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Ye X, Yang Y, Zhao X, Fang Q, Ye G. The state of parasitoid wasp genomics. Trends Parasitol 2024:S1471-4922(24)00218-6. [PMID: 39227194 DOI: 10.1016/j.pt.2024.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/12/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024]
Abstract
Parasitoid wasps represent a group of parasitic insects with high species diversity that have played a pivotal role in biological control and evolutionary studies. Over the past 20 years, developments in genomics have greatly enhanced our understanding of the biology of these species. Technological leaps in sequencing have facilitated the improvement of genome quality and quantity, leading to the availability of hundreds of parasitoid wasp genomes. Here, we summarize recent progress in parasitoid wasp genomics, focusing on the evolution of genome size (GS) and the genomic basis of several key traits. We also discuss the contributions of genomics in studying venom evolution and endogenization of viruses. Finally, we advocate for increased sequencing and functional research to better understand parasitoid biology and enhance biological control.
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Affiliation(s)
- Xinhai Ye
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China.
| | - Yi Yang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xianxin Zhao
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.
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Biswas T, Vogel H, Biedermann PHW, Lehenberger M, Yuvaraj JK, Andersson MN. Few chemoreceptor genes in the ambrosia beetle Trypodendron lineatum may reflect its specialized ecology. BMC Genomics 2024; 25:764. [PMID: 39107741 PMCID: PMC11302349 DOI: 10.1186/s12864-024-10678-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Chemoreception is crucial for insect fitness, underlying for instance food-, host-, and mate finding. Chemicals in the environment are detected by receptors from three divergent gene families: odorant receptors (ORs), gustatory receptors (GRs), and ionotropic receptors (IRs). However, how the chemoreceptor gene families evolve in parallel with ecological specializations remains poorly understood, especially in the order Coleoptera. Hence, we sequenced the genome and annotated the chemoreceptor genes of the specialised ambrosia beetle Trypodendron lineatum (Coleoptera, Curculionidae, Scolytinae) and compared its chemoreceptor gene repertoires with those of other scolytines with different ecological adaptations, as well as a polyphagous cerambycid species. RESULTS We identified 67 ORs, 38 GRs, and 44 IRs in T. lineatum ('Tlin'). Across gene families, T. lineatum has fewer chemoreceptors compared to related scolytines, the coffee berry borer Hypothenemus hampei and the mountain pine beetle Dendroctonus ponderosae, and clearly fewer receptors than the polyphagous cerambycid Anoplophora glabripennis. The comparatively low number of chemoreceptors is largely explained by the scarcity of large receptor lineage radiations, especially among the bitter taste GRs and the 'divergent' IRs, and the absence of alternatively spliced GR genes. Only one non-fructose sugar receptor was found, suggesting several sugar receptors have been lost. Also, we found no orthologue in the 'GR215 clade', which is widely conserved across Coleoptera. Two TlinORs are orthologous to ORs that are functionally conserved across curculionids, responding to 2-phenylethanol (2-PE) and green leaf volatiles (GLVs), respectively. CONCLUSIONS Trypodendron lineatum reproduces inside the xylem of decaying conifers where it feeds on its obligate fungal mutualist Phialophoropsis ferruginea. Like previous studies, our results suggest that stenophagy correlates with small chemoreceptor numbers in wood-boring beetles; indeed, the few GRs may be due to its restricted fungal diet. The presence of TlinORs orthologous to those detecting 2-PE and GLVs in other species suggests these compounds are important for T. lineatum. Future functional studies should test this prediction, and chemoreceptor annotations should be conducted on additional ambrosia beetle species to investigate whether few chemoreceptors is a general trait in this specialized group of beetles.
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Affiliation(s)
- Twinkle Biswas
- Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden
| | - Heiko Vogel
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Peter H W Biedermann
- Chair of Forest Entomology and Protection, University of Freiburg, Stegen-Wittental, Germany
| | | | | | - Martin N Andersson
- Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden.
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Yang D, Li D, Jiang L, Lin J, Yue G, Xiao K, Hao X, Ji Q, Hong Y, Cai P, Yang J. Antennal transcriptome analysis of Psyttalia incisi (silvestri) (Hymenoptera: Braconidae): identification and tissue expression profiling of candidate odorant-binding protein genes. Mol Biol Rep 2024; 51:333. [PMID: 38393425 DOI: 10.1007/s11033-024-09281-3] [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: 10/21/2023] [Accepted: 01/23/2024] [Indexed: 02/25/2024]
Abstract
BACKGROUND Olfaction plays an important role in host-seeking by parasitoids, as they can sense chemical signals using sensitive chemosensory systems. Psyttalia incisi (Silvestri) (Hymenoptera: Braconidae) is the dominant parasitoid of Bactrocera dorsalis (Hendel) in fruit-producing regions of southern China. The olfactory behavior of P. incisi has been extensively studied; however, the chemosensory mechanisms of this species are not fully understood. RESULTS Bioinformatics analysis of 64,515 unigenes from the antennal transcriptome of both male and female adults P. incisi identified 87 candidate chemosensory genes. These included 13 odorant-binding proteins (OBPs), seven gustatory receptors (GRs), 55 odorant receptors (ORs), 10 ionotropic receptors (IRs), and two sensory neuron membrane proteins (SNMPs). Phylogenetic trees were constructed to predict evolutionary relationships between these chemosensory genes in hymenopterans. Moreover, the tissue expression profiles of 13 OBPs were analyzed by quantitative real-time PCR, revealing high expression of seven OBPs (1, 3, 6, 7, 8, 12, and 13) in the antennae. CONCLUSION This study represents the first identification of chemosensory genes and the determination of their expression patterns in different tissues of P. incisi. These results contribute to a better understanding of the function of the chemosensory system of this parasitoid species.
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Affiliation(s)
- Deqing Yang
- Institute of Biological Control, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Biopesticide and Chemical Biology, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Horticulture, College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Dongliang Li
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
- Department of Horticulture, College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Lili Jiang
- Institute of Biological Control, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Biopesticide and Chemical Biology, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jia Lin
- Institute of Biological Control, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Biopesticide and Chemical Biology, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guoqing Yue
- Institute of Biological Control, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Biopesticide and Chemical Biology, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kang Xiao
- Institute of Biological Control, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Biopesticide and Chemical Biology, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuxing Hao
- Institute of Biological Control, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Biopesticide and Chemical Biology, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinge Ji
- Institute of Biological Control, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Biopesticide and Chemical Biology, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongcong Hong
- Department of Horticulture, College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Pumo Cai
- Institute of Biological Control, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China.
- Key Laboratory of Biopesticide and Chemical Biology, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China.
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China.
- Department of Horticulture, College of Tea and Food Science, Wuyi University, Wuyishan, China.
| | - Jianquan Yang
- Institute of Biological Control, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China.
- Key Laboratory of Biopesticide and Chemical Biology, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China.
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China.
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Wulff JP, Traverso LM, Latorre-Estivalis JM, Segura DF, Lanzavecchia SB. Identification of candidate genes associated with host-seeking behavior in the parasitoid wasp Diachasmimorpha longicaudata. BMC Genomics 2024; 25:147. [PMID: 38321385 PMCID: PMC10848486 DOI: 10.1186/s12864-024-10034-6] [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: 04/14/2023] [Accepted: 01/20/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Diachasmimorpha longicaudata is a hymenopteran fruit fly endoparasitoid. Females of this species find their hosts for oviposition by using complex sensorial mechanisms in response to physical and chemical stimuli associated with the host and host habitat. Ecological and behavioral aspects related to host-seeking behavior for oviposition have been extensively studied in D. longicaudata, including the identification of volatile organic compounds acting as attractants to females. In this sense, molecular mechanisms of chemoreception have been explored in this species, including a preliminary characterization of odorant-binding proteins (OBPs), chemosensory proteins (CSPs) and odorant receptors (ORs), among other proteins. Functional assays on OBP and CSP have been conducted as a first approach to identify molecular mechanisms associated with the female host-seeking behavior for oviposition. The aims of the present study were to identify the D. longicaudata sensory gene repertoire expressed in the antenna of sexually mature and mated individuals of both sexes, and subsequently, characterize transcripts differentially expressed in the antennae of females to identify candidate genes associated with the female host-seeking behavior for oviposition. RESULTS A total of 33,745 predicted protein-coding sequences were obtained from a de novo antennal transcriptome assembly. Ten sensory-related gene families were annotated as follows: 222 ORs, 44 ionotropic receptors (IRs), 25 gustatory receptors (GRs), 9 CSPs, 13 OBPs, 2 ammonium transporters (AMTs), 8 pickpocket (PPKs) receptors, 16 transient receptor potential (TRP) channels, 12 CD36/SNMPs and 3 Niemann-Pick type C2 like proteins (NPC2-like). The differential expression analysis revealed 237 and 151 transcripts up- and downregulated, respectively, between the female and male antennae. Ninety-seven differentially expressed transcripts corresponded to sensory-related genes including 88 transcripts being upregulated (87 ORs and one TRP) and nine downregulated (six ORs, two CSPs and one OBP) in females compared to males. CONCLUSIONS The sensory gene repertoire of D. longicaudata was similar to that of other taxonomically related parasitoid wasps. We identified a high number of ORs upregulated in the female antenna. These results may indicate that this gene family has a central role in the chemoreception of sexually mature females during the search for hosts and host habitats for reproductive purposes.
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Affiliation(s)
- Juan P Wulff
- Entomology and Plant Pathology, NCSU, Raleigh, NC, USA.
| | - Lucila M Traverso
- Laboratorio de Neurobiología de Insectos (LNI), Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CENEXA, CONICET, La Plata, Bs As, Argentina
| | - Jose M Latorre-Estivalis
- Laboratorio de Insectos Sociales, Biología Molecular y Neurociencias (IFIBYNE), Instituto de Fisiología, Universidad de Buenos Aires - CONICET, Bs As, Buenos Aires, Argentina
| | - Diego F Segura
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética Ewald A. Favret (INTA) gv-IABIMO (CONICET), Hurlingham, Bs As, Argentina
- Facultad de Ciencias Agrarias y Veterinarias, Universidad del Salvador, Bs As, Argentina
| | - Silvia B Lanzavecchia
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética Ewald A. Favret (INTA) gv-IABIMO (CONICET), Hurlingham, Bs As, Argentina
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Vertacnik KL, Herrig DK, Godfrey RK, Hill T, Geib SM, Unckless RL, Nelson DR, Linnen CR. Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae). Ecol Evol 2023; 13:e10506. [PMID: 37791292 PMCID: PMC10542623 DOI: 10.1002/ece3.10506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 10/05/2023] Open
Abstract
A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a noneusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high-quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under-sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.
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Affiliation(s)
- Kim L. Vertacnik
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
| | | | - R. Keating Godfrey
- McGuire Center for Lepidoptera and Biodiversity, University of FloridaGainesvilleFloridaUSA
| | - Tom Hill
- National Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Scott M. Geib
- Tropical Crop and Commodity Protection Research UnitUnited States Department of Agriculture: Agriculture Research Service Pacific Basin Agricultural Research CenterHiloHawaiiUSA
| | - Robert L. Unckless
- Department of Molecular BiosciencesUniversity of KansasLawrenceKansasUSA
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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Inwood SN, Skelly J, Guhlin JG, Harrop TWR, Goldson SL, Dearden PK. Chromosome-level genome assemblies of two parasitoid biocontrol wasps reveal the parthenogenesis mechanism and an associated novel virus. BMC Genomics 2023; 24:440. [PMID: 37543591 PMCID: PMC10403939 DOI: 10.1186/s12864-023-09538-4] [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: 05/22/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Biocontrol is a key technology for the control of pest species. Microctonus parasitoid wasps (Hymenoptera: Braconidae) have been released in Aotearoa New Zealand as biocontrol agents, targeting three different pest weevil species. Despite their value as biocontrol agents, no genome assemblies are currently available for these Microctonus wasps, limiting investigations into key biological differences between the different species and strains. METHODS AND FINDINGS Here we present high-quality genomes for Microctonus hyperodae and Microctonus aethiopoides, assembled with short read sequencing and Hi-C scaffolding. These assemblies have total lengths of 106.7 Mb for M. hyperodae and 129.2 Mb for M. aethiopoides, with scaffold N50 values of 9 Mb and 23 Mb respectively. With these assemblies we investigated differences in reproductive mechanisms, and association with viruses between Microctonus wasps. Meiosis-specific genes are conserved in asexual Microctonus, with in-situ hybridisation validating expression of one of these genes in the ovaries of asexual Microctonus aethiopoides. This implies asexual reproduction in these Microctonus wasps involves meiosis, with the potential for sexual reproduction maintained. Investigation of viral gene content revealed candidate genes that may be involved in virus-like particle production in M. aethiopoides, as well as a novel virus infecting M. hyperodae, for which a complete genome was assembled. CONCLUSION AND SIGNIFICANCE These are the first published genomes for Microctonus wasps which have been deployed as biocontrol agents, in Aotearoa New Zealand. These assemblies will be valuable resources for continued investigation and monitoring of these biocontrol systems. Understanding the biology underpinning Microctonus biocontrol is crucial if we are to maintain its efficacy, or in the case of M. hyperodae to understand what may have influenced the significant decline of biocontrol efficacy. The potential for sexual reproduction in asexual Microctonus is significant given that empirical modelling suggests this asexual reproduction is likely to have contributed to biocontrol decline. Furthermore the identification of a novel virus in M. hyperodae highlights a previously unknown aspect of this biocontrol system, which may contribute to premature mortality of the host pest. These findings have potential to be exploited in future in attempt to increase the effectiveness of M. hyperodae biocontrol.
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Affiliation(s)
- Sarah N Inwood
- Bioprotection Aotearoa and Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand
| | - John Skelly
- Bioprotection Aotearoa and Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand
- Humble Bee Bio, Wellington, Aotearoa, New Zealand
| | - Joseph G Guhlin
- Genomics Aotearoa, University of Otago, Dunedin, Aotearoa, New Zealand
| | - Thomas W R Harrop
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Stephen L Goldson
- Biocontrol and Biosecurity Group, AgResearch Limited, Lincoln, Aotearoa, New Zealand
| | - Peter K Dearden
- Bioprotection Aotearoa and Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand.
- Genomics Aotearoa, University of Otago, Dunedin, Aotearoa, New Zealand.
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Zhao X, Liu Y. Current Knowledge on Bee Innate Immunity Based on Genomics and Transcriptomics. Int J Mol Sci 2022; 23:ijms232214278. [PMID: 36430757 PMCID: PMC9692672 DOI: 10.3390/ijms232214278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/28/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
As important pollinators, bees play a critical role in maintaining the balance of the ecosystem and improving the yield and quality of crops. However, in recent years, the bee population has significantly declined due to various pathogens and environmental stressors including viruses, bacteria, parasites, and increased pesticide application. The above threats trigger or suppress the innate immunity of bees, their only immune defense system, which is essential to maintaining individual health and that of the colony. In addition, bees can be divided into solitary and eusocial bees based on their life traits, and eusocial bees possess special social immunities, such as grooming behavior, which cooperate with innate immunity to maintain the health of the colony. The omics approach gives us an opportunity to recognize the distinctive innate immunity of bees. In this regard, we summarize innate bee immunity from a genomic and transcriptomic perspective. The genetic characteristics of innate immunity were revealed by the multiple genomes of bees with different kinds of sociality, including honeybees, bumblebees, wasps, leaf-cutter bees, and so on. Further substantial transcriptomic data of different tissues from diverse bees directly present the activation or suppression of immune genes under the infestation of pathogens or toxicity of pesticides.
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Affiliation(s)
- Xiaomeng Zhao
- College of Engineering, Hebei Normal University, Shijiazhuang 050024, China
| | - Yanjie Liu
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
- Correspondence:
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Ma Y, Guo Z, Wang L, Wang B, Huang T, Tang B, Zhang G, Zhou Q. The genome of the rice planthopper egg parasitoid wasps Anagrus nilaparvatae casts light on the chemo- and mechanosensation in parasitism. BMC Genomics 2022; 23:541. [PMID: 35902811 PMCID: PMC9331105 DOI: 10.1186/s12864-022-08656-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mymaridae is an ancient insect group and is a basal lineage of the superfamily Chalcidoidea. Species of Mymaridae have great potential for biological control. Anagrus nilaparvatae, a representative species of Mymaridae, is ideal for controlling rice planthopper due to its high rate of parasitism and ability to find hosts efficiently in paddy ridges and fields. RESULTS Using both PacBio single-molecule real-time and Illumina sequencing, we sequenced and assembled the whole genome of A. nilaparvatae, a first for the family Mymaridae. The assembly consists of 394 scaffolds, totaling 488.8 Mb. The assembly is of high continuity and completeness, indicated by the N50 value of 25.4 Mb and 98.2% mapping rate of Benchmarking Universal Single-Copy Orthologs. In total, 16,894 protein-coding genes in the genome were annotated. A phylogenomic tree constructed for A. nilaparvatae and other 12 species of Hymenoptera confirmed that the family Mymaridae is sister to all remaining chalcidoids. The divergence time between A. nilaparvatae and the other seven Chalcidoidea species was dated at ~ 126.9 Mya. Chemoreceptor and mechanoreceptor genes are important in explaining parasitic behavior. We identified 17 odorant binding proteins, 11 chemosensory proteins, four Niemann-Pick type C2 proteins, 88 olfactory receptors, 12 gustatory receptors, 22 ionotropic receptors and 13 sensory neuron membrane proteins in the genome of A. nilaparvatae, which are associated with the chemosensory functions. Strikingly, there is only one pickpocket receptors and nine transient receptor potential genes in the genome that have a mechanosensory function. CONCLUSIONS We obtained a high-quality genome assembly for A. nilaparvatae using PacBio single-molecule real-time sequencing, which provides phylogenomic insights for its evolutionary history. The small numbers of chemo- and mechanosensory genes in A. nilaparvatae indicate the species-specific host detection and oviposition behavior of A. nilaparvatae might be regulated by relatively simple molecular pathways.
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Affiliation(s)
- Ying Ma
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,School of Agriculture, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zixiao Guo
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liyang Wang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Bingyang Wang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Tingfa Huang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Bingjie Tang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Guren Zhang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiang Zhou
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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Kamiyama T, Shimada-Niwa Y, Tanaka H, Katayama M, Kuwabara T, Mori H, Kunihisa A, Itoh T, Toyoda A, Niwa R. Whole-genome sequencing analysis and protocol for RNA interference of the endoparasitoid wasp Asobara japonica. DNA Res 2022; 29:6605221. [PMID: 35686927 PMCID: PMC9233498 DOI: 10.1093/dnares/dsac019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Asobara japonica is an endoparasitic wasp that parasitizes Drosophila flies. It synthesizes various toxic components in the venom gland and injects them into host larvae during oviposition. To identify and characterize these toxic components for enabling parasitism, we performed the whole-genome sequencing (WGS) and devised a protocol for RNA interference (RNAi) with A. japonica. Because it has a parthenogenetic lineage due to Wolbachia infection, we generated a clonal strain from a single wasp to obtain highly homogenous genomic DNA. The WGS analysis revealed that the estimated genome size was 322 Mb with a heterozygosity of 0.132%. We also performed RNA-seq analyses for gene annotation. Based on the qualified WGS platform, we cloned ebony-Aj, which encodes the enzyme N-β-alanyl dopamine synthetase, which is involved in melanin production. The microinjection of double-stranded RNA (dsRNA) targeting ebony-Aj led to body colour changes in adult wasps, phenocopying ebony-Dm mutants. Furthermore, we identified putative venom genes as a target of RNAi, confirming that dsRNA injection-based RNAi specifically suppressed the expression of the target gene in wasp adults. Taken together, our results provide a powerful genetic toolkit for studying the molecular mechanisms of parasitism.
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Affiliation(s)
- Takumi Kamiyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
| | - Yuko Shimada-Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
- Precursory Research for Embryonic Science and Technology (PREST), Japan Science and Technology Agency (JST) , Tokyo 102-0076, Japan
| | - Hiroyuki Tanaka
- Department of Biological Information, Tokyo Institute of Technology , Meguro, Tokyo 152-8550, Japan
| | - Minami Katayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Takayoshi Kuwabara
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Hitoha Mori
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Akari Kunihisa
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology , Meguro, Tokyo 152-8550, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics , Mishima, Shizuoka 411-8540, Japan
| | - Ryusuke Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
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10
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Davison HR, Pilgrim J, Wybouw N, Parker J, Pirro S, Hunter-Barnett S, Campbell PM, Blow F, Darby AC, Hurst GDD, Siozios S. Genomic diversity across the Rickettsia and 'Candidatus Megaira' genera and proposal of genus status for the Torix group. Nat Commun 2022; 13:2630. [PMID: 35551207 PMCID: PMC9098888 DOI: 10.1038/s41467-022-30385-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/29/2022] [Indexed: 11/09/2022] Open
Abstract
Members of the bacterial genus Rickettsia were originally identified as causative agents of vector-borne diseases in mammals. However, many Rickettsia species are arthropod symbionts and close relatives of 'Candidatus Megaira', which are symbiotic associates of microeukaryotes. Here, we clarify the evolutionary relationships between these organisms by assembling 26 genomes of Rickettsia species from understudied groups, including the Torix group, and two genomes of 'Ca. Megaira' from various insects and microeukaryotes. Our analyses of the new genomes, in comparison with previously described ones, indicate that the accessory genome diversity and broad host range of Torix Rickettsia are comparable to those of all other Rickettsia combined. Therefore, the Torix clade may play unrecognized roles in invertebrate biology and physiology. We argue this clade should be given its own genus status, for which we propose the name 'Candidatus Tisiphia'.
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Affiliation(s)
- Helen R Davison
- Institute of Infection, Veterinary and Ecological sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jack Pilgrim
- Institute of Infection, Veterinary and Ecological sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Nicky Wybouw
- Terrestrial Ecology Unit, Department of Biology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Joseph Parker
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA, 91125, USA
| | | | - Simon Hunter-Barnett
- Institute of Infection, Veterinary and Ecological sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Paul M Campbell
- Institute of Infection, Veterinary and Ecological sciences, University of Liverpool, Liverpool, L69 7ZB, UK
- School of Health and Life Sciences, Faculty of Biology Medicine and Health, the University of Manchester, Manchester, UK
| | - Frances Blow
- Institute of Infection, Veterinary and Ecological sciences, University of Liverpool, Liverpool, L69 7ZB, UK
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Alistair C Darby
- Institute of Infection, Veterinary and Ecological sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Stefanos Siozios
- Institute of Infection, Veterinary and Ecological sciences, University of Liverpool, Liverpool, L69 7ZB, UK.
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11
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Al-Jalely BH, Wang P, Liao Y, Xu W. Identification and characterization of olfactory genes in the parasitoid wasp Diadegma semiclausum (Hellén) (Hymenoptera: Ichneumonidae). BULLETIN OF ENTOMOLOGICAL RESEARCH 2022; 112:187-196. [PMID: 34474703 DOI: 10.1017/s0007485321000675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Diadegma semiclausum is an important parasitoid wasp and widely used in the biological control of the diamondback moth, Plutella xylostella, one of the most destructive pests of cruciferous plants. Insect olfactory system is critical in guiding behaviors including feeding, mating, and oviposition, in which odorant binding proteins (OBPs) and odorant receptors (ORs) are two key components. However, limited attention has been paid to D. semiclausum olfactory genes. In this study, a transcriptome sequencing was performed on the RNA samples extracted from D. semiclausum male and female adult antennae. A total of 17 putative OBP and 67 OR genes were annotated and further compared to OBPs and ORs from P. xylostella, and other hemipteran parasitoid species. The expression patterns of D. semiclausum OBPs between male and female antennae were examined using reverse transcription polymerase chain reaction (RT-PCR) and quantitative real-time PCR. Six OBPs (DsemOBP 6, 7, 8, 9, 10, and 14) demonstrated significantly higher expression levels in females than in males, which may assist in female D. semiclausum host-seeking and oviposition behaviors. This study advances our understanding of the olfactory system of D. semiclausum at the molecular level and paves the way for future functional studies aiming at increasing the efficacy to control P. xylostella by using D. semiclausum.
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Affiliation(s)
- Basman H Al-Jalely
- Food Futures Institute, Murdoch University, Perth, WA6150, Australia
- College of Agricultural Engineering Sciences, University of Baghdad, Baghdad, Iraq
| | - Penghao Wang
- Food Futures Institute, Murdoch University, Perth, WA6150, Australia
| | - Yalin Liao
- Food Futures Institute, Murdoch University, Perth, WA6150, Australia
| | - Wei Xu
- Food Futures Institute, Murdoch University, Perth, WA6150, Australia
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12
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Zhang H, Wang JY, Wan NF, Chen YJ, Ji XY, Jiang JX. Identification and expression profile of odorant-binding proteins in the parasitic wasp Microplitis pallidipes using PacBio long-read sequencing. Parasite 2022; 29:53. [PMID: 36350195 PMCID: PMC9645227 DOI: 10.1051/parasite/2022053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/21/2022] [Indexed: 11/11/2022] Open
Abstract
Microplitis pallidipes Szépligeti (Hymenoptera: Braconidae) is an important parasitic wasp of second and third-instar noctuid larvae such as the insect pests Spodoptera exigua, Spodoptera litura, and Spodoptera frugiperda. As in other insects, M. pallidipes has a chemosensory recognition system that is critical to foraging, mating, oviposition, and other behaviors. Odorant-binding proteins (OBPs) are important to the system, but those of M. pallidipes have not been determined. This study used PacBio long-read sequencing to identify 170,980 M. pallidipes unigenes and predicted 129,381 proteins. Following retrieval of possible OBP sequences, we removed those that were redundant or non-full-length and eventually cloned five OBP sequences: MpOBP2, MpOBP3, MpOBP8, MpOBP10, and MpPBP 429, 429, 459, 420, and 429 bp in size, respectively. Each M. pallidipes OBP had six conserved cysteine residues. Phylogenetic analysis revealed that the five OBPs were located at different branches of the phylogenetic tree. Additionally, tissue expression profiles indicated that MpOBP2 and MpPBP were mainly expressed in the antennae of male wasps, while MpOBP3, MpOBP8, and MpOBP10 were mainly expressed in the antennae of female wasps. MpOBP3 was also highly expressed in the legs of female wasps. Temporal profiles revealed that the expression of each M. pallidipes OBP peaked at different days after emergence to adulthood. In conclusion, we identified five novel odorant-binding proteins of M. pallidipes and demonstrated biologically relevant differences in expression patterns.
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Affiliation(s)
- Hao Zhang
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Engineering Research Centre of Low-Carbon Agriculture Shanghai 201403 China
| | - Jin-Yan Wang
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Engineering Research Centre of Low-Carbon Agriculture Shanghai 201403 China
| | - Nian-Feng Wan
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology Shanghai 200237 China
| | - Yi-Juan Chen
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Engineering Research Centre of Low-Carbon Agriculture Shanghai 201403 China
| | - Xiang-Yun Ji
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Engineering Research Centre of Low-Carbon Agriculture Shanghai 201403 China
- Corresponding authors: ;
| | - Jie-Xian Jiang
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Engineering Research Centre of Low-Carbon Agriculture Shanghai 201403 China
- Corresponding authors: ;
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13
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Walsh AT, Triant DA, Le Tourneau JJ, Shamimuzzaman M, Elsik CG. Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. Nucleic Acids Res 2021; 50:D1032-D1039. [PMID: 34747465 PMCID: PMC8728238 DOI: 10.1093/nar/gkab1018] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 01/02/2023] Open
Abstract
We report an update of the Hymenoptera Genome Database (HGD; http://HymenopteraGenome.org), a genomic database of hymenopteran insect species. The number of species represented in HGD has nearly tripled, with fifty-eight hymenopteran species, including twenty bees, twenty-three ants, eleven wasps and four sawflies. With a reorganized website, HGD continues to provide the HymenopteraMine genomic data mining warehouse and JBrowse/Apollo genome browsers integrated with BLAST. We have computed Gene Ontology (GO) annotations for all species, greatly enhancing the GO annotation data gathered from UniProt with more than a ten-fold increase in the number of GO-annotated genes. We have also generated orthology datasets that encompass all HGD species and provide orthologue clusters for fourteen taxonomic groups. The new GO annotation and orthology data are available for searching in HymenopteraMine, and as bulk file downloads.
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Affiliation(s)
- Amy T Walsh
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Deborah A Triant
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | | | - Md Shamimuzzaman
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Christine G Elsik
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.,Division of Plant Science & Technology, University of Missouri, Columbia, MO 65211, USA.,MU Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA
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14
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Olfactory Sensilla and Olfactory Genes in the Parasitoid Wasp Trichogramma pretiosum Riley (Hymenoptera: Trichogrammatidae). INSECTS 2021; 12:insects12110998. [PMID: 34821797 PMCID: PMC8620382 DOI: 10.3390/insects12110998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Parasitic wasps are the major natural enemies of many organisms, and therefore they are broadly used in the biological control of numerous agricultural and horticultural pests. For example, Trichogramma pretiosum Riley (Hymenoptera: Trichogrammatidae) is a tiny natural egg parasitoid of various agricultural pest insects, including Plutella xylostella, Helicoverpa armigera, Spodoptera frugiperda and Ectomyelois ceratoniae. However, how T. pretiosum seek and localise host insect eggs is still not clear. The olfactory system is critical in guiding insect behaviours, including mating, feeding and oviposition, which play pivotal roles in the interactions between parasitoid wasps and their hosts. This project aimed to investigate T. pretiosum major olfactory tissue (antennae) and the olfactory genes, including odorant binding proteins (OBPs) and odorant receptors (ORs). T. pretiosum adult antennae were examined under scanning electron microscopy, and four types of olfactory sensilla were observed. Using T. pretiosum genome, 22 OBPs and 105 ORs were identified, which were further compared with olfactory genes of other Hymenoptera insect species. The expression patterns of OBPs between T. pretiosum male and female adults were examined to identify female- or male-specific OBPs. This study enriches our knowledge of T. pretiosum olfactory system and will help better use it in the integrated pest management (IPM) for many insect pest species. Abstract Trichogramma pretiosum Riley (Hymenoptera: Trichogrammatidae) is a tiny natural egg parasitoid of several agricultural pest insects, which has been widely used in the biological control for Plutella xylostella, Helicoverpa armigera, Spodoptera frugiperda and Ectomyelois ceratoniae. However, limited studies have been conducted on T. pretiosum olfactory system, which is critical in regulating insect behaviours. In this study, T. pretiosum adult antennae were investigated under ascanning electron microscopy (SEM). Four types of olfactory sensilla were observed, including chaetica sensilla (CS), trichoid sensilla (TS), faleate sensilla (FS) and placoid sensilla (PS). Using T. pretiosum genome, 22 putative odorant binding proteins (OBPs) and 105 odorant receptors (ORs) were identified, which were further compared with olfactory genes of Apis mellifera, Nasonia vitripennis and Diachasma alloeum. The expression patterns of OBPs between T. pretiosum male and female adults were examined by quantitative real time PCR (qRT-PCR) approaches. Three female-specific OBPs (TpreOBP19, TpreOBP15 and TpreOBP3) were identified, which may play crucial roles in T. pretiosum host-seeking and oviposition behaviours. This study enriches our knowledge of T. pretiosum olfactory genes and improves our understanding of its olfactory system.
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15
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Ulrich GF, Zemp N, Vorburger C, Boulain H. Quantitative trait locus analysis of parasitoid counteradaptation to symbiont-conferred resistance. Heredity (Edinb) 2021; 127:219-232. [PMID: 34012059 PMCID: PMC8322320 DOI: 10.1038/s41437-021-00444-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 02/04/2023] Open
Abstract
Insect hosts and parasitoids are engaged in an intense struggle of antagonistic coevolution. Infection with heritable bacterial endosymbionts can substantially increase the resistance of aphids to parasitoid wasps, which exerts selection on parasitoids to overcome this symbiont-conferred protection (counteradaptation). Experimental evolution in the laboratory has produced counteradapted populations of the parasitoid wasp Lysiphlebus fabarum. These populations can parasitize black bean aphids (Aphis fabae) protected by the bacterial endosymbiont Hamiltonella defensa, which confers high resistance against L. fabarum. We used two experimentally evolved parasitoid populations to study the genetic architecture of the counteradaptation to symbiont-conferred resistance by QTL analysis. With simple crossing experiments, we showed that the counteradaptation is a recessive trait depending on the maternal genotype. Based on these results, we designed a customized crossing scheme to genotype a mapping population phenotyped for the ability to parasitize Hamiltonella-protected aphids. Using 1835 SNP markers obtained by ddRAD sequencing, we constructed a high-density linkage map consisting of six linkage groups (LGs) with an overall length of 828.3 cM and an average marker spacing of 0.45 cM. We identified a single QTL associated with the counteradaptation to Hamiltonella in L. fabarum on linkage group 2. Out of 120 genes located in this QTL, several genes encoding putative venoms may represent candidates for counteradaptation, as parasitoid wasps inject venoms into their hosts during oviposition.
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Affiliation(s)
- Gabriel F. Ulrich
- grid.418656.80000 0001 1551 0562EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland ,grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, Universitätsstrasse 16, 8092 Zürich, Switzerland
| | - Niklaus Zemp
- Genetic Diversity Centre, Department of Environmental Systems Sciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Christoph Vorburger
- grid.418656.80000 0001 1551 0562EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland ,grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, Universitätsstrasse 16, 8092 Zürich, Switzerland
| | - Hélène Boulain
- grid.418656.80000 0001 1551 0562EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland ,grid.9851.50000 0001 2165 4204Present Address: Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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16
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Burke GR, Hines HM, Sharanowski BJ. The Presence of Ancient Core Genes Reveals Endogenization from Diverse Viral Ancestors in Parasitoid Wasps. Genome Biol Evol 2021; 13:evab105. [PMID: 33988720 PMCID: PMC8325570 DOI: 10.1093/gbe/evab105] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
The Ichneumonoidea (Ichneumonidae and Braconidae) is an incredibly diverse superfamily of parasitoid wasps that includes species that produce virus-like entities in their reproductive tracts to promote successful parasitism of host insects. Research on these entities has traditionally focused upon two viral genera Bracovirus (in Braconidae) and Ichnovirus (in Ichneumonidae). These viruses are produced using genes known collectively as endogenous viral elements (EVEs) that represent historical, now heritable viral integration events in wasp genomes. Here, new genome sequence assemblies for 11 species and 6 publicly available genomes from the Ichneumonoidea were screened with the goal of identifying novel EVEs and characterizing the breadth of species in lineages with known EVEs. Exhaustive similarity searches combined with the identification of ancient core genes revealed sequences from both known and novel EVEs. One species harbored a novel, independently derived EVE related to a divergent large double-stranded DNA (dsDNA) virus that manipulates behavior in other hymenopteran species. Although bracovirus or ichnovirus EVEs were identified as expected in three species, the absence of ichnoviruses in several species suggests that they are independently derived and present in two younger, less widespread lineages than previously thought. Overall, this study presents a novel bioinformatic approach for EVE discovery in genomes and shows that three divergent virus families (nudiviruses, the ancestors of ichnoviruses, and Leptopilina boulardi Filamentous Virus-like viruses) are recurrently acquired as EVEs in parasitoid wasps. Virus acquisition in the parasitoid wasps is a common process that has occurred in many more than two lineages from a diverse range of arthropod-infecting dsDNA viruses.
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Affiliation(s)
- Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Heather M Hines
- Department of Biology and Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
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17
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Wulff JP, Segura DF, Devescovi F, Muntaabski I, Milla FH, Scannapieco AC, Cladera JL, Lanzavecchia SB. Identification and characterization of soluble binding proteins associated with host foraging in the parasitoid wasp Diachasmimorpha longicaudata. PLoS One 2021; 16:e0252765. [PMID: 34138896 PMCID: PMC8211293 DOI: 10.1371/journal.pone.0252765] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 05/22/2021] [Indexed: 11/19/2022] Open
Abstract
The communication and reproduction of insects are driven by chemical sensing. During this process, chemical compounds are transported across the sensillum lymph to the sensory neurons assisted by different types of soluble binding proteins: odorant-binding proteins (OBPs); chemosensory proteins (CSPs); some members of ML-family proteins (MD-2 (myeloid differentiation factor-2)-related Lipid-recognition), also known as NPC2-like proteins. Potential transcripts involved in chemosensing were identified by an in silico analysis of whole-body female and male transcriptomes of the parasitic wasp Diachasmimorpha longicaudata. This analysis facilitated the characterization of fourteen OBPs (all belonging to the Classic type), seven CSPs (and two possible isoforms), and four NPC2-like proteins. A differential expression analysis by qPCR showed that eleven of these proteins (CSPs 2 and 8, OBPs 2, 3, 4, 5, 6, 9, 10, and 11, and NPC2b) were over-expressed in female antenna and two (CSP 1 and OBP 12) in the body without antennae. Foraging behavior trials (linked to RNA interference) suggest that OBPs 9, 10, and 11 are potentially involved in the female orientation to chemical cues associated with the host. OBP 12 seems to be related to physiological processes of female longevity regulation. In addition, transcriptional silencing of CSP 3 showed that this protein is potentially associated with the regulation of foraging behavior. This study supports the hypothesis that soluble binding proteins are potentially linked to fundamental physiological processes and behaviors in D. longicaudata. The results obtained here contribute useful information to increase the parasitoid performance as a biological control agent of fruit fly pest species.
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Affiliation(s)
- Juan P. Wulff
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética Ewald A. Favret (INTA) gv IABIMO (CONICET), Buenos Aires, Argentina
| | - Diego F. Segura
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética Ewald A. Favret (INTA) gv IABIMO (CONICET), Buenos Aires, Argentina
| | - Francisco Devescovi
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética Ewald A. Favret (INTA) gv IABIMO (CONICET), Buenos Aires, Argentina
| | - Irina Muntaabski
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética Ewald A. Favret (INTA) gv IABIMO (CONICET), Buenos Aires, Argentina
| | - Fabian H. Milla
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética Ewald A. Favret (INTA) gv IABIMO (CONICET), Buenos Aires, Argentina
| | - Alejandra C. Scannapieco
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética Ewald A. Favret (INTA) gv IABIMO (CONICET), Buenos Aires, Argentina
| | - Jorge L. Cladera
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética Ewald A. Favret (INTA) gv IABIMO (CONICET), Buenos Aires, Argentina
| | - Silvia B. Lanzavecchia
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética Ewald A. Favret (INTA) gv IABIMO (CONICET), Buenos Aires, Argentina
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18
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Pinto BJ, Weis JJ, Gamble T, Ode PJ, Paul R, Zaspel JM. A chromosome-level genome assembly of the parasitoid wasp, Cotesia glomerata (Hymenoptera: Braconidae). J Hered 2021; 112:558-564. [PMID: 34043785 DOI: 10.1093/jhered/esab032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
Hymenopterans make up about 20% of all animal species, but most are poorly known and lack high-quality genomic resources. One group of important, yet under-studied hymenopterans, are parasitoid wasps in the family Braconidae. Among this under-studied group are braconid wasps in the genus Cotesia; a clade of ~1,000 species routinely used in studies of physiology, ecology, biological control, and genetics. However, our ability to understand these organisms has been hindered by a lack of genomic resources. We helped bridge this gap by generating a high-quality genome assembly for the parasitoid wasp, Cotesia glomerata (Braconidae; Microgastrinae). We generated this assembly using multiple sequencing technologies, including Oxford Nanopore, whole-genome shotgun sequencing, and 3-D chromatin contact information (Hi-C). Our assembly is one of the most contiguous, complete, and publicly available hymenopteran genomes, represented by 3,355 scaffolds with a scaffold N50 of ~28Mb and a BUSCO score of ~99%. Given the genome sizes found in closely related species, our genome assembly was ~50% larger than expected, which was apparently induced by runaway amplification of three types of repetitive elements: simple repeats, Long Terminal Repeats (LTRs), and Long Interspersed Nuclear Elements (LINEs). This assembly is another step forward for genomics across this hyper-diverse, yet understudied, order of insects. The assembled genomic data and metadata files are publicly available via Figshare (https://doi.org/10.6084/m9.figshare.13010549).
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Affiliation(s)
- Brendan J Pinto
- Department of Integrative Biology, University of Texas at Austin, TX, USA.,Milwaukee Public Museum, Milwaukee, WI, USA
| | | | - Tony Gamble
- Milwaukee Public Museum, Milwaukee, WI, USA.,Department of Biological Sciences, Marquette University, Milwaukee, WI, USA.,Bell Museum of Natural History, University of Minnesota, St Paul, MN, USA
| | - Paul J Ode
- Colorado State University, Ft. Collins, CO, USA
| | - Ryan Paul
- Colorado State University, Ft. Collins, CO, USA
| | - Jennifer M Zaspel
- Milwaukee Public Museum, Milwaukee, WI, USA.,Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
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19
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Vallino M, Rossi M, Ottati S, Martino G, Galetto L, Marzachì C, Abbà S. Bacteriophage-Host Association in the Phytoplasma Insect Vector Euscelidius variegatus. Pathogens 2021; 10:pathogens10050612. [PMID: 34067814 PMCID: PMC8156552 DOI: 10.3390/pathogens10050612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/26/2022] Open
Abstract
Insect vectors transmit viruses and bacteria that can cause severe diseases in plants and economic losses due to a decrease in crop production. Insect vectors, like all other organisms, are colonized by a community of various microorganisms, which can influence their physiology, ecology, evolution, and also their competence as vectors. The important ecological meaning of bacteriophages in various ecosystems and their role in microbial communities has emerged in the past decade. However, only a few phages have been described so far in insect microbiomes. The leafhopper Euscelidius variegatus is a laboratory vector of the phytoplasma causing Flavescence dorée, a severe grapevine disease that threatens viticulture in Europe. Here, the presence of a temperate bacteriophage in E. variegatus (named Euscelidius variegatus phage 1, EVP-1) was revealed through both insect transcriptome analyses and electron microscopic observations. The bacterial host was isolated in axenic culture and identified as the bacterial endosymbiont of E. variegatus (BEV), recently assigned to the genus Candidatus Symbiopectobacterium. BEV harbors multiple prophages that become active in culture, suggesting that different environments can trigger different mechanisms, finely regulating the interactions among phages. Understanding the complex relationships within insect vector microbiomes may help in revealing possible microbe influences on pathogen transmission, and it is a crucial step toward innovative sustainable strategies for disease management in agriculture.
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Affiliation(s)
- Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
- Correspondence:
| | - Marika Rossi
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
| | - Sara Ottati
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Gabriele Martino
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Luciana Galetto
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
| | - Cristina Marzachì
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
| | - Simona Abbà
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
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20
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Li B, Du Z, Tian L, Zhang L, Huang Z, Wei S, Song F, Cai W, Yu Y, Yang H, Li H. Chromosome-level genome assembly of the aphid parasitoid Aphidius gifuensis using Oxford Nanopore sequencing and Hi-C technology. Mol Ecol Resour 2021; 21:941-954. [PMID: 33314728 PMCID: PMC7986076 DOI: 10.1111/1755-0998.13308] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022]
Abstract
Aphidius gifuensis is a parasitoid wasp that has been commercially bred and released in large scale as a biocontrol agent for the management of aphid pests. As a highly efficient endoparasitoid, it is also an important model for exploring mechanisms of parasitism. Currently, artificially bred populations of this wasp are facing rapid decline with undetermined cause, and mechanisms underlying its parasitoid strategy remain poorly understood. Exploring the mechanism behind its population decline and the host–parasitoid relationship is impeded partly due to the lack of a comprehensive genome data for this species. In this study, we constructed a high‐quality reference genome of A. gifuensis using Oxford Nanopore sequencing and Hi‐C (proximity ligation chromatin conformation capture) technology. The final genomic assembly was 156.9 Mb, with a contig N50 length of 3.93 Mb, the longest contig length of 10.4 Mb and 28.89% repetitive sequences. 99.8% of genome sequences were anchored onto six linkage groups. A total of 11,535 genes were predicted, of which 90.53% were functionally annotated. Benchmarking Universal Single‐Copy Orthologs (BUSCO) analysis showed the completeness of assembled genome is 98.3%. We found significantly expanded gene families involved in metabolic processes, transmembrane transport, cell signal communication and oxidoreductase activity, in particular ATP‐binding cassette (ABC) transporter, Cytochrome P450 and venom proteins. The olfactory receptors (ORs) showed significant contraction, which may be associated with the decrease in host recognition. Our study provides a solid foundation for future studies on the molecular mechanisms of population decline as well as host–parasitoid relationship for parasitoid wasps.
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Affiliation(s)
- Bingyan Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhenyong Du
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | | | | | - Shujun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yanbi Yu
- Yunnan Tobacco Company of China National Tobacco Corporation, Kunming, China
| | | | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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21
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Quicke DLJ, Butcher BA. Review of Venoms of Non-Polydnavirus Carrying Ichneumonoid Wasps. BIOLOGY 2021; 10:50. [PMID: 33445639 PMCID: PMC7828074 DOI: 10.3390/biology10010050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/23/2022]
Abstract
Parasitoids are predominantly insects that develop as larvae on or inside their host, also usually another insect, ultimately killing it after various periods of parasitism when both parasitoid larva and host are alive. The very large wasp superfamily Ichneumonoidea is composed of parasitoids of other insects and comprises a minimum of 100,000 species. The superfamily is dominated by two similarly sized families, Braconidae and Ichneumonidae, which are collectively divided into approximately 80 subfamilies. Of these, six have been shown to release DNA-containing virus-like particles, encoded within the wasp genome, classified in the virus family Polydnaviridae. Polydnaviruses infect and have profound effects on host physiology in conjunction with various venom and ovarial secretions, and have attracted an immense amount of research interest. Physiological interactions between the remaining ichneumonoids and their hosts result from adult venom gland secretions and in some cases, ovarian or larval secretions. Here we review the literature on the relatively few studies on the effects and chemistry of these ichneumonoid venoms and make suggestions for interesting future research areas. In particular, we highlight relatively or potentially easily culturable systems with features largely lacking in currently studied systems and whose study may lead to new insights into the roles of venom chemistry in host-parasitoid relationships as well as their evolution.
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Affiliation(s)
- Donald L. J. Quicke
- Integrative Ecology Laboratory, Department of Biology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan 10330, Thailand;
- Center of Excellence in Entomology, Bee Biology, Diversity of Insects and Mites, Chulalongkorn University, Phayathai Road, Pathumwan 10330, Thailand
| | - Buntika A. Butcher
- Integrative Ecology Laboratory, Department of Biology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan 10330, Thailand;
- Center of Excellence in Entomology, Bee Biology, Diversity of Insects and Mites, Chulalongkorn University, Phayathai Road, Pathumwan 10330, Thailand
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22
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Multiple origins of obligate nematode and insect symbionts by a clade of bacteria closely related to plant pathogens. Proc Natl Acad Sci U S A 2020; 117:31979-31986. [PMID: 33257562 DOI: 10.1073/pnas.2000860117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Obligate symbioses involving intracellular bacteria have transformed eukaryotic life, from providing aerobic respiration and photosynthesis to enabling colonization of previously inaccessible niches, such as feeding on xylem and phloem, and surviving in deep-sea hydrothermal vents. A major challenge in the study of obligate symbioses is to understand how they arise. Because the best studied obligate symbioses are ancient, it is especially challenging to identify early or intermediate stages. Here we report the discovery of a nascent obligate symbiosis in Howardula aoronymphium, a well-studied nematode parasite of Drosophila flies. We have found that H aoronymphium and its sister species harbor a maternally inherited intracellular bacterial symbiont. We never find the symbiont in nematode-free flies, and virtually all nematodes in the field and the laboratory are infected. Treating nematodes with antibiotics causes a severe reduction in fly infection success. The association is recent, as more distantly related insect-parasitic tylenchid nematodes do not host these endosymbionts. We also report that the Howardula nematode symbiont is a member of a widespread monophyletic group of invertebrate host-associated microbes that has independently given rise to at least four obligate symbioses, one in nematodes and three in insects, and that is sister to Pectobacterium, a lineage of plant pathogenic bacteria. Comparative genomic analysis of this group, which we name Candidatus Symbiopectobacterium, shows signatures of genome erosion characteristic of early stages of symbiosis, with the Howardula symbiont's genome containing over a thousand predicted pseudogenes, comprising a third of its genome.
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23
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Ferguson KB, Pannebakker BA, Centurión A, van den Heuvel J, Nieuwenhuis R, Becker FFM, Schijlen E, Thiel A, Zwaan BJ, Verhulst EC. Bracon brevicornis Genome Showcases the Potential of Linked-Read Sequencing in Identifying a Putative Complementary Sex Determiner Gene. Genes (Basel) 2020; 11:E1390. [PMID: 33255162 PMCID: PMC7759789 DOI: 10.3390/genes11121390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 11/18/2020] [Indexed: 01/24/2023] Open
Abstract
Bracon brevicornis is an ectoparasitoid of a wide range of larval-stage Lepidopterans, including several pests of important crops, such as the corn borer, Ostrinia nubilalis. It is also one of the earliest documented cases of complementary sex determination in Hymenoptera. Here, we present the linked-read-based genome of B. brevicornis, complete with an ab initio-derived annotation and protein comparisons with fellow braconids, Fopius arisanus and Diachasma alloeum. We demonstrate the potential of linked-read assemblies in exploring regions of heterozygosity and search for structural and homology-derived evidence of the complementary sex determiner gene (csd).
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Affiliation(s)
- Kim B. Ferguson
- Laboratory of Genetics, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (B.A.P.); (J.v.d.H.); (F.F.M.B.); (B.J.Z.)
| | - Bart A. Pannebakker
- Laboratory of Genetics, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (B.A.P.); (J.v.d.H.); (F.F.M.B.); (B.J.Z.)
| | - Alejandra Centurión
- Population and Evolutionary Ecology Group, Institute of Ecology, FB02, University of Bremen, 28359 Bremen, Germany; (A.C.); (A.T.)
| | - Joost van den Heuvel
- Laboratory of Genetics, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (B.A.P.); (J.v.d.H.); (F.F.M.B.); (B.J.Z.)
| | - Ronald Nieuwenhuis
- Bioscience, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (R.N.); (E.S.)
| | - Frank F. M. Becker
- Laboratory of Genetics, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (B.A.P.); (J.v.d.H.); (F.F.M.B.); (B.J.Z.)
| | - Elio Schijlen
- Bioscience, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (R.N.); (E.S.)
| | - Andra Thiel
- Population and Evolutionary Ecology Group, Institute of Ecology, FB02, University of Bremen, 28359 Bremen, Germany; (A.C.); (A.T.)
| | - Bas J. Zwaan
- Laboratory of Genetics, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (B.A.P.); (J.v.d.H.); (F.F.M.B.); (B.J.Z.)
| | - Eveline C. Verhulst
- Laboratory of Entomology, Wageningen University & Research, 6708PB Wageningen, The Netherlands;
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24
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Chen H, Lahey Z, Talamas EJ, Johnson NF. Identification and expression of chemosensory receptor genes in the egg parasitoid Trissolcus basalis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 37:100758. [PMID: 33202309 DOI: 10.1016/j.cbd.2020.100758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 11/17/2022]
Abstract
Parasitic wasps largely rely on chemosenses to locate resources. Understanding the evolution of their chemoreceptors can help elucidate the mechanisms underlying host adaptation and speciation. Trissolcus basalis is a biological control agent of the southern green stink bug, a pantropical pest, and is ideal for investigating the evolution of chemoreceptors. We identified 34 gustatory receptors, 170 odorant receptors, one odorant co-receptor, and 23 ionotropic receptors. Comparison with other Hymenoptera revealed species-specific expansions of 21 Grs and 53 Ors. Most of these Or expansions have 9 exons. Gender- and tissue-specific analyses showed that 5 Grs and 54 Ors are expressed only in antennae in both sexes, 66 Ors in female antennae only, and 4 Ors in male antennae alone. The identification and expression profile of chemosensory receptor genes in T. basalis helps in understanding the link between the evolution of chemoreceptors and speciation in parasitic wasps.
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Affiliation(s)
- Huayan Chen
- State Key Laboratory of Biocontrol, School of Life Sciences/School of Ecology, Sun Yat-sen University, Guangzhou 510275, China; Department of Entomology, The Ohio State University, 1315 Kinnear Road, Columbus, OH 43212, USA.
| | - Zachary Lahey
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 1315 Kinnear Road, Columbus, OH 43212, USA.
| | - Elijah J Talamas
- Department of Entomology, The Ohio State University, 1315 Kinnear Road, Columbus, OH 43212, USA; Florida Department of Agriculture and Consumer Services, The Doyle Conner Building, 1911 SW 34th St, Gainesville, Florida 32608, USA.
| | - Norman F Johnson
- Department of Entomology, The Ohio State University, 1315 Kinnear Road, Columbus, OH 43212, USA; Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 1315 Kinnear Road, Columbus, OH 43212, USA.
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25
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Rotenberg D, Baumann AA, Ben-Mahmoud S, Christiaens O, Dermauw W, Ioannidis P, Jacobs CGC, Vargas Jentzsch IM, Oliver JE, Poelchau MF, Rajarapu SP, Schneweis DJ, Snoeck S, Taning CNT, Wei D, Widana Gamage SMK, Hughes DST, Murali SC, Bailey ST, Bejerman NE, Holmes CJ, Jennings EC, Rosendale AJ, Rosselot A, Hervey K, Schneweis BA, Cheng S, Childers C, Simão FA, Dietzgen RG, Chao H, Dinh H, Doddapaneni HV, Dugan S, Han Y, Lee SL, Muzny DM, Qu J, Worley KC, Benoit JB, Friedrich M, Jones JW, Panfilio KA, Park Y, Robertson HM, Smagghe G, Ullman DE, van der Zee M, Van Leeuwen T, Veenstra JA, Waterhouse RM, Weirauch MT, Werren JH, Whitfield AE, Zdobnov EM, Gibbs RA, Richards S. Genome-enabled insights into the biology of thrips as crop pests. BMC Biol 2020; 18:142. [PMID: 33070780 PMCID: PMC7570057 DOI: 10.1186/s12915-020-00862-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. RESULTS We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. CONCLUSIONS Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.
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Affiliation(s)
- Dorith Rotenberg
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Aaron A Baumann
- Virology Section, College of Veterinary Medicine, University of Tennessee, A239 VTH, 2407 River Drive, Knoxville, TN, 37996, USA
| | - Sulley Ben-Mahmoud
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | - Olivier Christiaens
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Panagiotis Ioannidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Vassilika Vouton, 70013, Heraklion, Greece
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany
| | - Jonathan E Oliver
- Department of Plant Pathology, University of Georgia - Tifton Campus, Tifton, GA, 31793-5737, USA
| | | | - Swapna Priya Rajarapu
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Derek J Schneweis
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Simon Snoeck
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Department of Biology, University of Washington, Seattle, WA, 98105, USA
| | - Clauvis N T Taning
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Dong Wei
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China and Ghent University, Ghent, Belgium
| | | | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Samuel T Bailey
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | | | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
- Department of Biology, Mount St. Joseph University, Cincinnati, OH, 45233, USA
| | - Andrew Rosselot
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Kaylee Hervey
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Brandi A Schneweis
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Sammy Cheng
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | | | - Felipe A Simão
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China and Ghent University, Ghent, Belgium
| | - Diane E Ullman
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | | | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Jan A Veenstra
- INCIA UMR 5287 CNRS, University of Bordeaux, Pessac, France
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Swiss Institute of Bioinformatics, University of Lausanne, 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, 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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26
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Ye X, Xiong S, Teng Z, Yang Y, Wang J, Yu K, Wu H, Mei Y, Yan Z, Cheng S, Yin C, Wang F, Yao H, Fang Q, Song Q, Werren JH, Ye G, Li F. Amino acid synthesis loss in parasitoid wasps and other hymenopterans. eLife 2020; 9:e59795. [PMID: 33074103 PMCID: PMC7593089 DOI: 10.7554/elife.59795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/17/2020] [Indexed: 11/17/2022] Open
Abstract
Insects utilize diverse food resources which can affect the evolution of their genomic repertoire, including leading to gene losses in different nutrient pathways. Here, we investigate gene loss in amino acid synthesis pathways, with special attention to hymenopterans and parasitoid wasps. Using comparative genomics, we find that synthesis capability for tryptophan, phenylalanine, tyrosine, and histidine was lost in holometabolous insects prior to hymenopteran divergence, while valine, leucine, and isoleucine were lost in the common ancestor of Hymenoptera. Subsequently, multiple loss events of lysine synthesis occurred independently in the Parasitoida and Aculeata. Experiments in the parasitoid Cotesia chilonis confirm that it has lost the ability to synthesize eight amino acids. Our findings provide insights into amino acid synthesis evolution, and specifically can be used to inform the design of parasitoid artificial diets for pest control.
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Affiliation(s)
- Xinhai Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
- Department of Biology, University of RochesterRochesterUnited States
| | - Shijiao Xiong
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Ziwen Teng
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Yi Yang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Jiale Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Kaili Yu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Huizi Wu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Zhichao Yan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Sammy Cheng
- Department of Biology, University of RochesterRochesterUnited States
| | - Chuanlin Yin
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Fang Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Hongwei Yao
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Qi Fang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of MissouriColumbiaUnited States
| | - John H Werren
- Department of Biology, University of RochesterRochesterUnited States
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
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27
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Legeai F, Santos BF, Robin S, Bretaudeau A, Dikow RB, Lemaitre C, Jouan V, Ravallec M, Drezen JM, Tagu D, Baudat F, Gyapay G, Zhou X, Liu S, Webb BA, Brady SG, Volkoff AN. Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps. BMC Biol 2020; 18:89. [PMID: 32703219 PMCID: PMC7379367 DOI: 10.1186/s12915-020-00822-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/29/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Polydnaviruses (PDVs) are mutualistic endogenous viruses inoculated by some lineages of parasitoid wasps into their hosts, where they facilitate successful wasp development. PDVs include the ichnoviruses and bracoviruses that originate from independent viral acquisitions in ichneumonid and braconid wasps respectively. PDV genomes are fully incorporated into the wasp genomes and consist of (1) genes involved in viral particle production, which derive from the viral ancestor and are not encapsidated, and (2) proviral segments harboring virulence genes, which are packaged into the viral particle. To help elucidating the mechanisms that have facilitated viral domestication in ichneumonid wasps, we analyzed the structure of the viral insertions by sequencing the whole genome of two ichnovirus-carrying wasp species, Hyposoter didymator and Campoletis sonorensis. RESULTS Assemblies with long scaffold sizes allowed us to unravel the organization of the endogenous ichnovirus and revealed considerable dispersion of the viral loci within the wasp genomes. Proviral segments contained species-specific sets of genes and occupied distinct genomic locations in the two ichneumonid wasps. In contrast, viral machinery genes were organized in clusters showing highly conserved gene content and order, with some loci located in collinear wasp genomic regions. This genomic architecture clearly differs from the organization of PDVs in braconid wasps, in which proviral segments are clustered and viral machinery elements are more dispersed. CONCLUSIONS The contrasting structures of the two types of ichnovirus genomic elements are consistent with their different functions: proviral segments are vehicles for virulence proteins expected to adapt according to different host defense systems, whereas the genes involved in virus particle production in the wasp are likely more stable and may reflect ancestral viral architecture. The distinct genomic architectures seen in ichnoviruses versus bracoviruses reveal different evolutionary trajectories that have led to virus domestication in the two wasp lineages.
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Affiliation(s)
- Fabrice Legeai
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Bernardo F Santos
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
| | - Stéphanie Robin
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Anthony Bretaudeau
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Rebecca B Dikow
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
| | - Claire Lemaitre
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Véronique Jouan
- DGIMI, INRAE, University of Montpellier, 34095, Montpellier, France
| | - Marc Ravallec
- DGIMI, INRAE, University of Montpellier, 34095, Montpellier, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - Université de Tours, UFR des Sciences et Techniques, Parc de Grandmont, Tours, France
| | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
| | - Frédéric Baudat
- Institut de Génétique Humaine, CNRS, University of Montpellier, 34396, Montpellier, France
| | - Gabor Gyapay
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, People's Republic of China
| | - Bruce A Webb
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
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28
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Dennis AB, Ballesteros GI, Robin S, Schrader L, Bast J, Berghöfer J, Beukeboom LW, Belghazi M, Bretaudeau A, Buellesbach J, Cash E, Colinet D, Dumas Z, Errbii M, Falabella P, Gatti JL, Geuverink E, Gibson JD, Hertaeg C, Hartmann S, Jacquin-Joly E, Lammers M, Lavandero BI, Lindenbaum I, Massardier-Galata L, Meslin C, Montagné N, Pak N, Poirié M, Salvia R, Smith CR, Tagu D, Tares S, Vogel H, Schwander T, Simon JC, Figueroa CC, Vorburger C, Legeai F, Gadau J. Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. BMC Genomics 2020; 21:376. [PMID: 32471448 PMCID: PMC7257214 DOI: 10.1186/s12864-020-6764-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. RESULTS We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. CONCLUSIONS These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.
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Affiliation(s)
- Alice B Dennis
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland.
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland.
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
| | - Gabriel I Ballesteros
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Stéphanie Robin
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Jens Bast
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
- Institute of Zoology, Universität zu Köln, 50674, Köln, Germany
| | - Jan Berghöfer
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Maya Belghazi
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, PINT, PFNT, Marseille, France
| | - Anthony Bretaudeau
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jan Buellesbach
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Elizabeth Cash
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | | | - Zoé Dumas
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Mohammed Errbii
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Jean-Luc Gatti
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Biology, Georgia Southern University, Statesboro, GA, 30460, USA
| | - Corinne Hertaeg
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Department of Environmental Systems Sciences, D-USYS, ETH Zürich, Zürich, Switzerland
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Mark Lammers
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Blas I Lavandero
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Ina Lindenbaum
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nina Pak
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Marylène Poirié
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Rosanna Salvia
- Department of Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Chris R Smith
- Department of Biology, Earlham College, Richmond, IN, 47374, USA
| | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
| | - Sophie Tares
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | | | - Christian C Figueroa
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
| | - Christoph Vorburger
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Fabrice Legeai
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany.
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