Entomology and Nematology, University of California - Davis, Davis, CA, USA
| | - Greta Buckmeier
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Xiaoting Chen
- The Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Craig J Coates
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - Megan Davis
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Justin Dykema
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Scott J Emrich
- Department of Electrical Engineering & Computer Science, University of Tennessee, Knoxville, TN, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Evan N Jansen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Daniel Lawson
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | | | - Gareth L Maslen
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Dana Nayduch
- Arthropod-borne Animal Diseases Research Unit, USDA-ARS, Manhattan, KS, USA
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kennan J Oyen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Tyler J Raszick
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - José M C Ribeiro
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Timothy B Sackton
- Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Perot Saelao
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Sonja L Swiger
- Department of Entomology, Texas A&M AgriLife Research and Extension Center, Stephenville, TX, USA
| | - Sing-Hoi Sze
- Department of Computer Science & Engineering, Department of Biochemistry & Biophysics, Texas A & M University, College Station, TX, USA
| | - Aaron M Tarone
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - David B Taylor
- Agroecosystem Management Research Unit, USDA-ARS, Lincoln, NE, USA
| | - Wesley C Warren
- University of Missouri, Bond Life Sciences Center, Columbia, MO, USA
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Richard K Wilson
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,College of Medicine, Ohio State University, Columbus, OH, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
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14
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Bing XL, Zhao DS, Sun JT, Zhang KJ, Hong XY. Genomic Analysis of Wolbachia from Laodelphax striatellus (Delphacidae, Hemiptera) Reveals Insights into Its "Jekyll and Hyde" Mode of Infection Pattern. Genome Biol Evol 2020; 12:3818-3831. [PMID: 31958110 PMCID: PMC7046167 DOI: 10.1093/gbe/evaa006] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 12/26/2022] Open
Abstract
Wolbachia is a widely distributed intracellular bacterial endosymbiont among invertebrates. The wStriCN, the Wolbachia strain that naturally infects an agricultural pest Laodelphax striatellus, has a “Jekyll and Hyde” mode of infection pattern with positive and negative effects: It not only kills many offspring by inducing cytoplasmic incompatibility (CI) but also significantly increases host fecundity. In this study, we assembled the draft genome of wStriCN and compared it with other Wolbachia genomes to look for clues to its Jekyll and Hyde characteristics. The assembled wStriCN draft genome is 1.79 Mb in size, which is the largest Wolbachia genome in supergroup B. Phylogenomic analysis showed that wStriCN is closest to Wolbachia from Asian citrus psyllid Diaphorina citri. These strains formed a monophylogentic clade within supergroup B. Compared with other Wolbachia genomes, wStriCN contains the most diverse insertion sequence families, the largest amount of prophage sequences, and the most ankyrin domain protein coding genes. The wStriCN genome encodes components of multiple secretion systems, including Types I, II, IV, VI, Sec, and Tac. We detected three pairs of homologs for CI factors CifA and CifB. These proteins harbor the catalytic domains responsible for CI phenotypes but are phylogenetically and structurally distinct from all known Cif proteins. The genome retains pathways for synthesizing biotin and riboflavin, which may explain the beneficial roles of wStriCN in its host planthoppers, which feed on nutrient-poor plant sap. Altogether, the genomic sequencing of wStriCN provides insight into understanding the phylogeny and biology of Wolbachia.
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Affiliation(s)
- Xiao-Li Bing
- Department of Entomology, Nanjing Agricultural University, Jiangsu, China
| | - Dian-Shu Zhao
- Department of Entomology, Nanjing Agricultural University, Jiangsu, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Jiangsu, China
| | - Kai-Jun Zhang
- Department of Entomology, Nanjing Agricultural University, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Jiangsu, China
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15
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Lefoulon E, Clark T, Guerrero R, Cañizales I, Cardenas-Callirgos JM, Junker K, Vallarino-Lhermitte N, Makepeace BL, Darby AC, Foster JM, Martin C, Slatko BE. Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm. Microb Genom 2020; 6:mgen000487. [PMID: 33295865 PMCID: PMC8116671 DOI: 10.1099/mgen.0.000487] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/14/2020] [Indexed: 01/13/2023] Open
Abstract
Wolbachia are alpha-proteobacteria symbionts infecting a large range of arthropod species and two different families of nematodes. Interestingly, these endosymbionts are able to induce diverse phenotypes in their hosts: they are reproductive parasites within many arthropods, nutritional mutualists within some insects and obligate mutualists within their filarial nematode hosts. Defining Wolbachia 'species' is controversial and so they are commonly classified into 17 different phylogenetic lineages, termed supergroups, named A-F, H-Q and S. However, available genomic data remain limited and not representative of the full Wolbachia diversity; indeed, of the 24 complete genomes and 55 draft genomes of Wolbachia available to date, 84 % belong to supergroups A and B, exclusively composed of Wolbachia from arthropods. For the current study, we took advantage of a recently developed DNA-enrichment method to produce four complete genomes and two draft genomes of Wolbachia from filarial nematodes. Two complete genomes, wCtub and wDcau, are the smallest Wolbachia genomes sequenced to date (863 988 bp and 863 427 bp, respectively), as well as the first genomes representing supergroup J. These genomes confirm the validity of this supergroup, a controversial clade due to weaknesses of the multilocus sequence typing approach. We also produced the first draft Wolbachia genome from a supergroup F filarial nematode representative (wMhie), two genomes from supergroup D (wLsig and wLbra) and the complete genome of wDimm from supergroup C. Our new data confirm the paradigm of smaller Wolbachia genomes from filarial nematodes containing low levels of transposable elements and the absence of intact bacteriophage sequences, unlike many Wolbachia from arthropods, where both are more abundant. However, we observe differences among the Wolbachia genomes from filarial nematodes: no global co-evolutionary pattern, strong synteny between supergroup C and supergroup J Wolbachia, and more transposable elements observed in supergroup D Wolbachia compared to the other supergroups. Metabolic pathway analysis indicates several highly conserved pathways (haem and nucleotide biosynthesis, for example) as opposed to more variable pathways, such as vitamin B biosynthesis, which might be specific to certain host-symbiont associations. Overall, there appears to be no single Wolbachia-filarial nematode pattern of co-evolution or symbiotic relationship.
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Affiliation(s)
- Emilie Lefoulon
- Molecular Parasitology Group, New England Biolabs, Ipswich, MA, USA
- Present address: School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Travis Clark
- Molecular Parasitology Group, New England Biolabs, Ipswich, MA, USA
| | - Ricardo Guerrero
- Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Israel Cañizales
- Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela
- Ediciones La Fauna KPT SL, Madrid, Spain
| | - Jorge Manuel Cardenas-Callirgos
- Neotropical Parasitology Research Network - NEOPARNET, Asociación Peruana de Helmintología e Invertebrados Afines – APHIA, Peru
| | - Kerstin Junker
- Epidemiology, Parasites and Vectors, ARC-Onderstepoort Veterinary Institute, Onderstepoort 0110, South Africa
| | - Nathaly Vallarino-Lhermitte
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum National d’Histoire Naturelle, CNRS, Paris, France
| | - Benjamin L. Makepeace
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alistair C. Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jeremy M. Foster
- Molecular Parasitology Group, New England Biolabs, Ipswich, MA, USA
| | - Coralie Martin
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum National d’Histoire Naturelle, CNRS, Paris, France
| | - Barton E. Slatko
- Molecular Parasitology Group, New England Biolabs, Ipswich, MA, USA
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16
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Wang Z, Li H, Zhou X, Tang M, Sun L, Zhan S, Xiao Q. Comparative characterization of microbiota between the sibling species of tea geometrid moth Ectropis obliqua Prout and E. grisescens Warren. BULLETIN OF ENTOMOLOGICAL RESEARCH 2020; 110:684-693. [PMID: 32741378 DOI: 10.1017/s0007485320000164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
For a wide range of insect species, the microbiota has potential roles in determining host developmental programme, immunity and reproductive biology. The tea geometrid moths Ectropis obliqua and E. grisescens are two closely related species that mainly feed on tea leaves. Although they can mate, infertile hybrids are produced. Therefore, these species provide a pair of model species for studying the molecular mechanisms of microbiotal involvement in host reproductive biology. In this study, we first identified and compared the compositions of microbiota between these sibling species, revealing higher microbiotal diversity for E. grisescens. The microbiota of E. obliqua mainly comprised the phyla Firmicutes, Proteobacteria and Cyanobacteria, whereas that of E. grisescens was dominated by Proteobacteria, Actinobacteria and Firmicutes. At the genus level, the dominant microbiota of E. grisescens included Wolbachia, Enterobacter and Pseudomonas and that of E. obliqua included Melissococcus, Staphylococcus and Enterobacter. Furthermore, we verified the rate of Wolbachia to infect 80 samples from eight different geographical populations, and the results supported that only E. grisescens harboured Wolbachia. Taken together, our findings indicate significantly different microbiotal compositions for E. obliqua and E. grisescens, with Wolbachia possibly being a curial factor influencing the reproductive isolation of these species. This study provides new insight into the mechanisms by which endosymbiotic bacteria, particularly Wolbachia, interact with sibling species.
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Affiliation(s)
- Zhibo Wang
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Hong Li
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaogui Zhou
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Meijun Tang
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Liang Sun
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Shuai Zhan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Xiao
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
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17
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Laidoudi Y, Levasseur A, Medkour H, Maaloum M, Ben Khedher M, Sambou M, Bassene H, Davoust B, Fenollar F, Raoult D, Mediannikov O. An Earliest Endosymbiont, Wolbachia massiliensis sp. nov., Strain PL13 from the Bed Bug ( Cimex hemipterus), Type Strain of a New Supergroup T. Int J Mol Sci 2020; 21:E8064. [PMID: 33138055 PMCID: PMC7662661 DOI: 10.3390/ijms21218064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 02/06/2023] Open
Abstract
The symbiotic Wolbachia are the most sophisticated mutualistic bacterium among all insect-associated microbiota. Wolbachia-insect relationship fluctuates from the simple facultative/parasitic to an obligate nutritional-mutualistic association as it was the case of the bedbug-Wolbachia from Cimexlectularius. Understanding this association may help in the control of associated arthropods. Genomic data have proven to be reliable tools in resolving some aspects of these symbiotic associations. Although, Wolbachia appear to be fastidious or uncultivated bacteria which strongly limited their study. Here we proposed Drosophila S2 cell line for the isolation and culture model to study Wolbachia strains. We therefore isolated and characterized a novel Wolbachia strain associated with the bedbug Cimexhemipterus, designated as wChem strain PL13, and proposed Wolbachiamassiliensis sp. nov. strain wChem-PL13 a type strain of this new species from new supergroup T. Phylogenetically, T-supergroup was close to F and S-supergroups from insects and D-supergroup from filarial nematodes. We determined the 1,291,339-bp genome of wChem-PL13, which was the smallest insect-associated Wolbachia genomes. Overall, the wChem genome shared 50% of protein coding genes with the other insect-associated facultative Wolbachia strains. These findings highlight the diversity of Wolbachia genotypes as well as the Wolbachia-host relationship among Cimicinae subfamily. The wChem provides folate and riboflavin vitamins on which the host depends, while the bacteria had a limited translation mechanism suggesting its strong dependence to its hosts. However, the clear-cut distinction between mutualism and parasitism of the wChem in C. hemipterus cannot be yet ruled out.
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Affiliation(s)
- Younes Laidoudi
- Aix Marseille Univ, IRD, AP-HM, MEPHI, 13385 Marseille, France; (Y.L.); (A.L.); (H.M.); (M.B.K.); (B.D.); (D.R.)
- IHU Méditerranée Infection, 13385 Marseille, France;
| | - Anthony Levasseur
- Aix Marseille Univ, IRD, AP-HM, MEPHI, 13385 Marseille, France; (Y.L.); (A.L.); (H.M.); (M.B.K.); (B.D.); (D.R.)
- IHU Méditerranée Infection, 13385 Marseille, France;
| | - Hacène Medkour
- Aix Marseille Univ, IRD, AP-HM, MEPHI, 13385 Marseille, France; (Y.L.); (A.L.); (H.M.); (M.B.K.); (B.D.); (D.R.)
- IHU Méditerranée Infection, 13385 Marseille, France;
| | - Mossaab Maaloum
- Laboratory of Biology and Health, Faculty of Sciences Ben M’sik, Hassan II University, Sidi Othmane, Casablanca 7955, Morocco;
| | - Mariem Ben Khedher
- Aix Marseille Univ, IRD, AP-HM, MEPHI, 13385 Marseille, France; (Y.L.); (A.L.); (H.M.); (M.B.K.); (B.D.); (D.R.)
- IHU Méditerranée Infection, 13385 Marseille, France;
| | - Masse Sambou
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France, 13385 Marseille, France; (M.S.); (H.B.)
- Campus Commun UCAD-IRD of Hann, Dakar 10200, Senegal
| | - Hubert Bassene
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France, 13385 Marseille, France; (M.S.); (H.B.)
- Campus Commun UCAD-IRD of Hann, Dakar 10200, Senegal
| | - Bernard Davoust
- Aix Marseille Univ, IRD, AP-HM, MEPHI, 13385 Marseille, France; (Y.L.); (A.L.); (H.M.); (M.B.K.); (B.D.); (D.R.)
- IHU Méditerranée Infection, 13385 Marseille, France;
| | - Florence Fenollar
- IHU Méditerranée Infection, 13385 Marseille, France;
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France, 13385 Marseille, France; (M.S.); (H.B.)
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, 13385 Marseille, France; (Y.L.); (A.L.); (H.M.); (M.B.K.); (B.D.); (D.R.)
- IHU Méditerranée Infection, 13385 Marseille, France;
| | - Oleg Mediannikov
- Aix Marseille Univ, IRD, AP-HM, MEPHI, 13385 Marseille, France; (Y.L.); (A.L.); (H.M.); (M.B.K.); (B.D.); (D.R.)
- IHU Méditerranée Infection, 13385 Marseille, France;
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18
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Wang X, Xiong X, Cao W, Zhang C, Werren JH, Wang X. Phylogenomic Analysis of Wolbachia Strains Reveals Patterns of Genome Evolution and Recombination. Genome Biol Evol 2020; 12:2508-2520. [PMID: 33283864 PMCID: PMC7719230 DOI: 10.1093/gbe/evaa219] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 12/19/2022] Open
Abstract
Wolbachia are widespread intracellular bacteria that mediate many important biological processes in arthropod species. In this study, we identified 210 conserved single-copy genes in 33 genome-sequenced Wolbachia strains in the A–F supergroups. Phylogenomic analyses with these core genes indicate that all 33 Wolbachia strains maintain the supergroup relationship, which was classified previously based on the multilocus sequence typing (MLST) genes. Using an interclade recombination screening method, 14 inter-supergroup recombination events were discovered in six genes (2.9%) among 210 single-copy orthologs. This finding suggests a relatively low frequency of intergroup recombination. Interestingly, they have occurred not only between A and B supergroups (nine events) but also between A and E supergroups (five events). Maintenance of such transfers suggests possible roles in Wolbachia infection-related functions. Comparisons of strain divergence using the five genes of the MLST system show a high correlation (Pearson correlation coefficient r = 0.98) between MLST and whole-genome divergences, indicating that MLST is a reliable method for identifying related strains when whole-genome data are not available. The phylogenomic analysis and the identified core gene set in our study will serve as a valuable foundation for strain identification and the investigation of recombination and genome evolution in Wolbachia.
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Affiliation(s)
- Xiaozhu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University
| | - Xiao Xiong
- Department of Pathobiology, College of Veterinary Medicine, Auburn University.,Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wenqi Cao
- Department of Pathobiology, College of Veterinary Medicine, Auburn University
| | - Chao Zhang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | | | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University.,Alabama Agricultural Experiment Station, Auburn University.,Department of Entomology and Plant Pathobiology, Auburn University.,HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
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19
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Carneiro Dutra HL, Deehan MA, Frydman H. Wolbachia and Sirtuin-4 interaction is associated with alterations in host glucose metabolism and bacterial titer. PLoS Pathog 2020; 16:e1008996. [PMID: 33048997 PMCID: PMC7584242 DOI: 10.1371/journal.ppat.1008996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 10/23/2020] [Accepted: 09/18/2020] [Indexed: 12/30/2022] Open
Abstract
Wolbachia is an intracellular bacterial symbiont of arthropods notorious for inducing many reproductive manipulations that foster its dissemination. Wolbachia affects many aspects of host biology, including metabolism, longevity and physiology, being described as a nutrient provisioning or metabolic parasite, depending on the host-microbe association. Sirtuins (SIRTs) are a family of NAD+-dependent post-translational regulatory enzymes known to affect many of the same processes altered by Wolbachia, including aging and metabolism, among others. Despite a clear overlap in control of host-derived pathways and physiology, no work has demonstrated a link between these two regulators. We used genetically tractable Drosophila melanogaster to explore the role of sirtuins in shaping signaling pathways in the context of a host-symbiont model. By using transcriptional profiling and metabolic assays in the context of genetic knockouts/over-expressions, we examined the effect of several Wolbachia strains on host sirtuin expression across distinct tissues and timepoints. We also quantified the downstream effects of the sirtuin x Wolbachia interaction on host glucose metabolism, and in turn, how it impacted Wolbachia titer. Our results indicate that the presence of Wolbachia is associated with (1) reduced sirt-4 expression in a strain-specific manner, and (2) alterations in host glutamate dehydrogenase expression and ATP levels, key components of glucose metabolism. We detected high glucose levels in Wolbachia-infected flies, which further increased when sirt-4 was over-expressed. However, under sirt-4 knockout, flies displayed a hypoglycemic state not rescued to normal levels in the presence of Wolbachia. Finally, whole body sirt-4 over-expression resulted in reduced Wolbachia ovarian titer. Our results expand knowledge of Wolbachia-host associations in the context of a yet unexplored class of host post-translational regulatory enzymes with implications for conserved host signaling pathways and bacterial titer, factors known to impact host biology and the symbiont's ability to spread through populations.
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Affiliation(s)
| | - Mark Anthony Deehan
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Horacio Frydman
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- National Emerging Infectious Disease Laboratory, Boston University, Boston, Massachusetts, United States of America
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20
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Lindsey ARI. Sensing, Signaling, and Secretion: A Review and Analysis of Systems for Regulating Host Interaction in Wolbachia. Genes (Basel) 2020; 11:E813. [PMID: 32708808 PMCID: PMC7397232 DOI: 10.3390/genes11070813] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 12/18/2022] Open
Abstract
Wolbachia (Anaplasmataceae) is an endosymbiont of arthropods and nematodes that resides within host cells and is well known for manipulating host biology to facilitate transmission via the female germline. The effects Wolbachia has on host physiology, combined with reproductive manipulations, make this bacterium a promising candidate for use in biological- and vector-control. While it is becoming increasingly clear that Wolbachia's effects on host biology are numerous and vary according to the host and the environment, we know very little about the molecular mechanisms behind Wolbachia's interactions with its host. Here, I analyze 29 Wolbachia genomes for the presence of systems that are likely central to the ability of Wolbachia to respond to and interface with its host, including proteins for sensing, signaling, gene regulation, and secretion. Second, I review conditions under which Wolbachia alters gene expression in response to changes in its environment and discuss other instances where we might hypothesize Wolbachia to regulate gene expression. Findings will direct mechanistic investigations into gene regulation and host-interaction that will deepen our understanding of intracellular infections and enhance applied management efforts that leverage Wolbachia.
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Affiliation(s)
- Amelia R I Lindsey
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
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21
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Lefoulon E, Clark T, Borveto F, Perriat-Sanguinet M, Moulia C, Slatko BE, Gavotte L. Pseudoscorpion Wolbachia symbionts: diversity and evidence for a new supergroup S. BMC Microbiol 2020; 20:188. [PMID: 32605600 PMCID: PMC7325362 DOI: 10.1186/s12866-020-01863-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/18/2020] [Indexed: 11/29/2022] Open
Abstract
Background Wolbachia are the most widely spread endosymbiotic bacteria, present in a wide variety of insects and two families of nematodes. As of now, however, relatively little genomic data has been available. The Wolbachia symbiont can be parasitic, as described for many arthropod systems, an obligate mutualist, as in filarial nematodes or a combination of both in some organisms. They are currently classified into 16 monophyletic lineage groups (“supergroups”). Although the nature of these symbioses remains largely unknown, expanded Wolbachia genomic data will contribute to understanding their diverse symbiotic mechanisms and evolution. Results This report focuses on Wolbachia infections in three pseudoscorpion species infected by two distinct groups of Wolbachia strains, based upon multi-locus phylogenies. Geogarypus minor harbours wGmin and Chthonius ischnocheles harbours wCisc, both closely related to supergroup H, while Atemnus politus harbours wApol, a member of a novel supergroup S along with Wolbachia from the pseudoscorpion Cordylochernes scorpioides (wCsco). Wolbachia supergroup S is most closely related to Wolbachia supergroups C and F. Using target enrichment by hybridization with Wolbachia-specific biotinylated probes to capture large fragments of Wolbachia DNA, we produced two draft genomes of wApol. Annotation of wApol highlights presence of a biotin operon, which is incomplete in many sequenced Wolbachia genomes. Conclusions The present study highlights at least two symbiont acquisition events among pseudoscorpion species. Phylogenomic analysis indicates that the Wolbachia from Atemnus politus (wApol), forms a separate supergroup (“S”) with the Wolbachia from Cordylochernes scorpioides (wCsco). Interestingly, the biotin operon, present in wApol, appears to have been horizontally transferred multiple times along Wolbachia evolutionary history.
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Affiliation(s)
- Emilie Lefoulon
- Molecular Parasitology Group, Molecular Enzyme Division, New England Biolabs, Inc., Ipswich, USA.,School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, USA
| | - Travis Clark
- Molecular Parasitology Group, Molecular Enzyme Division, New England Biolabs, Inc., Ipswich, USA
| | - Fanni Borveto
- ISEM, University of Montpellier, Montpellier, France
| | | | | | - Barton E Slatko
- Molecular Parasitology Group, Molecular Enzyme Division, New England Biolabs, Inc., Ipswich, USA.
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22
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The Intracellular Symbiont Wolbachia pipientis Enhances Recombination in a Dose-Dependent Manner. INSECTS 2020; 11:insects11050284. [PMID: 32384776 PMCID: PMC7290356 DOI: 10.3390/insects11050284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
Wolbachia pipientis is an intracellular alphaproteobacterium that infects 40%-60% of insect species and is well known for host reproductive manipulations. Although Wolbachia are primarily maternally transmitted, evidence of horizontal transmission can be found in incongruent host-symbiont phylogenies and recent acquisitions of the same Wolbachia strain by distantly related species. Parasitoids and predator-prey interactions may indeed facilitate the transfer of Wolbachia between insect lineages, but it is likely that Wolbachia are acquired via introgression in many cases. Many hypotheses exist to explain Wolbachia prevalence and penetrance, such as nutritional supplementation, protection from parasites, protection from viruses, or direct reproductive parasitism. Using classical genetics, we show that Wolbachia increase recombination in infected lineages across two genomic intervals. This increase in recombination is titer-dependent as the wMelPop variant, which infects at higher load in Drosophila melanogaster, increases recombination 5% more than the wMel variant. In addition, we also show that Spiroplasma poulsonii, another bacterial intracellular symbiont of D. melanogaster, does not induce an increase in recombination. Our results suggest that Wolbachia infection specifically alters its host's recombination landscape in a dose-dependent manner.
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23
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Wang X, Xiong X, Cao W, Zhang C, Werren JH, Wang X. Genome Assembly of the A-Group Wolbachia in Nasonia oneida Using Linked-Reads Technology. Genome Biol Evol 2020; 11:3008-3013. [PMID: 31596462 PMCID: PMC6821208 DOI: 10.1093/gbe/evz223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2019] [Indexed: 12/26/2022] Open
Abstract
Wolbachia are obligate intracellular bacteria which commonly infect various nematode and arthropod species. Genome sequences have been generated from arthropod samples following enrichment for the intracellular bacteria, and genomes have also been assembled from arthropod whole-genome sequencing projects. However, these methods remain challenging for infections that occur at low titers in hosts. Here we report the first Wolbachia genome assembled from host sequences using 10× Genomics linked-reads technology. The high read depth attainable by this method allows for recovery of intracellular bacteria that are at low concentrations. Based on the depth differences (714× for the insect and 59× for the bacterium), we assembled the genome of a Wolbachia in the parasitoid jewel wasp species Nasonia oneida. The final draft assembly consists of 1,293, 06 bp in 47 scaffolds with 1,114 coding genes and 97.01% genome completeness assessed by checkM. Comparisons of the five Multi Locus Sequence Typing genes revealed that the sequenced Wolbachia genome is the A1 strain (henceforth wOneA1) previously reported in N. oneida. Pyrosequencing confirms that the wasp strain lacks A2 and B types previously detected in this insect, which were likely lost during laboratory culturing. Assembling bacterial genomes from host genome projects can provide an effective method for sequencing bacterial genomes, even when the infections occur at low density in sampled tissues.
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Affiliation(s)
| | - Xiao Xiong
- Department of Pathobiology, Auburn University.,Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wenqi Cao
- Department of Pathobiology, Auburn University
| | - Chao Zhang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | | | - Xu Wang
- Department of Pathobiology, Auburn University.,Alabama Agricultural Experiment Station, Auburn University.,HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.,Department of Entomology and Plant Pathology, Auburn University
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24
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Distinct epigenomic and transcriptomic modifications associated with Wolbachia-mediated asexuality. PLoS Pathog 2020; 16:e1008397. [PMID: 32187233 PMCID: PMC7105135 DOI: 10.1371/journal.ppat.1008397] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/30/2020] [Accepted: 02/11/2020] [Indexed: 11/19/2022] Open
Abstract
Wolbachia are maternally transmitted intracellular bacteria that induce a range of pathogenic and fitness-altering effects on insect and nematode hosts. In parasitoid wasps of the genus Trichogramma, Wolbachia infection induces asexual production of females, thus increasing transmission of Wolbachia. It has been hypothesized that Wolbachia infection accompanies a modification of the host epigenome. However, to date, data on genome-wide epigenomic changes associated with Wolbachia are limited, and are often confounded by background genetic differences. Here, we took sexually reproducing Trichogramma free of Wolbachia and introgressed their genome into a Wolbachia-infected cytoplasm, converting them to Wolbachia-mediated asexuality. Wolbachia was then cured from replicates of these introgressed lines, allowing us to examine the genome-wide effects of wasps newly converted to asexual reproduction while controlling for genetic background. We thus identified gene expression and DNA methylation changes associated with Wolbachia-infection. We found no overlaps between differentially expressed genes and differentially methylated genes, indicating that Wolbachia-infection associated DNA methylation change does not directly modulate levels of gene expression. Furthermore, genes affected by these mechanisms exhibit distinct evolutionary histories. Genes differentially methylated due to the infection tended to be evolutionarily conserved. In contrast, differentially expressed genes were significantly more likely to be unique to the Trichogramma lineage, suggesting host-specific transcriptomic responses to infection. Nevertheless, we identified several novel aspects of Wolbachia-associated DNA methylation changes. Differentially methylated genes included those involved in oocyte development and chromosome segregation. Interestingly, Wolbachia-infection was associated with higher levels of DNA methylation. Additionally, Wolbachia infection reduced overall variability in gene expression, even after accounting for the effect of DNA methylation. We also identified specific cases where alternative exon usage was associated with DNA methylation changes due to Wolbachia infection. These results begin to reveal distinct genes and molecular pathways subject to Wolbachia induced epigenetic modification and/or host responses to Wolbachia-infection. Wolbachia is an extremely common endosymbiotic infection of arthropods and nematodes. One of the reasons why Wolbachia can so successfully infect diverse species is the bacterium’s ability to profoundly alter the reproductive behavior of its host. It has been proposed that Wolbachia may modify host’s epigenetic programs to alter its reproductive behavior. However, it has been difficult to study how epigenetic programs change with Wolbachia infection, due to the confounding effects of genetic backgrounds. Here, we studied host transcriptome and epigenome changes associated with Wolbachia infection in a homogenous genetic background, by carrying out an innovative introgression scheme. By doing so, we show, for the first time, high-resolution molecular consequences of intracellular infection and offer insights into epigenetic and transcriptomic regulation of invertebrates.
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25
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Magro A, Lecompte E, Hemptinne J, Soares AO, Dutrillaux A, Murienne J, Fürsch H, Dutrillaux B. First case of parthenogenesis in ladybirds (Coleoptera: Coccinellidae) suggests new mechanisms for the evolution of asexual reproduction. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12339] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Alexandra Magro
- Laboratoire Evolution et Diversité biologique UMR EDB 5174 CNRS / UT3 / IRDToulouse France
- Ecole Nationale Supérieure de Formation de l'Enseignement Agricole Auzeville-Tolosane France
| | - Emilie Lecompte
- Laboratoire Evolution et Diversité biologique UMR EDB 5174 CNRS / UT3 / IRDToulouse France
- Université Toulouse III‐Paul Sabatier Toulouse France
| | - Jean‐Louis Hemptinne
- Laboratoire Evolution et Diversité biologique UMR EDB 5174 CNRS / UT3 / IRDToulouse France
- Ecole Nationale Supérieure de Formation de l'Enseignement Agricole Auzeville-Tolosane France
| | - Antonio O. Soares
- Centre for Ecology, Evolution and Environmental Changes Azorean Biodiversity Group University of the Azores Ponta Delgada, Azores Portugal
| | - Anne‐Marie Dutrillaux
- Institut de Systématique, Evolution, Biodiversité UMR ISYEB 7205 CNRS / MNHN / UPMC / EPHE Museum National d'Histoire Naturelle Paris France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité biologique UMR EDB 5174 CNRS / UT3 / IRDToulouse France
- Université Toulouse III‐Paul Sabatier Toulouse France
| | | | - Bernard Dutrillaux
- Institut de Systématique, Evolution, Biodiversité UMR ISYEB 7205 CNRS / MNHN / UPMC / EPHE Museum National d'Histoire Naturelle Paris France
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26
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Hellemans S, Kaczmarek N, Marynowska M, Calusinska M, Roisin Y, Fournier D. Bacteriome-associated Wolbachia of the parthenogenetic termite Cavitermes tuberosus. FEMS Microbiol Ecol 2019; 95:5247714. [PMID: 30551145 DOI: 10.1093/femsec/fiy235] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/13/2018] [Indexed: 11/13/2022] Open
Abstract
Wolbachia has deeply shaped the ecology and evolution of many arthropods, and interactions between the two partners are a continuum ranging from parasitism to mutualism. Non-dispersing queens of the termite Cavitermes tuberosus are parthenogenetically produced through gamete duplication, a mode of ploidy restoration generally induced by Wolbachia. These queens display a bacteriome-like structure in the anterior part of the mesenteron. Our study explores the possibility of a nutritional mutualistic, rather than a parasitic, association between Wolbachia and C. tuberosus. We found a unique strain (wCtub), nested in the supergroup F, in 28 nests collected in French Guiana, the island of Trinidad and the state of Paraíba, Brazil (over 3500 km). wCtub infects individuals regardless of caste, sex or reproductive (sexual versus parthenogenetic) origin. qPCR assays reveal that Wolbachia densities are higher in the bacteriome-like structure and in the surrounding gut compared to other somatic tissues. High-throughput 16S rRNA gene amplicon sequencing reveals that Wolbachia represents over 97% of bacterial reads present in the bacteriome structure. BLAST analyses of 16S rRNA, bioA (a gene of the biosynthetic pathway of B vitamins) and five multilocus sequence typing genes indicated that wCtub shares 99% identity with wCle, an obligate nutritional mutualist of the bedbug Cimex lectularius.
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Affiliation(s)
- Simon Hellemans
- Evolutionary Biology & Ecology, Université libre de Bruxelles, Avenue F.D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium
| | - Nicolas Kaczmarek
- Evolutionary Biology & Ecology, Université libre de Bruxelles, Avenue F.D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium
| | - Martyna Marynowska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, L-4422 Belvaux, Luxembourg
| | - Magdalena Calusinska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, L-4422 Belvaux, Luxembourg
| | - Yves Roisin
- Evolutionary Biology & Ecology, Université libre de Bruxelles, Avenue F.D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium
| | - Denis Fournier
- Evolutionary Biology & Ecology, Université libre de Bruxelles, Avenue F.D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium
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27
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Sharko FS, Nedoluzhko AV, Lê BM, Tsygankova SV, Boulygina ES, Rastorguev SM, Sokolov AS, Rodriguez F, Mazur AM, Polilov AA, Benton R, Evgen'ev MB, Arkhipova IR, Prokhortchouk EB, Skryabin KG. A partial genome assembly of the miniature parasitoid wasp, Megaphragma amalphitanum. PLoS One 2019; 14:e0226485. [PMID: 31869362 PMCID: PMC6927652 DOI: 10.1371/journal.pone.0226485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 11/26/2019] [Indexed: 12/18/2022] Open
Abstract
Body size reduction, also known as miniaturization, is an important evolutionary process that affects a number of physiological and phenotypic traits and helps animals conquer new ecological niches. However, this process is poorly understood at the molecular level. Here, we report genomic and transcriptomic features of arguably the smallest known insect-the parasitoid wasp, Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae). In contrast to expectations, we find that the genome and transcriptome sizes of this parasitoid wasp are comparable to other members of the Chalcidoidea superfamily. Moreover, compared to other chalcid wasps the gene content of M. amalphitanum is remarkably conserved. Intriguingly, we observed significant changes in M. amalphitanum transposable element dynamics over time, in which an initial burst was followed by suppression of activity, possibly due to a recent reinforcement of the genome defense machinery. Overall, while the M. amalphitanum genomic data reveal certain features that may be linked to the unusual biological properties of this organism, miniaturization is not associated with a large decrease in genome complexity.
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Affiliation(s)
- Fedor S. Sharko
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Artem V. Nedoluzhko
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Nord University, Faculty of Biosciences and Aquaculture, Bodø, Norway
| | - Brandon M. Lê
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | | | | | | | - Alexey S. Sokolov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Alexander M. Mazur
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Polilov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | | | - Irina R. Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Egor B. Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
| | - Konstantin G. Skryabin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
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28
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Gebiola M, Streicher JW, Rugman-Jones PF, Morse JG, Stouthamer R. Genome-wide analyses of single nucleotide polymorphisms reveal the consequences of traditional mass-rearing on genetic variation in Aphytis melinus (Hymenoptera: Aphelinidae): the danger of putting all eggs in one basket. PEST MANAGEMENT SCIENCE 2019; 75:3102-3112. [PMID: 30924276 DOI: 10.1002/ps.5427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/15/2019] [Accepted: 03/23/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Aphytis melinus DeBach (Hymenoptera: Aphelinidae) is a highly effective biocontrol agent of the California red scale Aonidiella aurantii (Maskell) (Hemiptera: Diaspididae). It is commercially reared and used for augmentative releases within integrated pest management programs. However, mass rearing of biocontrol agents can result in population bottlenecks and high levels of inbreeding and/or adaptation to the factitious rearing conditions. Although these factors can all negatively impact field performance of biocontrol agents, few empirical studies have examined the genetic consequences of mass rearing. We used double-digest RAD sequencing (ddRADseq) to investigate the effect of traditional mass rearing on genetic variation among insectary colonies of A. melinus relative to wild populations in native (Pakistan) and introduced (California) ranges. RESULTS Analyses of up to 9700 single nucleotide polymorphisms (SNPs) revealed that insectary populations had less genomic variation than introduced populations. This was evidenced by fewer private alleles, reduced heterozygosity, and greater missing data in the insectary populations. Further, California insectaries formed a distinct genomic cluster relative to the other samples, a surprising result given that the insectary colonies were putatively established at different times and from different source populations. These differences were evident across most data sets also after we filtered out contaminant DNA from the most common host species (Aspidiotus nerii Bouché and A. aurantii). CONCLUSION We hypothesize that this pattern would only result if: (i) directional selection for 'captive' phenotypes produces convergent patterns of genomic variation across insectaries; or (ii) the California insectary colonies were all founded from a unifying source population and/or that the insectaries regularly exchange 'genetic' stocks. We show that RADseq is an effective method to investigate the effects of mass rearing on genetics of biocontrol agents. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Marco Gebiola
- Department of Entomology, University of California, Riverside, CA, USA
| | | | | | - Joseph G Morse
- Department of Entomology, University of California, Riverside, CA, USA
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29
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Meany MK, Conner WR, Richter SV, Bailey JA, Turelli M, Cooper BS. Loss of cytoplasmic incompatibility and minimal fecundity effects explain relatively low Wolbachia frequencies in Drosophila mauritiana. Evolution 2019; 73:1278-1295. [PMID: 31001816 PMCID: PMC6554066 DOI: 10.1111/evo.13745] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/29/2019] [Indexed: 12/16/2022]
Abstract
Maternally transmitted Wolbachia bacteria infect about half of all insect species. Many Wolbachia cause cytoplasmic incompatibility (CI) and reduced egg hatch when uninfected females mate with infected males. Although CI produces a frequency-dependent fitness advantage that leads to high equilibrium Wolbachia frequencies, it does not aid Wolbachia spread from low frequencies. Indeed, the fitness advantages that produce initial Wolbachia spread and maintain non-CI Wolbachia remain elusive. wMau Wolbachia infecting Drosophila mauritiana do not cause CI, despite being very similar to CI-causing wNo from Drosophila simulans (0.068% sequence divergence over 682,494 bp), suggesting recent CI loss. Using draft wMau genomes, we identify a deletion in a CI-associated gene, consistent with theory predicting that selection within host lineages does not act to increase or maintain CI. In the laboratory, wMau shows near-perfect maternal transmission; but we find no significant effect on host fecundity, in contrast to published data. Intermediate wMau frequencies on the island of Mauritius are consistent with a balance between unidentified small, positive fitness effects and imperfect maternal transmission. Our phylogenomic analyses suggest that group-B Wolbachia, including wMau and wPip, diverged from group-A Wolbachia, such as wMel and wRi, 6-46 million years ago, more recently than previously estimated.
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Affiliation(s)
- Megan K. Meany
- Division of Biological Sciences, University of Montana,
Missoula, MT USA
| | - William R. Conner
- Division of Biological Sciences, University of Montana,
Missoula, MT USA
| | - Sophia V. Richter
- Division of Biological Sciences, University of Montana,
Missoula, MT USA
| | - Jessica A. Bailey
- Division of Biological Sciences, University of Montana,
Missoula, MT USA
| | - Michael Turelli
- Department of Evolution and Ecology, University of
California, Davis, CA USA
| | - Brandon S. Cooper
- Division of Biological Sciences, University of Montana,
Missoula, MT USA
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30
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Abstract
Microbial symbioses exhibit astounding adaptations, yet all symbionts face the problem of how to reliably associate with host offspring every generation. A common strategy is vertical transmission, in which symbionts are directly transmitted from the female to her offspring. The diversity of symbionts and vertical transmission mechanisms is as expansive as the diversity of eukaryotic host taxa that house them. However, there are several common themes among these mechanisms based on the degree to which symbionts associate with the host germline during transmission. In this review, we detail three distinct vertical transmission strategies, starting with associations that are transmitted from host somatic cells to offspring somatic cells, either due to lacking a germline or avoiding it. A second strategy involves somatically-localized symbionts that migrate into the germline during host development. The third strategy we discuss is one in which the symbiont maintains continuous association with the germline throughout development. Unexpectedly, the vast majority of documented vertically inherited symbionts rely on the second strategy: soma-to-germline migration. Given that not all eukaryotes contain a sequestered germline and instead produce offspring from somatic stem cell lineages, this soma-to-germline migration is discussed in the context of multicellular evolution. Lastly, as recent genomics data have revealed an abundance of horizontal gene transfer events from symbiotic and non-symbiotic bacteria to host genomes, we discuss their impact on eukaryotic host evolution.
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Affiliation(s)
- Shelbi L Russell
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States.
| | - Laura Chappell
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - William Sullivan
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
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31
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Dhaygude K, Nair A, Johansson H, Wurm Y, Sundström L. The first draft genomes of the ant Formica exsecta, and its Wolbachia endosymbiont reveal extensive gene transfer from endosymbiont to host. BMC Genomics 2019; 20:301. [PMID: 30991952 PMCID: PMC6469114 DOI: 10.1186/s12864-019-5665-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 04/02/2019] [Indexed: 02/05/2023] Open
Abstract
Background Adapting to changes in the environment is the foundation of species survival, and is usually thought to be a gradual process. However, transposable elements (TEs), epigenetic modifications, and/or genetic material acquired from other organisms by means of horizontal gene transfer (HGTs), can also lead to novel adaptive traits. Social insects form dense societies, which attract and maintain extra- and intracellular accessory inhabitants, which may facilitate gene transfer between species. The wood ant Formica exsecta (Formicidae; Hymenoptera), is a common ant species throughout the Palearctic region. The species is a well-established model for studies of ecological characteristics and evolutionary conflict. Results In this study, we sequenced and assembled draft genomes for F. exsecta and its endosymbiont Wolbachia. The F. exsecta draft genome is 277.7 Mb long; we identify 13,767 protein coding genes, for which we provide gene ontology and protein domain annotations. This is also the first report of a Wolbachia genome from ants, and provides insights into the phylogenetic position of this endosymbiont. We also identified multiple horizontal gene transfer events (HGTs) from Wolbachia to F. exsecta. Some of these HGTs have also occurred in parallel in multiple other insect genomes, highlighting the extent of HGTs in eukaryotes. Conclusion We present the first draft genome of ant F. exsecta, and its endosymbiont Wolbachia (wFex), and show considerable rates of gene transfer from the symbiont to the host. We expect that especially the F. exsecta genome will be valuable resource in further exploration of the molecular basis of the evolution of social organization. Electronic supplementary material The online version of this article (10.1186/s12864-019-5665-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kishor Dhaygude
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and environmental sciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland.
| | - Abhilash Nair
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and environmental sciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Helena Johansson
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and environmental sciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Yannick Wurm
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Liselotte Sundström
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and environmental sciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
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32
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Genome organisation and comparative genomics of four novel Wolbachia genome assemblies from Indian Drosophila host. Funct Integr Genomics 2019; 19:617-632. [PMID: 30798391 DOI: 10.1007/s10142-019-00664-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 11/12/2018] [Accepted: 02/04/2019] [Indexed: 10/27/2022]
Abstract
Wolbachia has long been known to share an endosymbiotic relationship with its host as an obligate intracellular organism. Wolbachia diversity as different supergroups is found to be host-specific in most cases except a few, where the host species is seen to accommodate multiple strains. Besides, the Wolbachia genome must have undergone several changes in response to the evolving host genome in order to adapt and establish a strong association with its host, thus making a distinctive Wolbachia-host alliance. The present study focusses on four novel genome assembly and genome-wide sequence variations of Indian Wolbachia strains, i.e. wMel and wRi isolated from two different Drosophila hosts. The genome assembly has an average size of ~ 1.1 Mb and contains ~ 1100 genes, which is comparable with the previously sequenced Wolbachia genomes. The comparative genomics analysis of these genomes and sequence-wide comparison of some functionally significant genes, i.e. ankyrin repeats, Wsp and T4SS, highlight their sequence similarities and dissimilarities, further supporting the strain-specific association of Wolbachia to its host. Interestingly, some of the sequence variations are also found to be restricted to only Indian Wolbachia strains. Further analysis of prophage and their flanking regions in the Wolbachia genome reveals the presence of several functional genes which may assist the phage to reside inside the bacterial host, thus providing a trade-off for the endosymbiont-host association. Understanding this endosymbiont genome in different eco-geographical conditions has become imperative for the recent use of Wolbachia in medical entomology as a vector-control agent.
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33
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Kampfraath AA, Klasson L, Anvar SY, Vossen RHAM, Roelofs D, Kraaijeveld K, Ellers J. Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model. BMC Genomics 2019; 20:106. [PMID: 30727958 PMCID: PMC6364476 DOI: 10.1186/s12864-019-5492-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/29/2019] [Indexed: 12/11/2022] Open
Abstract
Background Theory predicts that dependency within host-endosymbiont interactions results in endosymbiont genome size reduction. Unexpectedly, the largest Wolbachia genome was found in the obligate, parthenogenesis-associated wFol. In this study, we investigate possible processes underlying this genome expansion by comparing a re-annotated wFol genome to other Wolbachia genomes. In addition, we also search for candidate genes related to parthenogenesis induction (PI). Results Within wFol, we found five phage WO regions representing 25.4% of the complete genome, few pseudogenized genes, and an expansion of DNA-repair genes in comparison to other Wolbachia. These signs of genome conservation were mirrored in the wFol host, the springtail F. candida, which also had an expanded DNA-repair gene family and many horizontally transferred genes. Across all Wolbachia genomes, there was a strong correlation between gene numbers of Wolbachia strains and their hosts. In order to identify genes with a potential link to PI, we assembled the genome of an additional PI strain, wLcla. Comparisons between four PI Wolbachia, including wFol and wLcla, and fourteen non-PI Wolbachia yielded a small set of potential candidate genes for further investigation. Conclusions The strong similarities in genome content of wFol and its host, as well as the correlation between host and Wolbachia gene numbers suggest that there may be some form of convergent evolution between endosymbiont and host genomes. If such convergent evolution would be strong enough to overcome the evolutionary forces causing genome reduction, it would enable expanded genomes within long-term obligate endosymbionts. Electronic supplementary material The online version of this article (10.1186/s12864-019-5492-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A A Kampfraath
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - L Klasson
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - S Y Anvar
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - R H A M Vossen
- Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - D Roelofs
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - K Kraaijeveld
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - J Ellers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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34
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Lindsey ARI, Rice DW, Bordenstein SR, Brooks AW, Bordenstein SR, Newton ILG. Evolutionary Genetics of Cytoplasmic Incompatibility Genes cifA and cifB in Prophage WO of Wolbachia. Genome Biol Evol 2018; 10:434-451. [PMID: 29351633 PMCID: PMC5793819 DOI: 10.1093/gbe/evy012] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2018] [Indexed: 12/20/2022] Open
Abstract
The bacterial endosymbiont Wolbachia manipulates arthropod reproduction to facilitate its maternal spread through host populations. The most common manipulation is cytoplasmic incompatibility (CI): Wolbachia-infected males produce modified sperm that cause embryonic mortality, unless rescued by embryos harboring the same Wolbachia. The genes underlying CI, cifA and cifB, were recently identified in the eukaryotic association module of Wolbachia’s prophage WO. Here, we use transcriptomic and genomic approaches to address three important evolutionary facets of the cif genes. First, we assess whether or not cifA and cifB comprise a classic toxin–antitoxin operon in wMel and show that the two genes exhibit striking, transcriptional differences across host development. They can produce a bicistronic message despite a predicted hairpin termination element in their intergenic region. Second, cifA and cifB strongly coevolve across the diversity of phage WO. Third, we provide new domain and functional predictions across homologs within Wolbachia, and show that amino acid sequences vary substantially across the genus. Finally, we investigate conservation of cifA and cifB and find frequent degradation and loss of the genes in strains that no longer induce CI. Taken together, we demonstrate that cifA and cifB exhibit complex transcriptional regulation in wMel, provide functional annotations that broaden the potential mechanisms of CI induction, and report recurrent erosion of cifA and cifB in non-CI strains, thus expanding our understanding of the most widespread form of reproductive parasitism.
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Affiliation(s)
| | - Danny W Rice
- Department of Biology, Indiana University, Bloomington
| | | | - Andrew W Brooks
- Department of Biological Sciences, Vanderbilt University.,Vanderbilt Genetics Institute, Vanderbilt University
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University.,Vanderbilt Genetics Institute, Vanderbilt University.,Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University.,Department of Pathology, Microbiology and Immunology, Vanderbilt University
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35
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Pascar J, Chandler CH. A bioinformatics approach to identifying Wolbachia infections in arthropods. PeerJ 2018; 6:e5486. [PMID: 30202647 PMCID: PMC6126470 DOI: 10.7717/peerj.5486] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 07/30/2018] [Indexed: 11/20/2022] Open
Abstract
Wolbachia is the most widespread endosymbiont, infecting >20% of arthropod species, and capable of drastically manipulating the host's reproductive mechanisms. Conventionally, diagnosis has relied on PCR amplification; however, PCR is not always a reliable diagnostic technique due to primer specificity, strain diversity, degree of infection and/or tissue sampled. Here, we look for evidence of Wolbachia infection across a wide array of arthropod species using a bioinformatic approach to detect the Wolbachia genes ftsZ, wsp, and the groE operon in next-generation sequencing samples available through the NCBI Sequence Read Archive. For samples showing signs of infection, we attempted to assemble entire Wolbachia genomes, and in order to better understand the relationships between hosts and symbionts, phylogenies were constructed using the assembled gene sequences. Out of the 34 species with positively identified infections, eight species of arthropod had not previously been recorded to harbor Wolbachia infection. All putative infections cluster with known representative strains belonging to supergroup A or B, which are known to only infect arthropods. This study presents an efficient bioinformatic approach for post-sequencing diagnosis and analysis of Wolbachia infection in arthropods.
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Affiliation(s)
- Jane Pascar
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, United States of America
- Department of Biology, Syracuse University, Syracuse, NY, United States of America
| | - Christopher H. Chandler
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, United States of America
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36
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Chung M, Small ST, Serre D, Zimmerman PA, Dunning Hotopp JC. Draft genome sequence of the Wolbachia endosymbiont of Wuchereria bancrofti wWb. Pathog Dis 2018; 75:4584485. [PMID: 29099918 PMCID: PMC5827699 DOI: 10.1093/femspd/ftx115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/31/2017] [Indexed: 11/18/2022] Open
Abstract
The draft genome assembly of the Wolbachia endosymbiont of
Wuchereria bancrofti (wWb) consists of 1060 850 bp in
100 contigs and contains 961 ORFs, with a single copy of the 5S rRNA, 16S rRNA and 23S
rRNA and each of the 34 tRNA genes. Phylogenetic core genome analyses show
wWb to cluster with other strains in supergroup D of the
Wolbachia phylogeny, while being most closely related to the
Wolbachia endosymbiont of Brugia malayi strain TRS
(wBm). The wWb and wBm genomes share
779 orthologous clusters with wWb having 101 unclustered genes and
wBm having 23 unclustered genes. The higher number of unclustered genes
in the wWb genome likely reflects the fragmentation of the draft
genome.
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Affiliation(s)
- Matthew Chung
- Institute for Genome Sciences, University of Maryland, Baltimore, MD 21201, USA.,Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Scott T Small
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH 44106, USA.,Eck Institute for Global Health, University of Notre Dame, South Bend, IN 46556, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland, Baltimore, MD 21201, USA.,Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Peter A Zimmerman
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Julie C Dunning Hotopp
- Institute for Genome Sciences, University of Maryland, Baltimore, MD 21201, USA.,Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
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37
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Lindsey ARI, Kelkar YD, Wu X, Sun D, Martinson EO, Yan Z, Rugman-Jones PF, Hughes DST, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni HV, Worley KC, Muzny DM, Ye G, Gibbs RA, Richards S, Yi SV, Stouthamer R, Werren JH. Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum. BMC Biol 2018; 16:54. [PMID: 29776407 PMCID: PMC5960102 DOI: 10.1186/s12915-018-0520-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/20/2018] [Indexed: 12/25/2022] Open
Abstract
Background Trichogrammatids are minute parasitoid wasps that develop within other insect eggs. They are less than half a millimeter long, smaller than some protozoans. The Trichogrammatidae are one of the earliest branching families of Chalcidoidea: a diverse superfamily of approximately half a million species of parasitoid wasps, proposed to have evolved from a miniaturized ancestor. Trichogramma are frequently used in agriculture, released as biological control agents against major moth and butterfly pests. Additionally, Trichogramma are well known for their symbiotic bacteria that induce asexual reproduction in infected females. Knowledge of the genome sequence of Trichogramma is a major step towards further understanding its biology and potential applications in pest control. Results We report the 195-Mb genome sequence of Trichogramma pretiosum and uncover signatures of miniaturization and adaptation in Trichogramma and related parasitoids. Comparative analyses reveal relatively rapid evolution of proteins involved in ribosome biogenesis and function, transcriptional regulation, and ploidy regulation. Chalcids also show loss or especially rapid evolution of 285 gene clusters conserved in other Hymenoptera, including many that are involved in signal transduction and embryonic development. Comparisons between sexual and asexual lineages of Trichogramma pretiosum reveal that there is no strong evidence for genome degradation (e.g., gene loss) in the asexual lineage, although it does contain a lower repeat content than the sexual lineage. Trichogramma shows particularly rapid genome evolution compared to other hymenopterans. We speculate these changes reflect adaptations to miniaturization, and to life as a specialized egg parasitoid. Conclusions The genomes of Trichogramma and related parasitoids are a valuable resource for future studies of these diverse and economically important insects, including explorations of parasitoid biology, symbiosis, asexuality, biological control, and the evolution of miniaturization. Understanding the molecular determinants of parasitism can also inform mass rearing of Trichogramma and other parasitoids for biological control. Electronic supplementary material The online version of this article (10.1186/s12915-018-0520-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amelia R I Lindsey
- Department of Entomology, University of California Riverside, Riverside, California, 92521, USA. .,Present Address: Department of Biology, Indiana University, Bloomington, Indiana, 47405, USA.
| | - Yogeshwar D Kelkar
- Department of Biology, University of Rochester, Rochester, New York, 14627, USA
| | - Xin Wu
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Dan Sun
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Ellen O Martinson
- Department of Biology, University of Rochester, Rochester, New York, 14627, USA.,Present Address: Department of Entomology, University of Georgia, Athens, Georgia, 30602, USA
| | - Zhichao Yan
- Department of Biology, University of Rochester, Rochester, New York, 14627, USA.,State Key Laboratory of Rice Biology & Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Paul F Rugman-Jones
- Department of Entomology, University of California Riverside, Riverside, California, 92521, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Soojin V Yi
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Richard Stouthamer
- Department of Entomology, University of California Riverside, Riverside, California, 92521, USA.
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, New York, 14627, USA.
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38
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Lindsey ARI, Kelkar YD, Wu X, Sun D, Martinson EO, Yan Z, Rugman-Jones PF, Hughes DST, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni HV, Worley KC, Muzny DM, Ye G, Gibbs RA, Richards S, Yi SV, Stouthamer R, Werren JH. Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum. BMC Biol 2018. [DOI: 10.1186/s12915-018-0520-9 10.1186/s12915-018-0520-9 [pii]] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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39
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Duplouy A, Hornett EA. Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts. PeerJ 2018; 6:e4629. [PMID: 29761037 PMCID: PMC5947162 DOI: 10.7717/peerj.4629] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/27/2018] [Indexed: 12/18/2022] Open
Abstract
The Lepidoptera is one of the most widespread and recognisable insect orders. Due to their remarkable diversity, economic and ecological importance, moths and butterflies have been studied extensively over the last 200 years. More recently, the relationship between Lepidoptera and their heritable microbial endosymbionts has received increasing attention. Heritable endosymbionts reside within the host’s body and are often, but not exclusively, inherited through the female line. Advancements in molecular genetics have revealed that host-associated microbes are both extremely prevalent among arthropods and highly diverse. Furthermore, heritable endosymbionts have been repeatedly demonstrated to play an integral role in many aspects of host biology, particularly host reproduction. Here, we review the major findings of research of heritable microbial endosymbionts of butterflies and moths. We promote the Lepidoptera as important models in the study of reproductive manipulations employed by heritable endosymbionts, with the mechanisms underlying male-killing and feminisation currently being elucidated in moths and butterflies. We also reveal that the vast majority of research undertaken of Lepidopteran endosymbionts concerns Wolbachia. While this highly prevalent bacterium is undoubtedly important, studies should move towards investigating the presence of other, and interacting endosymbionts, and we discuss the merits of examining the microbiome of Lepidoptera to this end. We finally consider the importance of understanding the influence of endosymbionts under global environmental change and when planning conservation management of endangered Lepidoptera species.
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Affiliation(s)
- Anne Duplouy
- Organismal and Evolutionary Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Emily A Hornett
- Department of Zoology, University of Cambridge, Cambridge, UK
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40
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Lindsey ARI, Stouthamer R. The effects of outbreeding on a parasitoid wasp fixed for infection with a parthenogenesis-inducing Wolbachia symbiont. Heredity (Edinb) 2017; 119:411-417. [PMID: 28902190 DOI: 10.1038/hdy.2017.53] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 02/08/2023] Open
Abstract
Trichogramma wasps can be rendered asexual by infection with the maternally inherited symbiont Wolbachia. Previous studies indicate the Wolbachia strains infecting Trichogramma wasps are host-specific, inferred by failed horizontal transfer of Wolbachia to novel Trichogramma hosts. Additionally, Trichogramma can become dependent upon their Wolbachia infection for the production of female offspring, leaving them irreversibly asexual, further linking host and symbiont. We hypothesized Wolbachia strains infecting irreversibly asexual, resistant to horizontal transfer Trichogramma would show adaptation to a particular host genetic background. To test this, we mated Wolbachia-dependent females with males from a Wolbachia-naïve population to create heterozygous wasps. We measured sex ratios and fecundity, a proxy for Wolbachia fitness, produced by heterozygous wasps, and by their recombinant offspring. We find a heterozygote advantage, resulting in higher fitness for Wolbachia, as wasps will produce more offspring without any reduction in the proportion of females. While recombinant wasps did not differ in total fecundity after 10 days, recombinants produced fewer offspring early on, leading to an increased female-biased sex ratio for the whole brood. Despite the previously identified barriers to horizontal transfer of Wolbachia to and from Trichogramma pretiosum, there were no apparent barriers for Wolbachia to induce parthenogenesis in these non-native backgrounds. This is likely due to the route of infection being introgression rather than horizontal transfer, and possibly the co-evolution of Wolbachia with the mitochondria rather than the nuclear genome. These results help to elucidate the mechanisms by which Wolbachia adapt to hosts and the evolution of host-symbiont phenotypes.
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Affiliation(s)
- A R I Lindsey
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - R Stouthamer
- Department of Entomology, University of California Riverside, Riverside, CA, USA
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41
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Wilmes M, Meier K, Schiefer A, Josten M, Otten CF, Klöckner A, Henrichfreise B, Vollmer W, Hoerauf A, Pfarr K. AmiD Is a Novel Peptidoglycan Amidase in Wolbachia Endosymbionts of Drosophila melanogaster. Front Cell Infect Microbiol 2017; 7:353. [PMID: 28824885 PMCID: PMC5543032 DOI: 10.3389/fcimb.2017.00353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/21/2017] [Indexed: 11/13/2022] Open
Abstract
Wolbachia endobacteria are obligate intracellular bacteria with a highly reduced genome infecting many arthropod and filarial species, in which they manipulate arthropod reproduction to increase their transmission and are essential for nematode development and survival. The Wolbachia genome encodes all enzymes required for the synthesis of the cell wall building block lipid II, although a peptidoglycan-like structure has not been detected. Despite the ability to synthesize lipid II, Wolbachia from arthropods and nematodes have only a subset of genes encoding enzymes involved in the periplasmic processing of lipid II and peptidoglycan recycling, with arthropods having two more than nematodes. We functionally analyzed the activity of the putative cell wall hydrolase AmiD from the Wolbachia endosymbiont of Drosophila melanogaster, an enzyme not encoded by the nematode endobacteria. Wolbachia AmiD has Zn2+-dependent amidase activity and cleaves intact peptidoglycan, monomeric lipid II and anhydromuropeptides, substrates that are generated during bacterial growth. AmiD may have been maintained in arthropod Wolbachia to avoid host immune recognition by degrading cell wall fragments in the periplasm. This is the first description of a wolbachial lipid II processing enzyme putatively expressed in the periplasm.
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Affiliation(s)
- Miriam Wilmes
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital BonnBonn, Germany
| | - Kirstin Meier
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital BonnBonn, Germany
| | - Andrea Schiefer
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital BonnBonn, Germany
| | - Michaele Josten
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital BonnBonn, Germany
| | - Christian F Otten
- Institute for Cell and Molecular Bioscience, Newcastle UniversityNewcastle upon Tyne, United Kingdom
| | - Anna Klöckner
- Institute for Pharmaceutical Microbiology, University of BonnBonn, Germany
| | | | - Waldemar Vollmer
- Institute for Cell and Molecular Bioscience, Newcastle UniversityNewcastle upon Tyne, United Kingdom
| | - Achim Hoerauf
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital BonnBonn, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-CologneBonn, Germany
| | - Kenneth Pfarr
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital BonnBonn, Germany
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Balado M, Benzekri H, Labella AM, Claros MG, Manchado M, Borrego JJ, Osorio CR, Lemos ML. Genomic analysis of the marine fish pathogen Photobacterium damselae subsp. piscicida: Insertion sequences proliferation is associated with chromosomal reorganisations and rampant gene decay. INFECTION GENETICS AND EVOLUTION 2017; 54:221-229. [PMID: 28688976 DOI: 10.1016/j.meegid.2017.07.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 01/25/2023]
Abstract
Photobacterium damselae subsp. piscicida (Pdp) is an intracellular fish pathogen that causes photobacteriosis, a disease proven deadly in farmed fish worldwide. This work focuses on the analysis of genome sequences, chromosomes structure and gene contents of two strains from Sparus aurata (DI21) and Solea senegalensis (L091106-03H), isolated on the Spanish Atlantic coast. The comparative genomic analysis revealed that DI21 and L091106-03H share 98% of their genomes, including two virulence plasmids: pPHDP70 encoding siderophore piscibactin synthesis and pPHDP10 encoding the apoptotic toxin AIP56. Both genomes harbour a surprisingly large number of IS elements accounting for 12-17% of the total genome, representing an IS density of 0.15 elements per kb, one of the highest IS density values in a bacterial pathogen. This massive proliferation of ISs is responsible for the generation of a high number of pseudogenes that caused extensive loss of biological functions. Pseudogene formation is one of the main features of Pdp genome that explains most of the ecological and phenotypic differences with respect to its sibling subspecies P. damselae subsp. damselae and to other Vibrionaceae. Evidence was also found proving the existence of two chromosomal configurations depending on the origin of the strains: an European and an Asian/American types of genome organisation, reinforcing the idea of the existence of two geographically-linked clonal lineages in Pdp. In short, our study suggests that the host-dependent lifestyle of Pdp allowed massive IS proliferation and gene decay processes, which are major evolutionary forces in the shaping of the Pdp genome.
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Affiliation(s)
- Miguel Balado
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Hicham Benzekri
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Alejandro M Labella
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - M Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Manuel Manchado
- IFAPA Centro El Toruño, Junta de Andalucía, El Puerto de Santa María, Cádiz, Spain
| | - Juan J Borrego
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Carlos R Osorio
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
| | - Manuel L Lemos
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
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Lindsey ARI, Stouthamer R. Penetrance of symbiont-mediated parthenogenesis is driven by reproductive rate in a parasitoid wasp. PeerJ 2017; 5:e3505. [PMID: 28663939 PMCID: PMC5490460 DOI: 10.7717/peerj.3505] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/06/2017] [Indexed: 12/30/2022] Open
Abstract
Trichogramma wasps are tiny parasitoids of lepidopteran eggs, used extensively for biological control. They are often infected with the bacterial symbiont Wolbachia, which converts Trichogramma to an asexual mode of reproduction, whereby females develop from unfertilized eggs. However, this Wolbachia-induced parthenogenesis is not always complete, and previous studies have noted that infected females will produce occasional males in the lab. The conditions that reduce penetrance of the parthenogenesis phenotype are not well understood. We hypothesized that more ecologically relevant conditions of limited host access will sustain female-biased sex ratios. After restricting access to host eggs, we found a strong relationship between reproductive rate and sex ratio. By limiting reproduction to one hour a day, wasps could sustain up to 100% effective parthenogenesis for one week, with no significant impact on total fecundity. Reproductive output in the first 24-hours appears to be critical to the total sex ratio of the entire brood. Limiting oviposition in that period resulted in more effective parthenogenesis after one week, again without any significant impact on total fecundity. Our data suggest that this phenomenon may be due to the depletion of Wolbachia when oviposition occurs continuously, whereas Wolbachia titers may recover when offspring production is limited. In addition to the potential to improve mass rearing of Trichogramma for biological control, findings from this study help elucidate the context-dependent nature of a pervasive symbiotic relationship.
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Affiliation(s)
- Amelia R I Lindsey
- Department of Entomology, University of California, Riverside, Riverside, CA, United States of America
| | - Richard Stouthamer
- Department of Entomology, University of California, Riverside, Riverside, CA, United States of America
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