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Pavithran S, Murugan M, Mannu J, Sathyaseelan C, Balasubramani V, Harish S, Natesan S. Salivary gland transcriptomics of the cotton aphid Aphis gossypii and comparative analysis with other sap-sucking insects. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 116:e22123. [PMID: 38860775 DOI: 10.1002/arch.22123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/08/2024] [Accepted: 05/17/2024] [Indexed: 06/12/2024]
Abstract
Aphids are sap-sucking insects responsible for crop losses and a severe threat to crop production. Proteins in the aphid saliva are integral in establishing an interaction between aphids and plants and are responsible for host plant adaptation. The cotton aphid, Aphis gossypii (Hemiptera: Aphididae) is a major pest of Gossypium hirsutum. Despite extensive studies of the salivary proteins of various aphid species, the components of A. gossypii salivary glands are unknown. In this study, we identified 123,008 transcripts from the salivary gland of A. gossypii. Among those, 2933 proteins have signal peptides with no transmembrane domain known to be secreted from the cell upon feeding. The transcriptome includes proteins with more comprehensive functions such as digestion, detoxification, regulating host defenses, regulation of salivary glands, and a large set of uncharacterized proteins. Comparative analysis of salivary proteins of different aphids and other insects with A. gossypii revealed that 183 and 88 orthologous clusters were common in the Aphididae and non-Aphididae groups, respectively. The structure prediction for highly expressed salivary proteins indicated that most possess an intrinsically disordered region. These results provide valuable reference data for exploring novel functions of salivary proteins in A. gossypii with their host interactions. The identified proteins may help develop a sustainable way to manage aphid pests.
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Affiliation(s)
- Shanmugasundram Pavithran
- Department of Agricultural Entomology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, India
| | - Marimuthu Murugan
- Department of Agricultural Entomology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, India
| | - Jayakanthan Mannu
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Chakkarai Sathyaseelan
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas, USA
| | - Venkatasamy Balasubramani
- Department of Agricultural Entomology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, India
| | - Sankarasubramanian Harish
- Department of Plant Pathology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, India
| | - Senthil Natesan
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
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Ravigné V, Rodrigues LR, Charlery de la Masselière M, Facon B, Kuczyński L, Radwan J, Skoracka A, Magalhães S. Understanding the joint evolution of dispersal and host specialisation using phytophagous arthropods as a model group. Biol Rev Camb Philos Soc 2024; 99:219-237. [PMID: 37724465 DOI: 10.1111/brv.13018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Theory generally predicts that host specialisation and dispersal should evolve jointly. Indeed, many models predict that specialists should be poor dispersers to avoid landing on unsuitable hosts while generalists will have high dispersal abilities. Phytophagous arthropods are an excellent group to test this prediction, given extensive variation in their host range and dispersal abilities. Here, we explore the degree to which the empirical literature on this group is in accordance with theoretical predictions. We first briefly outline the theoretical reasons to expect such a correlation. We then report empirical studies that measured both dispersal and the degree of specialisation in phytophagous arthropods. We find a correlation between dispersal and levels of specialisation in some studies, but with wide variation in this result. We then review theoretical attributes of species and environment that may blur this correlation, namely environmental grain, temporal heterogeneity, habitat selection, genetic architecture, and coevolution between plants and herbivores. We argue that theoretical models fail to account for important aspects, such as phenotypic plasticity and the impact of selective forces stemming from other biotic interactions, on both dispersal and specialisation. Next, we review empirical caveats in the study of this interplay. We find that studies use different measures of both dispersal and specialisation, hampering comparisons. Moreover, several studies do not provide independent measures of these two traits. Finally, variation in these traits may occur at scales that are not being considered. We conclude that this correlation is likely not to be expected from large-scale comparative analyses as it is highly context dependent and should not be considered in isolation from the factors that modulate it, such as environmental scale and heterogeneity, intrinsic traits or biotic interactions. A stronger crosstalk between theoretical and empirical studies is needed to understand better the prevalence and basis of the correlation between dispersal and specialisation.
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Affiliation(s)
- Virginie Ravigné
- CIRAD, UMR PHIM, - PHIM, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, TA A-120/K, Campus international de Baillarguet, avenue du Campus d'Agropolis, Montpellier Cedex 5, 34398, France
| | - Leonor R Rodrigues
- cE3c: Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, edifício C2, Lisboa, 1749-016, Portugal
| | - Maud Charlery de la Masselière
- cE3c: Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, edifício C2, Lisboa, 1749-016, Portugal
| | - Benoît Facon
- CBGP, INRAE, IRD, CIRAD, Institut Agro, University of Montpellier, 755 avenue du Campus Agropolis, CS 34988, Montferrier sur Lez cedex, 30016, France
| | - Lechosław Kuczyński
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Sara Magalhães
- cE3c: Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, edifício C2, Lisboa, 1749-016, Portugal
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Shih PY, Sugio A, Simon JC. Molecular Mechanisms Underlying Host Plant Specificity in Aphids. ANNUAL REVIEW OF ENTOMOLOGY 2023; 68:431-450. [PMID: 36228134 DOI: 10.1146/annurev-ento-120220-020526] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Aphids are serious pests of agricultural and ornamental plants and important model systems for hemipteran-plant interactions. The long evolutionary history of aphids with their host plants has resulted in a variety of systems that provide insight into the different adaptation strategies of aphids to plants and vice versa. In the past, various plant-aphid interactions have been documented, but lack of functional tools has limited molecular studies on the mechanisms of plant-aphid interactions. Recent technological advances have begun to reveal plant-aphid interactions at the molecular level and to increase our knowledge of the mechanisms of aphid adaptation or specialization to different host plants. In this article, we compile and analyze available information on plant-aphid interactions, discuss the limitations of current knowledge, and argue for new research directions. We advocate for more work that takes advantage of natural systems and recently established molecular techniques to obtain a comprehensive view of plant-aphid interaction mechanisms.
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Affiliation(s)
- Po-Yuan Shih
- INRAE (National Institute of Agriculture, Food and Environment), UMR IGEPP, Le Rheu, France; , ,
| | - Akiko Sugio
- INRAE (National Institute of Agriculture, Food and Environment), UMR IGEPP, Le Rheu, France; , ,
| | - Jean-Christophe Simon
- INRAE (National Institute of Agriculture, Food and Environment), UMR IGEPP, Le Rheu, France; , ,
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Ollivier R, Glory I, Cloteau R, Le Gallic JF, Denis G, Morlière S, Miteul H, Rivière JP, Lesné A, Klein A, Aubert G, Kreplak J, Burstin J, Pilet-Nayel ML, Simon JC, Sugio A. A major-effect genetic locus, ApRVII, controlling resistance against both adapted and non-adapted aphid biotypes in pea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1511-1528. [PMID: 35192006 DOI: 10.1007/s00122-022-04050-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
KEY MESSAGE A genome-wide association study for pea resistance against a pea-adapted biotype and a non-adapted biotype of the aphid, Acyrthosiphon pisum, identified a genomic region conferring resistance to both biotypes. In a context of reduced insecticide use, the development of cultivars resistant to insect pests is crucial for an integrated pest management. Pea (Pisum sativum) is a crop of major importance among cultivated legumes, for the supply of dietary proteins and nitrogen in low-input cropping systems. However, yields of the pea crop have become unstable due to plant parasites. The pea aphid (Acyrthosiphon pisum) is an insect pest species forming a complex of biotypes, each one adapted to feed on one or a few related legume species. This study aimed to identify resistance to A. pisum and the underlying genetic determinism by examining a collection of 240 pea genotypes. The collection was screened against a pea-adapted biotype and a non-adapted biotype of A. pisum to characterize their resistant phenotype. Partial resistance was observed in some pea genotypes exposed to the pea-adapted biotype. Many pea genotypes were completely resistant to non-adapted biotype, but some exhibited partial susceptibility. A genome-wide association study, using pea exome-capture sequencing data, enabled the identification of the major-effect quantitative trait locus ApRVII on the chromosome 7. ApRVII includes linkage disequilibrium blocks significantly associated with resistance to one or both of the two aphid biotypes studied. Finally, we identified candidate genes underlying ApRVII that are potentially involved in plant-aphid interactions and marker haplotypes linked with aphid resistance. This study sets the ground for the functional characterization of molecular pathways involved in pea defence to the aphids but also is a step forward for breeding aphid-resistant cultivars.
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Affiliation(s)
- Rémi Ollivier
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Isabelle Glory
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Romuald Cloteau
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | | | - Gaëtan Denis
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | | | - Henri Miteul
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | | | - Angélique Lesné
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Anthony Klein
- Agroécologie, INRAE, AgroSup Dijon, Univ Bourgogne-Franche-Comté, 21065, Dijon, France
| | - Grégoire Aubert
- Agroécologie, INRAE, AgroSup Dijon, Univ Bourgogne-Franche-Comté, 21065, Dijon, France
| | - Jonathan Kreplak
- Agroécologie, INRAE, AgroSup Dijon, Univ Bourgogne-Franche-Comté, 21065, Dijon, France
| | - Judith Burstin
- Agroécologie, INRAE, AgroSup Dijon, Univ Bourgogne-Franche-Comté, 21065, Dijon, France
| | | | | | - Akiko Sugio
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France.
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Villarroel CA, González-González A, Alvarez-Baca JK, Villarreal P, Ballesteros GI, Figueroa CC, Cubillos FA, Ramírez CC. Genome sequencing of a predominant clonal lineage of the grain aphid Sitobion avenae. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 143:103742. [PMID: 35183733 DOI: 10.1016/j.ibmb.2022.103742] [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] [Received: 11/23/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
The English grain aphid, Sitobion avenae, is a cosmopolitan pest that feeds on cereals, provoking substantial yield losses by injuring plant tissue and by vectoring plant viruses. Here we report a highly complete, de novo draft genome of the grain aphid using long-read sequencing. We generated an assembly of 2740 contigs with a N50 of 450 kb. We compared this draft genome with that of other aphid species, inspecting gene family evolution, genome-wide positive selection, and searched for horizontal gene transfer events. In addition, we described a recent copy number variant expansion of gene families involving aconitase, ABC transporter, and esterase genes that could be associated with resistance to insecticides and plant chemical defenses. This S. avenae genome obtained from a predominant invasive genotype can provide a framework for studying the spatial-temporal success of these clonal lineages in invaded agroecosystems.
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Affiliation(s)
- Carlos A Villarroel
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; Instituto de Investigación Interdisciplinaria (I3), Universidad de Talca, Talca, Chile; Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
| | | | | | - Pablo Villarreal
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile; Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile
| | - Gabriel I Ballesteros
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; Instituto de Investigación Interdisciplinaria (I3), Universidad de Talca, Talca, Chile
| | - Christian C Figueroa
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; Centro de Ecología Molecular y Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Francisco A Cubillos
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile; Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile
| | - Claudio C Ramírez
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; Centro de Ecología Molecular y Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
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Thorpe P, Escudero‐Martinez CM, Eves‐van den Akker S, Bos JIB. Transcriptional changes in the aphid species Myzus cerasi under different host and environmental conditions. INSECT MOLECULAR BIOLOGY 2020; 29:271-282. [PMID: 31846128 PMCID: PMC7317760 DOI: 10.1111/imb.12631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/22/2019] [Accepted: 12/02/2019] [Indexed: 06/01/2023]
Abstract
Aphids feature complex life cycles, which in the case of many agriculturally important species involve primary and secondary host plant species. Whilst host alternation between primary and secondary host can occur in the field depending on host availability and the environment, aphid populations maintained as laboratory stocks generally are kept under conditions that allow asexual reproduction by parthenogenesis on secondary hosts. We used Myzus cerasi (black cherry aphid) to assess aphid transcriptional differences between populations collected from primary hosts in the field and those adapted to secondary hosts under controlled environment conditions. Transfer of M. cerasi collected from local cherry trees to reported secondary host species resulted in low survival rates. Moreover, aphids were unable to survive on the secondary host land cress, unless first adapted to another secondary host, cleavers. Transcriptome analyses of the different aphid populations (field collected and adapted) revealed extensive transcriptional plasticity to a change in environment, with predominantly genes involved in redox reactions differentially regulated. Most of the differentially expressed genes were duplicated and we found evidence for differential exon usage. Our data suggest that aphid adaptation to different environments may pose a major hurdle and leads to extensive gene expression changes.
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Affiliation(s)
- P. Thorpe
- Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
| | - C. M. Escudero‐Martinez
- Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
- Division of Plant SciencesSchool of Life Sciences, University of DundeeDundeeUK
| | | | - J. I. B. Bos
- Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
- Division of Plant SciencesSchool of Life Sciences, University of DundeeDundeeUK
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Fazalova V, Nevado B. Low Spontaneous Mutation Rate and Pleistocene Radiation of Pea Aphids. Mol Biol Evol 2020; 37:2045-2051. [DOI: 10.1093/molbev/msaa066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Abstract
Accurate estimates of divergence times are essential to understand the evolutionary history of species. It allows linking evolutionary histories of the diverging lineages with past geological, climatic, and other changes in environment and shed light on the processes involved in speciation. The pea aphid radiation includes multiple host races adapted to different legume host plants. It is thought that diversification in this system occurred very recently, over the past 8,000–16,000 years. This young age estimate was used to link diversification in pea aphids to the onset of human agriculture, and led to the establishment of the pea aphid radiation as a model system in the study of speciation with gene flow. Here, we re-examine the age of the pea aphid radiation, by combining a mutation accumulation experiment with a genome-wide estimate of divergence between distantly related pea aphid host races. We estimate the spontaneous mutation rate for pea aphids as 2.7×10-10 per haploid genome per parthenogenic generation. Using this estimate of mutation rate and the genome-wide genetic differentiation observed between pea aphid host races, we show that the pea aphid radiation is much more ancient than assumed previously, predating Neolithic agriculture by several hundreds of thousands of years. Our results rule out human agriculture as the driver of diversification of the pea aphid radiation, and call for re-assessment of the role of allopatric isolation during Pleistocene climatic oscillations in divergence of the pea aphid complex.
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Affiliation(s)
- Varvara Fazalova
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Qiu L, He L, Tan X, Zhang Z, Wang Y, Li X, He H, Ding W, Li Y. Identification and phylogenetics of Spodoptera frugiperda chemosensory proteins based on antennal transcriptome data. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 34:100680. [PMID: 32278289 DOI: 10.1016/j.cbd.2020.100680] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 02/28/2020] [Accepted: 03/01/2020] [Indexed: 12/12/2022]
Abstract
Understanding the interaction between the insect olfactory system and the environment is crucial for fully explaining the molecular mechanisms underlying insect behavior, and providing new strategies for integrated pest management. Although there is good evidence that olfactory proteins play a vital role in mediating insect behaviors, the olfactory mechanism of insects remains poorly understood. We identified a total of 71 chemosensory genes; 25 odorant-binding proteins (OBPs), 27 odorant receptors (ORs), 8 ionotropic receptors (IRs), 8 chemosensory proteins (CSPs) and 3 sensory neuron membrane proteins (SNMPs), in the antennae of male and female fall armyworms, Spodoptera frugiperda, an invasive global pest that causes significant economic damage worldwide. We used differential gene expression (DGE) and fragments per kilobase per million fragments (FPKM) values to compare the transcript levels of candidate chemosensory genes, and qRT-PCR to compare the expression levels of the OR gene, in male and female antennae. The expression of candidate OR genes in male and female antennae was consistent with the DGE data, and the expression of the SfruCL4419.Contig1-All and SfruUnigene1070-All genes was sex-biased. These results not only provide new information on the olfactory mechanism of S. frugiperda, and insects in general, but also suggest new gene targets for pest control.
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Affiliation(s)
- Lin Qiu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Li He
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Xiaoping Tan
- Plant Protection and Inspection Station, Agriculture and Rural Department of Hunan Province, Changsha 410005, China
| | - Zhengbing Zhang
- Plant Protection and Inspection Station, Agriculture and Rural Department of Hunan Province, Changsha 410005, China
| | - Yong Wang
- Plant Protection and Inspection Station, Agriculture and Rural Department of Hunan Province, Changsha 410005, China
| | - Xinwen Li
- Plant Protection and Inspection Station, Agriculture and Rural Department of Hunan Province, Changsha 410005, China
| | - Hualiang He
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Wenbing Ding
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Engineering & Technology Research Center for Biopesticide and Formulation Processing, Changsha 410128, China
| | - Youzhi Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Engineering & Technology Research Center for Biopesticide and Formulation Processing, Changsha 410128, China.
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Li Y, Park H, Smith TE, Moran NA. Gene Family Evolution in the Pea Aphid Based on Chromosome-Level Genome Assembly. Mol Biol Evol 2020; 36:2143-2156. [PMID: 31173104 PMCID: PMC6759078 DOI: 10.1093/molbev/msz138] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genome structural variations, including duplications, deletions, insertions, and inversions, are central in the evolution of eukaryotic genomes. However, structural variations present challenges for high-quality genome assembly, hampering efforts to understand the evolution of gene families and genome architecture. An example is the genome of the pea aphid (Acyrthosiphon pisum) for which the current assembly is composed of thousands of short scaffolds, many of which are known to be misassembled. Here, we present an improved version of the A. pisum genome based on the use of two long-range proximity ligation methods. The new assembly contains four long scaffolds (40-170 Mb), corresponding to the three autosomes and the X chromosome of A. pisum, and encompassing 86% of the new assembly. Assembly accuracy is supported by several quality assessments. Using this assembly, we identify the chromosomal locations and relative ages of duplication events, and the locations of horizontally acquired genes. The improved assembly illuminates the mode of gene family evolution by providing proximity information between paralogs. By estimating nucleotide polymorphism and coverage depth from resequencing data, we determined that many short scaffolds not assembling to chromosomes represent hemizygous regions, which are especially frequent on the highly repetitive X chromosome. Aligning the X-linked aphicarus region, responsible for male wing dimorphism, to the new assembly revealed a 50-kb deletion that cosegregates with the winged male phenotype in some clones. These results show that long-range scaffolding methods can substantially improve assemblies of repetitive genomes and facilitate study of gene family evolution and structural variation.
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Affiliation(s)
- Yiyuan Li
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Hyunjin Park
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Thomas E Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
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10
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Ma L, Li MY, Chang CY, Chen FF, Hu Y, Liu XD. The host range of Aphis gossypii is dependent on aphid genetic background and feeding experience. PeerJ 2019; 7:e7774. [PMID: 31579627 PMCID: PMC6768058 DOI: 10.7717/peerj.7774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 08/27/2019] [Indexed: 01/12/2023] Open
Abstract
Background A polyphagous insect herbivore has a wide range of host plants. However, it has been found that many polyphagous herbivores commonly exhibit a strong preference for a subset of species in their broad host range, and various host biotypes exist in herbivore populations. Nutrition and secondary metabolites in plants affect herbivore preference and performance, but it is still not clear which factors determine the host range and host preference of polyphagous herbivores. Method Cotton-melon aphids, Aphis gossypii Glover, collected from cotton and cucumber crops, were used in this study. The genetic backgrounds of these aphids were detected using microsatellite PCR and six genotypes were evaluated. Performance of these six aphid genotypes on excised leaves and plants of cotton and cucumber seedlings were examined through a reciprocal transplant experiment. In order to detect whether the feeding experience on artificial diet would alter aphid host range, the six genotypes of aphids fed on artificial diet for seven days were transferred onto cotton and cucumber leaves, and then their population growth on these two host plants was surveyed. Results Aphids from cotton and cucumber plants could not colonize the excised leaves and intact plants of cucumber and cotton seedlings, respectively. All six genotypes of aphids collected from cotton and cucumber plants could survive and produce offspring on artificial diet, which lacked plant secondary metabolites. The feeding experience on the artificial diet did not alter the ability of all six genotypes to use their native host plants. However, after feeding on this artificial diet for seven days, two aphid genotypes from cotton and one from cucumber acquired the ability to use both of the excised leaves from cucumber and cotton plants. The two aphid genotypes from cotton conditioned by the feeding experience on artificial diet and then reared on excised cucumber leaves for >12 generations still maintained the ability to use intact cotton plants but did not establish a population on cucumber plants. However, one cucumber genotype conditioned by artificial diet and then reared on excised cotton leaves could use both the intact cotton and cucumber plants, showing that the expansion of host range was mediated by feeding experience. Conclusion Feeding experience on artificial diet induced the expansion of host range of the cucurbit-specialized A. gossypii, and this expansion was genotype-specific. We speculated that feeding on a constant set of host plants in the life cycle of aphids may contribute to the formation of host specialization.
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Affiliation(s)
- Lin Ma
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Meng-Yue Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Chun-Yan Chang
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Fang-Fang Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Yang Hu
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xiang-Dong Liu
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
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Sanchez-Arcos C, Kai M, Svatoš A, Gershenzon J, Kunert G. Untargeted Metabolomics Approach Reveals Differences in Host Plant Chemistry Before and After Infestation With Different Pea Aphid Host Races. FRONTIERS IN PLANT SCIENCE 2019; 10:188. [PMID: 30873192 PMCID: PMC6403166 DOI: 10.3389/fpls.2019.00188] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 02/05/2019] [Indexed: 05/11/2023]
Abstract
The pea aphid (Acyrthosiphon pisum), a phloem-sucking insect, has undergone a rapid radiation together with the domestication and anthropogenic range expansion of several of its legume host plants. This insect species is a complex of at least 15 genetically different host races that can all develop on the universal host plant Vicia faba. However, each host race is specialized on a particular plant species, such as Medicago sativa, Trifolium pratense, or Pisum sativum, which makes it an attractive model insect to study ecological speciation. Previous work revealed that pea aphid host plants produce a specific phytohormone profile depending on the host plant - host race combination. Native aphid races induce lower defense hormone levels in their host plant than non-native pea aphid races. Whether these changes in hormone levels also lead to changes in other metabolites is still unknown. We used a mass spectrometry-based untargeted metabolomic approach to identify plant chemical compounds that vary among different host plant-host race combinations and might therefore, be involved in pea aphid host race specialization. We found significant differences among the metabolic fingerprints of the four legume species studied prior to aphid infestation, which correlated with aphid performance. After infestation, the metabolic profiles of M. sativa and T. pratense plants infested with their respective native aphid host race were consistently different from profiles after infestation with non-native host races and from uninfested control plants. The metabolic profiles of P. sativum plants infested with their native aphid host race were also different from plants infested with non-native host races, but not different from uninfested control plants. The compounds responsible for these differences were putatively identified as flavonoids, saponins, non-proteinogenic amino acids and peptides among others. As members of these compound classes are known for their activity against insects and aphids in particular, they may be responsible for the differential performance of host races on native vs. non-native host plants. We conclude that the untargeted metabolomic approach is suitable to identify candidate compounds involved in the specificity of pea aphid - host plant interactions.
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Affiliation(s)
- Carlos Sanchez-Arcos
- Department of Biochemistry, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Marco Kai
- Research Group Mass Spectrometry/Proteomics, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry/Proteomics, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Grit Kunert
- Department of Biochemistry, Max-Planck Institute for Chemical Ecology, Jena, Germany
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12
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Long-Term Population Studies Uncover the Genome Structure and Genetic Basis of Xenobiotic and Host Plant Adaptation in the Herbivore Tetranychus urticae. Genetics 2019; 211:1409-1427. [PMID: 30745439 DOI: 10.1534/genetics.118.301803] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/02/2019] [Indexed: 01/11/2023] Open
Abstract
Pesticide resistance arises rapidly in arthropod herbivores, as can host plant adaptation, and both are significant problems in agriculture. These traits have been challenging to study as both are often polygenic and many arthropods are genetically intractable. Here, we examined the genetic architecture of pesticide resistance and host plant adaptation in the two-spotted spider mite, Tetranychus urticae, a global agricultural pest. We show that the short generation time and high fecundity of T. urticae can be readily exploited in experimental evolution designs for high-resolution mapping of quantitative traits. As revealed by selection with spirodiclofen, an acetyl-CoA carboxylase inhibitor, in populations from a cross between a spirodiclofen-resistant and a spirodiclofen-susceptible strain, and which also differed in performance on tomato, we found that a limited number of loci could explain quantitative resistance to this compound. These were resolved to narrow genomic intervals, suggesting specific candidate genes, including acetyl-CoA carboxylase itself, clustered and copy variable cytochrome P450 genes, and NADPH cytochrome P450 reductase, which encodes a redox partner for cytochrome P450s. For performance on tomato, candidate genomic regions for response to selection were distinct from those responding to the synthetic compound and were consistent with a more polygenic architecture. In accomplishing this work, we exploited the continuous nature of allele frequency changes across experimental populations to resolve the existing fragmented T. urticae draft genome to pseudochromosomes. This improved assembly was indispensable for our analyses, as it will be for future research with this model herbivore that is exceptionally amenable to genetic studies.
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13
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Boulain H, Legeai F, Jaquiéry J, Guy E, Morlière S, Simon JC, Sugio A. Differential Expression of Candidate Salivary Effector Genes in Pea Aphid Biotypes With Distinct Host Plant Specificity. FRONTIERS IN PLANT SCIENCE 2019; 10:1301. [PMID: 31695713 PMCID: PMC6818229 DOI: 10.3389/fpls.2019.01301] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/18/2019] [Indexed: 05/13/2023]
Abstract
Effector proteins play crucial roles in determining the outcome of various plant-parasite interactions. Aphids inject salivary effector proteins into plants to facilitate phloem feeding, but some proteins might trigger defense responses in certain plants. The pea aphid, Acyrthosiphon pisum, forms multiple biotypes, and each biotype is specialized to feed on a small number of closely related legume species. Interestingly, all the previously identified biotypes can feed on Vicia faba; hence, it serves as a universal host plant of A. pisum. We hypothesized that the salivary effector proteins have a key role in determining the compatibility between specific host species and A. pisum biotypes and that each biotype produces saliva containing a specific mixture of effector proteins due to differential expression of encoding genes. As the first step to address these hypotheses, we conducted two sets of RNA-seq experiments. RNA-seq analysis of dissected salivary glands (SGs) from reference alfalfa- and pea-specialized A. pisum lines revealed common and line-specific repertoires of candidate salivary effector genes. Based on the results, we created an extended catalogue of A. pisum salivary effector candidates. Next, we used aphid head samples, which contain SGs, to examine biotype-specific expression patterns of candidate salivary genes. RNA-seq analysis of head samples of alfalfa- and pea-specialized biotypes, each represented by three genetically distinct aphid lines reared on either a universal or specific host plant, showed that a majority of the candidate salivary effector genes was expressed in both biotypes at a similar level. Nonetheless, we identified small sets of genes that were differentially regulated in a biotype-specific manner. Little host plant effect (universal vs. specific) was observed on the expression of candidate salivary genes. Analysis of previously obtained genome re-sequenced data of the two biotypes revealed the copy number variations that might explain the differential expression of some candidate salivary genes. In addition, at least four candidate effector genes that were present in the alfalfa biotype but might not be encoded in the pea biotype were identified. This work sets the stage for future functional characterization of candidate genes potentially involved in the determination of plant specificity of pea aphid biotypes.
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Affiliation(s)
- Hélène Boulain
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Fabrice Legeai
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
- University of Rennes 1, Inria, CNRS, IRISA, Rennes, France
| | - Julie Jaquiéry
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Endrick Guy
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Stéphanie Morlière
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Jean-Christophe Simon
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Akiko Sugio
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
- *Correspondence: Akiko Sugio,
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14
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Kahnt B, Theodorou P, Soro A, Hollens-Kuhr H, Kuhlmann M, Pauw A, Paxton RJ. Small and genetically highly structured populations in a long-legged bee, Rediviva longimanus, as inferred by pooled RAD-seq. BMC Evol Biol 2018; 18:196. [PMID: 30567486 PMCID: PMC6300007 DOI: 10.1186/s12862-018-1313-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 11/28/2018] [Indexed: 11/10/2022] Open
Abstract
Adaptation to local host plants may impact a pollinator's population genetic structure by reducing gene flow and driving population genetic differentiation, representing an early stage of ecological speciation. South African Rediviva longimanus bees exhibit elongated forelegs, a bizarre adaptation for collecting oil from floral spurs of their Diascia hosts. Furthermore, R. longimanus foreleg length (FLL) differs significantly among populations, which has been hypothesised to result from selection imposed by inter-population variation in Diascia floral spur length. Here, we used a pooled restriction site-associated DNA sequencing (pooled RAD-seq) approach to investigate the population genetic structure of R. longimanus and to test if phenotypic differences in FLL translate into increased genetic differentiation (i) between R. longimanus populations and (ii) between phenotypes across populations. We also inferred the effects of demographic processes on population genetic structure and tested for genetic markers underpinning local adaptation. RESULTS: Populations showed marked genetic differentiation (average FST = 0.165), though differentiation was not statistically associated with differences between populations in FLL. All populations exhibited very low genetic diversity and were inferred to have gone through recent bottleneck events, suggesting extremely low effective population sizes. Genetic differentiation between samples pooled by leg length (short versus long) rather than by population of origin was even higher (FST = 0.260) than between populations, suggesting reduced interbreeding between long and short-legged individuals. Signatures of selection were detected in 1119 (3.8%) of a total of 29,721 SNP markers, CONCLUSIONS: Populations of R. longimanus appear to be small, bottlenecked and isolated. Though we could not detect the effect of local adaptation (FLL in response to floral spurs of host plants) on population genetic differentiation, short and long legged bees appeared to be partially differentiated, suggesting incipient ecological speciation. To test this hypothesis, greater resolution through the use of individual-based whole-genome analyses is now needed to quantify the degree of reproductive isolation between long and short legged bees between and even within populations.
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Affiliation(s)
- Belinda Kahnt
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
| | - Panagiotis Theodorou
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Antonella Soro
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Hilke Hollens-Kuhr
- Institute of Landscape Ecology, Westfälische Wilhelms-Universität Münster, Heisenbergstraße 2, 48149, Münster, Germany
| | - Michael Kuhlmann
- Zoological Museum, Kiel University, Hegewischstr. 3, 24105, Kiel, Germany
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Anton Pauw
- Department of Botany and Zoology, Stellenbosch University, Matieland, 7602, South Africa
| | - Robert J Paxton
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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15
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Boulain H, Legeai F, Guy E, Morlière S, Douglas NE, Oh J, Murugan M, Smith M, Jaquiéry J, Peccoud J, White FF, Carolan JC, Simon JC, Sugio A. Fast Evolution and Lineage-Specific Gene Family Expansions of Aphid Salivary Effectors Driven by Interactions with Host-Plants. Genome Biol Evol 2018; 10:1554-1572. [PMID: 29788052 PMCID: PMC6012102 DOI: 10.1093/gbe/evy097] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2018] [Indexed: 12/31/2022] Open
Abstract
Effector proteins play crucial roles in plant-parasite interactions by suppressing plant defenses and hijacking plant physiological responses to facilitate parasite invasion and propagation. Although effector proteins have been characterized in many microbial plant pathogens, their nature and role in adaptation to host plants are largely unknown in insect herbivores. Aphids rely on salivary effector proteins injected into the host plants to promote phloem sap uptake. Therefore, gaining insight into the repertoire and evolution of aphid effectors is key to unveiling the mechanisms responsible for aphid virulence and host plant specialization. With this aim in mind, we assembled catalogues of putative effectors in the legume specialist aphid, Acyrthosiphon pisum, using transcriptomics and proteomics approaches. We identified 3,603 candidate effector genes predicted to be expressed in A. pisum salivary glands (SGs), and 740 of which displayed up-regulated expression in SGs in comparison to the alimentary tract. A search for orthologs in 17 arthropod genomes revealed that SG-up-regulated effector candidates of A. pisum are enriched in aphid-specific genes and tend to evolve faster compared with the whole gene set. We also found that a large fraction of proteins detected in the A. pisum saliva belonged to three gene families, of which certain members show evidence consistent with positive selection. Overall, this comprehensive analysis suggests that the large repertoire of effector candidates in A. pisum constitutes a source of novelties promoting plant adaptation to legumes.
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Affiliation(s)
- Hélène Boulain
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Fabrice Legeai
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France.,Inria/IRISA GenScale, Campus de Beaulieu, Rennes, France
| | - Endrick Guy
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Stéphanie Morlière
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Nadine E Douglas
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.,UCD School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Jonghee Oh
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
| | - Marimuthu Murugan
- Community Science College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Michael Smith
- Department of Entomology, Kansas State University, Manhattan, Kansas
| | - Julie Jaquiéry
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Jean Peccoud
- UMR CNRS 7267 Ecologie et Biologie des Interactions, équipe Ecologie Evolution Symbiose, Université de Poitiers, Poitiers, France
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, Florida
| | - James C Carolan
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Jean-Christophe Simon
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Akiko Sugio
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
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16
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Jaquiéry J, Peccoud J, Ouisse T, Legeai F, Prunier-Leterme N, Gouin A, Nouhaud P, Brisson JA, Bickel R, Purandare S, Poulain J, Battail C, Lemaitre C, Mieuzet L, Le Trionnaire G, Simon JC, Rispe C. Disentangling the Causes for Faster-X Evolution in Aphids. Genome Biol Evol 2018; 10:507-520. [PMID: 29360959 PMCID: PMC5798017 DOI: 10.1093/gbe/evy015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2018] [Indexed: 12/22/2022] Open
Abstract
The faster evolution of X chromosomes has been documented in several species, and results from the increased efficiency of selection on recessive alleles in hemizygous males and/or from increased drift due to the smaller effective population size of X chromosomes. Aphids are excellent models for evaluating the importance of selection in faster-X evolution because their peculiar life cycle and unusual inheritance of sex chromosomes should generally lead to equivalent effective population sizes for X and autosomes. Because we lack a high-density genetic map for the pea aphid, whose complete genome has been sequenced, we first assigned its entire genome to the X or autosomes based on ratios of sequencing depth in males (X0) to females (XX). Then, we computed nonsynonymous to synonymous substitutions ratios (dN/dS) for the pea aphid gene set and found faster evolution of X-linked genes. Our analyses of substitution rates, together with polymorphism and expression data, showed that relaxed selection is likely to be the greatest contributor to faster-X because a large fraction of X-linked genes are expressed at low rates and thus escape selection. Yet, a minor role for positive selection is also suggested by the difference between substitution rates for X and autosomes for male-biased genes (but not for asexual female-biased genes) and by lower Tajima’s D for X-linked compared with autosomal genes with highly male-biased expression patterns. This study highlights the relevance of organisms displaying alternative chromosomal inheritance to the understanding of forces shaping genome evolution.
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Affiliation(s)
- Julie Jaquiéry
- INRA UMR IGEPP Domaine de la Motte, Le Rheu, France.,CNRS UMR 6553 ECOBIO, Université de Rennes 1, France
| | - Jean Peccoud
- CNRS UMR 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, France
| | | | - Fabrice Legeai
- INRA UMR IGEPP Domaine de la Motte, Le Rheu, France.,INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Rennes, France
| | | | - Anais Gouin
- INRA UMR IGEPP Domaine de la Motte, Le Rheu, France.,INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Rennes, France
| | - Pierre Nouhaud
- Institute of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | | | - Ryan Bickel
- Department of Biology, University of Rochester
| | - Swapna Purandare
- Multidisciplinary Center for Advance Research and Studies (MCARS), Jamia Millia Islamia, New Delhi, India
| | - Julie Poulain
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Christophe Battail
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Centre National de Génotypage (CNG), Evry, France
| | - Claire Lemaitre
- INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Rennes, France
| | | | | | | | - Claude Rispe
- BIOEPAR, INRA, ONIRIS, La Chantrerie, Nantes, France
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17
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Guyomar C, Legeai F, Jousselin E, Mougel C, Lemaitre C, Simon JC. Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches. MICROBIOME 2018; 6:181. [PMID: 30305166 PMCID: PMC6180509 DOI: 10.1186/s40168-018-0562-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/20/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact. RESULTS We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host. CONCLUSIONS We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.
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Affiliation(s)
- Cervin Guyomar
- INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France
- Université Rennes 1, Inria, CNRS, IRISA, F-35000, Rennes, France
| | - Fabrice Legeai
- INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France
- Université Rennes 1, Inria, CNRS, IRISA, F-35000, Rennes, France
| | - Emmanuelle Jousselin
- INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, Montpellier, France
| | - Christophe Mougel
- INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France
| | - Claire Lemaitre
- Université Rennes 1, Inria, CNRS, IRISA, F-35000, Rennes, France
| | - Jean-Christophe Simon
- INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France.
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18
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Nouhaud P, Gautier M, Gouin A, Jaquiéry J, Peccoud J, Legeai F, Mieuzet L, Smadja CM, Lemaitre C, Vitalis R, Simon JC. Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races. Mol Ecol 2018; 27:3287-3300. [PMID: 30010213 DOI: 10.1111/mec.14799] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 06/01/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
Identifying the genomic bases of adaptation to novel environments is a long-term objective in evolutionary biology. Because genetic differentiation is expected to increase between locally adapted populations at the genes targeted by selection, scanning the genome for elevated levels of differentiation is a first step towards deciphering the genomic architecture underlying adaptive divergence. The pea aphid Acyrthosiphon pisum is a model of choice to address this question, as it forms a large complex of plant-specialized races and cryptic species, resulting from recent adaptive radiation. Here, we characterized genomewide polymorphisms in three pea aphid races specialized on alfalfa, clover and pea crops, respectively, which we sequenced in pools (poolseq). Using a model-based approach that explicitly accounts for selection, we identified 392 genomic hotspots of differentiation spanning 47.3 Mb and 2,484 genes (respectively, 9.12% of the genome size and 8.10% of its genes). Most of these highly differentiated regions were located on the autosomes, and overall differentiation was weaker on the X chromosome. Within these hotspots, high levels of absolute divergence between races suggest that these regions experienced less gene flow than the rest of the genome, most likely by contributing to reproductive isolation. Moreover, population-specific analyses showed evidence of selection in every host race, depending on the hotspot considered. These hotspots were significantly enriched for candidate gene categories that control host-plant selection and use. These genes encode 48 salivary proteins, 14 gustatory receptors, 10 odorant receptors, five P450 cytochromes and one chemosensory protein, which represent promising candidates for the genetic basis of host-plant specialization and ecological isolation in the pea aphid complex. Altogether, our findings open new research directions towards functional studies, for validating the role of these genes on adaptive phenotypes.
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Affiliation(s)
| | - Mathieu Gautier
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
| | - Anaïs Gouin
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Fabrice Legeai
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554) - CNRS - IRD - EPHE - CIRAD -Université de Montpellier, Montpellier, France
| | | | - Renaud Vitalis
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
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19
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Simon JC, Peccoud J. Rapid evolution of aphid pests in agricultural environments. CURRENT OPINION IN INSECT SCIENCE 2018; 26:17-24. [PMID: 29764656 DOI: 10.1016/j.cois.2017.12.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/05/2017] [Accepted: 12/30/2017] [Indexed: 05/19/2023]
Abstract
Aphids constitute a major group of crop pests that inflict serious damages to plants, both directly by ingesting phloem and indirectly as vectors of numerous diseases. In response to intense and repeated human-induced pressures, such as insecticide treatments, the use of resistant plants and biological agents, aphids have developed a series of evolutionary responses relying on adaptation and phenotypic plasticity. In this review, we highlight some remarkable evolutionary responses to anthropogenic pressures in agroecosystems and discuss the mechanisms underlying the ecological and evolutionary success of aphids. We outline the peculiar mode of reproduction, the polyphenism for biologically important traits and the diverse and flexible associations with microbial symbionts as key determinants of adaptive potential and pest status of aphids.
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Affiliation(s)
- Jean-Christophe Simon
- INRA, Institute of Genetics, Environment and Plant Protection (IGEPP-Joint Research Unit 1349), Domaine de la Motte, BP 35327, 35653 Le Rheu, France.
| | - Jean Peccoud
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions (EBI-Joint Research Unit 7267, CNRS), 86000 Poitiers, France
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20
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Acevedo FE, Peiffer M, Ray S, Meagher R, Luthe DS, Felton GW. Intraspecific differences in plant defense induction by fall armyworm strains. THE NEW PHYTOLOGIST 2018; 218:310-321. [PMID: 29332318 DOI: 10.1111/nph.14981] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/05/2017] [Indexed: 05/06/2023]
Abstract
The underlying adaptive mechanisms by which insect strains are associated with specific plants are largely unknown. In this study, we investigated the role of herbivore-induced defenses in the host plant association of fall armyworm (Spodoptera frugiperda) strains. We tested the expression of herbivore-induced defense-related genes and the activity of plant-defensive proteins in maize and Bermuda grass upon feeding by fall armyworm strains. The rice strain caterpillars induced greater accumulation of proteinase inhibitors in maize than the corn strain caterpillars. In Bermuda grass, feeding by the corn strain suppressed induction of trypsin inhibitor activity whereas the rice strain induced greater activity levels. Differences in elicitation of these plant defenses by the two strains seems to be due to differences in the activity levels of the salivary enzyme phospholipase C. The levels of plant defense responses were negatively correlated with caterpillar growth, indicating a fitness effect. Our results indicate that specific elicitors in the saliva of fall armyworm stains trigger differential levels of plant defense responses that affect caterpillar growth and thus may influence host plant associations in field conditions. The composition and secretion of plant defense elicitors may have a strong influence in the host plant association of insect herbivores.
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Affiliation(s)
- Flor E Acevedo
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Michelle Peiffer
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Swayamjit Ray
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Robert Meagher
- Center for Medical, Agricultural and Veterinary Entomology, USDA-ARS, Gainesville, FL, 32608, USA
| | - Dawn S Luthe
- Department of Plant Science, Pennsylvania State University, University Park, PA, 16802, USA
| | - Gary W Felton
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802, USA
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21
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Population genomics and comparisons of selective signatures in two invasions of melon fly, Bactrocera cucurbitae (Diptera: Tephritidae). Biol Invasions 2017. [DOI: 10.1007/s10530-017-1621-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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22
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Hopkins DP, Cameron DD, Butlin RK. The chemical signatures underlying host plant discrimination by aphids. Sci Rep 2017; 7:8498. [PMID: 28819265 PMCID: PMC5561273 DOI: 10.1038/s41598-017-07729-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 07/04/2017] [Indexed: 12/26/2022] Open
Abstract
The diversity of phytophagous insects is largely attributable to speciation involving shifts between host plants. These shifts are mediated by the close interaction between insects and plant metabolites. However, there has been limited progress in understanding the chemical signatures that underlie host preferences. We use the pea aphid (Acyrthosiphon pisum) to address this problem. Host-associated races of pea aphid discriminate between plant species in race-specific ways. We combined metabolomic profiling of multiple plant species with behavioural tests on two A. pisum races, to identify metabolites that explain variation in either acceptance or discrimination. Candidate compounds were identified using tandem mass spectrometry. Our results reveal a small number of compounds that explain a large proportion of variation in the differential acceptability of plants to A. pisum races. Two of these were identified as L-phenylalanine and L-tyrosine but it may be that metabolically-related compounds directly influence insect behaviour. The compounds implicated in differential acceptability were not related to the set correlated with general acceptability of plants to aphids, regardless of host race. Small changes in response to common metabolites may underlie host shifts. This study opens new opportunities for understanding the mechanistic basis of host discrimination and host shifts in insects.
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Affiliation(s)
- David P Hopkins
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Duncan D Cameron
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Roger K Butlin
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, S10 2TN, UK.
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23
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Cui N, Yang PC, Guo K, Kang L, Cui F. Large-scale gene expression reveals different adaptations of Hyalopterus persikonus to winter and summer host plants. INSECT SCIENCE 2017; 24:431-442. [PMID: 28547891 DOI: 10.1111/1744-7917.12336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/15/2016] [Accepted: 03/14/2016] [Indexed: 06/07/2023]
Abstract
Host alternation, an obligatory seasonal shifting between host plants of distant genetic relationship, has had significant consequences for the diversification and success of the superfamily of aphids. However, the underlying molecular mechanism remains unclear. In this study, the molecular mechanism of host alternation was explored through a large-scale gene expression analysis of the mealy aphid Hyalopterus persikonus on winter and summer host plants. More than four times as many unigenes of the mealy aphid were significantly upregulated on summer host Phragmites australis than on winter host Rosaceae plants. In order to identify gene candidates related to host alternation, the differentially expressed unigenes of H. persikonus were compared to salivary gland expressed genes and secretome of Acyrthosiphon pisum. Genes involved in ribosome and oxidative phosphorylation and with molecular functions of heme-copper terminal oxidase activity, hydrolase activity and ribosome binding were potentially upregulated in salivary glands of H. persikonus on the summer host. Putative secretory proteins, such as detoxification enzymes (carboxylesterases and cytochrome P450s), antioxidant enzymes (peroxidase and superoxide dismutase), glutathione peroxidase, glucose dehydrogenase, angiotensin-converting enzyme, cadherin, and calreticulin, were highly expressed in H. persikonus on the summer host, while a SCP GAPR-1-like family protein and a salivary sheath protein were highly expressed in the aphids on winter hosts. These results shed light on phenotypic plasticity in host utilization and seasonal adaptation of aphids.
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Affiliation(s)
- Na Cui
- State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng-Cheng Yang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Kun Guo
- State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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24
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Sikkink KL, Kobiela ME, Snell-Rood EC. Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study. BMC Genomics 2017; 18:412. [PMID: 28549454 PMCID: PMC5446745 DOI: 10.1186/s12864-017-3787-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/11/2017] [Indexed: 12/30/2022] Open
Abstract
Background Agricultural environments have long presented an opportunity to study evolution in action, and genomic approaches are opening doors for testing hypotheses about adaptation to crops, pesticides, and fertilizers. Here, we begin to develop the cabbage white butterfly (Pieris rapae) as a system to test questions about adaptation to novel, agricultural environments. We focus on a population in the north central United States as a unique case study: here, canola, a host plant, has been grown during the entire flight period of the butterfly over the last three decades. Results First, we show that the agricultural population has diverged phenotypically relative to a nonagricultural population: when reared on a host plant distantly related to canola, the agricultural population is smaller and more likely to go into diapause than the nonagricultural population. Second, drawing from deep sequencing runs from six individuals from the agricultural population, we assembled the gut transcriptome of this population. Then, we sequenced RNA transcripts from the midguts of 96 individuals from this canola agricultural population and the nonagricultural population in order to describe patterns of genomic divergence between the two. While population divergence is low, 235 genes show evidence of significant differentiation between populations. These genes are significantly enriched for cofactor and small molecule metabolic processes, and many genes also have transporter or catalytic activity. Analyses of population structure suggest the agricultural population contains a subset of the genetic variation in the nonagricultural population. Conclusions Taken together, our results suggest that adaptation of cabbage whites to an agricultural environment occurred at least in part through selection on standing genetic variation. Both the phenotypic and genetic data are consistent with the idea that this pest has adapted to an abundant and predictable agricultural resource through a narrowing of niche breadth and loss of genetic variants rather than de novo gain of adaptive alleles. The present research develops genomic resources to pave the way for future studies using cabbage whites as a model contributing to our understanding of adaptation to agricultural environments. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3787-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kristin L Sikkink
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul, MN, 55108, USA.
| | - Megan E Kobiela
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul, MN, 55108, USA
| | - Emilie C Snell-Rood
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul, MN, 55108, USA
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25
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Zhang YC, Lei HX, Miao NH, Liu XD. Comparative Transcriptional Analysis of the Host-Specialized Aphids Aphis gossypii (Hemiptera: Aphididae). JOURNAL OF ECONOMIC ENTOMOLOGY 2017; 110:702-710. [PMID: 28334183 DOI: 10.1093/jee/tox029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Indexed: 06/06/2023]
Abstract
Host specialization is an ubiquitous character in aphid populations. Many polyphagous aphid populations usually consist of several subpopulations that have strong fidelity to a specific host or a subset of host range. Host specialization is an evolutional result of food habit of insects. However, genetic basis and molecular mechanism of host specialization are still unclear. In this study, we presented a comparative analysis on global gene expression profiles of three lineages of Aphis gossypii Glover: cotton-specialized (CO), cucurbit-specialized (CU), and CU reared on cowpea (CU-cowpea), using RNA-Seq method. More than 157 million clean reads and 38,398 different unigenes were generated from transcriptomes of these three aphid lineages. The 1,106 down- and 2,835 up-regulated genes were found between CO and CU, and 812 down- and 14,492 up-regulated genes between CU-cowpea and CU. Differentially expressed genes between CO and CU were enriched in sugar metabolism, immune system process, pathogen infection or symbiosis, and salivary secretion. Genes associated with cytochrome P450, major facilitator superfamily, and salivary effector were differentially expressed between CO and CU, which might be involved in determining host specialization. UDP-glycosyltransferases genes were sensitive to host shift. Carboxylesterases and digestion-related protease genes were related to both the host specialization and host shift of aphids. Expression levels of 22 out of 24 genes of CO and CU measured by RT-qPCR method were as similar as the results from RNA-seq method. This study provides a road map for future study on molecular mechanism of host specialization in aphids.
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Affiliation(s)
- Yuan-Chen Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China (; ; ; )
| | - Hai-Xia Lei
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China (; ; ; )
| | - Ning-Hui Miao
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China (; ; ; )
| | - Xiang-Dong Liu
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China (; ; ; )
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26
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Lund KT, Riaz S, Walker MA. Population Structure, Diversity and Reproductive Mode of the Grape Phylloxera (Daktulosphaira vitifoliae) across Its Native Range. PLoS One 2017; 12:e0170678. [PMID: 28125736 PMCID: PMC5268464 DOI: 10.1371/journal.pone.0170678] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/09/2017] [Indexed: 11/25/2022] Open
Abstract
Grape Phylloxera, Daktulosphaira vitifoliae, is a gall-forming insect that feeds on the leaves and roots of many Vitis species. The roots of the cultivated V. vinifera cultivars and hybrids are highly susceptible to grape phylloxera feeding damage. The native range of this insect covers most of North America, and it is particularly abundant in the eastern and central United States. Phylloxera was introduced from North America to almost all grape-growing regions across five of the temperate zone continents. It devastated vineyards in each of these regions causing large-scale disruptions to grape growers, wine makers and national economies. In order to understand the population diversity of grape phylloxera in its native range, more than 500 samples from 19 States and 34 samples from the introduced range (northern California, Europe and South America) were genotyped with 32 simple sequence repeat markers. STRUCTURE, a model based clustering method identified five populations within these samples. The five populations were confirmed by a neighbor-joining tree and principal coordinate analysis (PCoA). These populations were distinguished by their Vitis species hosts and their geographic locations. Samples collected from California, Europe and South America traced back to phylloxera sampled in the northeastern United States on V. riparia, with some influence from phylloxera collected along the Atlantic Coast and Central Plains on V. vulpina. Reproductive statistics conclusively confirmed that sexual reproduction is common in the native range and is combined with cyclical parthenogenesis. Native grape phylloxera populations were identified to be under Hardy-Weinberg equilibrium. The identification of admixed samples between many of these populations indicates that shared environments facilitate sexual reproduction between different host associated populations to create new genotypes of phylloxera. This study also found that assortative mating might occur across the sympatric range of the V. vulpina west and V. cinerea populations.
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Affiliation(s)
- Karl T. Lund
- Department of Viticulture and Enology, University of California, Davis, California, United States of America
| | - Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, California, United States of America
| | - M. Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, California, United States of America
- * E-mail:
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27
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Vorburger C, Herzog J, Rouchet R. Aphid specialization on different summer hosts is associated with strong genetic differentiation and unequal symbiont communities despite a common mating habitat. J Evol Biol 2017; 30:762-772. [PMID: 28055138 DOI: 10.1111/jeb.13040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 12/06/2016] [Accepted: 01/02/2017] [Indexed: 01/03/2023]
Abstract
Specialization on different host plants can promote evolutionary diversification of herbivorous insects. Work on pea aphids (Acyrthosiphon pisum) has contributed significantly to the understanding of this process, demonstrating that populations associated with different host plants exhibit performance trade-offs across hosts, show adaptive host choice and genetic differentiation and possess different communities of bacterial endosymbionts. Populations specialized on different secondary host plants during the parthenogenetic summer generations are also described for the black bean aphid (Aphis fabae complex) and are usually treated as different (morphologically cryptic) subspecies. In contrast to pea aphids, however, host choice and mate choice are decoupled in black bean aphids, because populations from different summer hosts return to the same primary host plant to mate and lay overwintering eggs. This could counteract evolutionary divergence, and it is currently unknown to what extent black bean aphids using different summer hosts are indeed differentiated. We addressed this question by microsatellite genotyping and endosymbiont screening of black bean aphids collected in summer from the goosefoot Chenopodium album (subspecies A. f. fabae) and from thistles of the genus Cirsium (subspecies A. f. cirsiiacanthoides) across numerous sites in Switzerland and France. Our results show clearly that aphids from Cirsium and Chenopodium exhibit strong and geographically consistent genetic differentiation and that they differ in their frequencies of infection with particular endosymbionts. The dependence on a joint winter host has thus not prevented the evolutionary divergence into summer host-adapted populations that appear to have evolved mechanisms of reproductive isolation within a common mating habitat.
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Affiliation(s)
- C Vorburger
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - J Herzog
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - R Rouchet
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
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28
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Sanchez-Arcos C, Reichelt M, Gershenzon J, Kunert G. Modulation of Legume Defense Signaling Pathways by Native and Non-native Pea Aphid Clones. FRONTIERS IN PLANT SCIENCE 2016; 7:1872. [PMID: 28018405 PMCID: PMC5156717 DOI: 10.3389/fpls.2016.01872] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/28/2016] [Indexed: 05/25/2023]
Abstract
The pea aphid (Acyrthosiphon pisum) is a complex of at least 15 genetically different host races that are native to specific legume plants, but can all develop on the universal host plant Vicia faba. Despite much research, it is still unclear why pea aphid host races (biotypes) are able to colonize their native hosts while other host races are not. All aphids penetrate the plant and salivate into plant cells when they test plant suitability. Thus plants might react differently to the various pea aphid host races. To find out whether legume species vary in their defense responses to different pea aphid host races, we measured the amounts of salicylic acid (SA), the jasmonic acid-isoleucine conjugate (JA-Ile), other jasmonate precursors and derivatives, and abscisic acid (ABA) in four different species (Medicago sativa, Trifolium pratense, Pisum sativum, V. faba) after infestation by native and non-native pea aphid clones of various host races. Additionally, we assessed the performance of the clones on the four plant species. On M. sativa and T. pratense, non-native clones that were barely able to survive or reproduce, triggered a strong SA and JA-Ile response, whereas infestation with native clones led to lower levels of both phytohormones. On P. sativum, non-native clones, which survived or reproduced to a certain extent, induced fluctuating SA and JA-Ile levels, whereas the native clone triggered only a weak SA and JA-Ile response. On the universal host V. faba all aphid clones triggered only low SA levels initially, but induced clone-specific patterns of SA and JA-Ile later on. The levels of the active JA-Ile conjugate and of the other JA-pathway metabolites measured showed in many cases similar patterns, suggesting that the reduction in JA signaling was due to an effect upstream of OPDA. ABA levels were downregulated in all aphid clone-plant combinations and were therefore probably not decisive factors for aphid-plant compatibility. Our results suggest that A. pisum clones manipulate plant-defense signaling to their own advantage, and perform better on their native hosts due to their ability to modulate the SA- and JA-defense signaling pathways.
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Affiliation(s)
| | | | | | - Grit Kunert
- Department of Biochemistry, Max Planck Institute for Chemical EcologyJena, Germany
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29
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Eyres I, Duvaux L, Gharbi K, Tucker R, Hopkins D, Simon JC, Ferrari J, Smadja CM, Butlin RK. Targeted re-sequencing confirms the importance of chemosensory genes in aphid host race differentiation. Mol Ecol 2016; 26:43-58. [PMID: 27552184 PMCID: PMC6849616 DOI: 10.1111/mec.13818] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 01/01/2023]
Abstract
Host‐associated races of phytophagous insects provide a model for understanding how adaptation to a new environment can lead to reproductive isolation and speciation, ultimately enabling us to connect barriers to gene flow to adaptive causes of divergence. The pea aphid (Acyrthosiphon pisum) comprises host races specializing on legume species and provides a unique system for examining the early stages of diversification along a gradient of genetic and associated adaptive divergence. As host choice produces assortative mating, understanding the underlying mechanisms of choice will contribute directly to understanding of speciation. As host choice in the pea aphid is likely mediated by smell and taste, we use capture sequencing and SNP genotyping to test for the role of chemosensory genes in the divergence between eight host plant species across the continuum of differentiation and sampled at multiple locations across western Europe. We show high differentiation of chemosensory loci relative to control loci in a broad set of pea aphid races and localities, using a model‐free approach based on principal component analysis. Olfactory and gustatory receptors form the majority of highly differentiated genes and include loci that were already identified as outliers in a previous study focusing on the three most closely related host races. Consistent indications that chemosensory genes may be good candidates for local adaptation and barriers to gene flow in the pea aphid open the way to further investigations aiming to understand their impact on gene flow and to determine their precise functions in response to host plant metabolites.
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Affiliation(s)
- Isobel Eyres
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
| | - Ludovic Duvaux
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, EH9 3JT, Edinburgh, UK
| | - Rachel Tucker
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
| | - David Hopkins
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
| | - Jean-Christophe Simon
- Institut de Génétique, Environnement et Protection des Plantes, UMR 1349 IGEPP, Domaine de la Motte, INRA, 35653, Le Rheu Cedex, France
| | - Julia Ferrari
- Department of Biology, University of York, York YO10 5DD, UK
| | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554 CNRS-IRD-CIRAD-Université de Montpellier), Université de Montpellier, cc065, Place Bataillon, Campus Triolet, 34095, Montpellier Cedex 05, France
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
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30
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Eyres I, Jaquiéry J, Sugio A, Duvaux L, Gharbi K, Zhou JJ, Legeai F, Nelson M, Simon JC, Smadja CM, Butlin R, Ferrari J. Differential gene expression according to race and host plant in the pea aphid. Mol Ecol 2016; 25:4197-215. [PMID: 27474484 DOI: 10.1111/mec.13771] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 12/28/2022]
Abstract
Host-race formation in phytophagous insects is thought to provide the opportunity for local adaptation and subsequent ecological speciation. Studying gene expression differences amongst host races may help to identify phenotypes under (or resulting from) divergent selection and their genetic, molecular and physiological bases. The pea aphid (Acyrthosiphon pisum) comprises host races specializing on numerous plants in the Fabaceae and provides a unique system for examining the early stages of diversification along a gradient of genetic and associated adaptive divergence. In this study, we examine transcriptome-wide gene expression both in response to environment and across pea aphid races selected to cover the range of genetic divergence reported in this species complex. We identify changes in expression in response to host plant, indicating the importance of gene expression in aphid-plant interactions. Races can be distinguished on the basis of gene expression, and higher numbers of differentially expressed genes are apparent between more divergent races; these expression differences between host races may result from genetic drift and reproductive isolation and possibly divergent selection. Expression differences related to plant adaptation include a subset of chemosensory and salivary genes. Genes showing expression changes in response to host plant do not make up a large portion of between-race expression differences, providing confirmation of previous studies' findings that genes involved in expression differences between diverging populations or species are not necessarily those showing initial plasticity in the face of environmental change.
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Affiliation(s)
- Isobel Eyres
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
| | - Julie Jaquiéry
- CNRS UMR 6553 ECOBIO, Université de Rennes 1, Avenue du Général Leclerc, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Akiko Sugio
- INRA, Institut de Génétique, Environnement et Protection des Plantes, UMR 1349 IGEPP, Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Ludovic Duvaux
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Jing-Jiang Zhou
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Fabrice Legeai
- INRA, Institut de Génétique, Environnement et Protection des Plantes, UMR 1349 IGEPP, Domaine de la Motte, 35653, Le Rheu Cedex, France
| | | | - Jean-Christophe Simon
- INRA, Institut de Génétique, Environnement et Protection des Plantes, UMR 1349 IGEPP, Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554 CNRS-IRD-CIRAD-Université de Montpellier), Université Montpellier 2, cc065, Place Bataillon, 34095, Montpellier Cedex 05, France
| | - Roger Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
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31
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Gloss AD, Groen SC, Whiteman NK. A genomic perspective on the generation and maintenance of genetic diversity in herbivorous insects. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016; 47:165-187. [PMID: 28736510 DOI: 10.1146/annurev-ecolsys-121415-032220] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the processes that generate and maintain genetic variation within populations is a central goal in evolutionary biology. Theory predicts that some of this variation is maintained as a consequence of adapting to variable habitats. Studies in herbivorous insects have played a key role in confirming this prediction. Here, we highlight theoretical and conceptual models for the maintenance of genetic diversity in herbivorous insects, empirical genomic studies testing these models, and pressing questions within the realm of evolutionary and functional genomic studies. To address key gaps, we propose an integrative approach combining population genomic scans for adaptation, genome-wide characterization of targets of selection through experimental manipulations, mapping the genetic architecture of traits influencing fitness, and functional studies. We also stress the importance of studying the maintenance of genetic variation across biological scales-from variation within populations to divergence among populations-to form a comprehensive view of adaptation in herbivorous insects.
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Affiliation(s)
- Andrew D Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
| | - Simon C Groen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
| | - Noah K Whiteman
- Department of Integrative Biology, University of California-Berkeley, Berkeley, California
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Guy E, Boulain H, Aigu Y, Le Pennec C, Chawki K, Morlière S, Schädel K, Kunert G, Simon JC, Sugio A. Optimization of Agroinfiltration in Pisum sativum Provides a New Tool for Studying the Salivary Protein Functions in the Pea Aphid Complex. FRONTIERS IN PLANT SCIENCE 2016; 7:1171. [PMID: 27555856 PMCID: PMC4977312 DOI: 10.3389/fpls.2016.01171] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/20/2016] [Indexed: 05/06/2023]
Abstract
Aphids are piercing-sucking insect pests and feed on phloem sap. During feeding, aphids inject a battery of salivary proteins into host plant. Some of these proteins function like effectors of microbial pathogens and influence the outcome of plant-aphid interactions. The pea aphid (Acyrthosiphon pisum) is the model aphid and encompasses multiple biotypes each specialized to one or a few legume species, providing an opportunity to investigate the underlying mechanisms of the compatibility between plants and aphid biotypes. We aim to identify the aphid factors that determine the compatibility with host plants, hence involved in the host plant specialization process, and hypothesize that salivary proteins are one of those factors. Agrobacterium-mediated transient gene expression is a powerful tool to perform functional analyses of effector (salivary) proteins in plants. However, the tool was not established for the legume species that A. pisum feeds on. Thus, we decided to optimize the method for legume plants to facilitate the functional analyses of A. pisum salivary proteins. We screened a range of cultivars of pea (Pisum sativum) and alfalfa (Medicago sativa). None of the M. sativa cultivars was suitable for agroinfiltration under the tested conditions; however, we established a protocol for efficient transient gene expression in two cultivars of P. sativum, ZP1109 and ZP1130, using A. tumefaciens AGL-1 strain and the pEAQ-HT-DEST1 vector. We confirmed that the genes are expressed from 3 to 10 days post-infiltration and that aphid lines of the pea adapted biotype fed and reproduced on these two cultivars while lines of alfalfa and clover biotypes did not. Thus, the pea biotype recognizes these two cultivars as typical pea plants. By using a combination of ZP1109 and an A. pisum line, we defined an agroinfiltration procedure to examine the effect of in planta expression of selected salivary proteins on A. pisum fitness and demonstrated that transient expression of one candidate salivary gene increased the fecundity of the aphids. This result confirms that the agroinfiltration can be used to perform functional analyses of salivary proteins in P. sativum and consequently to study the molecular mechanisms underlying host specialization in the pea aphid complex.
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Affiliation(s)
- Endrick Guy
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Hélène Boulain
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Yoann Aigu
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Charlotte Le Pennec
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Khaoula Chawki
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Stéphanie Morlière
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Kristina Schädel
- Department of Biochemistry, Max Planck Institute for Chemical EcologyJena, Germany
| | - Grit Kunert
- Department of Biochemistry, Max Planck Institute for Chemical EcologyJena, Germany
| | - Jean-Christophe Simon
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Akiko Sugio
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
- *Correspondence: Akiko Sugio,
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van Bel AJE, Will T. Functional Evaluation of Proteins in Watery and Gel Saliva of Aphids. FRONTIERS IN PLANT SCIENCE 2016; 7:1840. [PMID: 28018380 PMCID: PMC5156713 DOI: 10.3389/fpls.2016.01840] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/22/2016] [Indexed: 05/20/2023]
Abstract
Gel and watery saliva are regarded as key players in aphid-pIant interactions. The salivary composition seems to be influenced by the variable environment encountered by the stylet tip. Milieu sensing has been postulated to provide information needed for proper stylet navigation and for the required switches between gel and watery saliva secretion during stylet progress. Both the chemical and physical factors involved in sensing of the stylet's environment are discussed. To investigate the salivary proteome, proteins were collected from dissected gland extracts or artificial diets in a range of studies. We discuss the advantages and disadvantages of either collection method. Several proteins were identified by functional assays or by use of proteomic tools, while most of their functions still remain unknown. These studies disclosed the presence of at least two proteins carrying numerous sulfhydryl groups that may act as the structural backbone of the salivary sheath. Furthermore, cell-wall degrading proteins such a pectinases, pectin methylesterases, polygalacturonases, and cellulases as well as diverse Ca2+-binding proteins (e.g., regucalcin, ARMET proteins) were detected. Suppression of the plant defense may be a common goal of salivary proteins. Salivary proteases are likely involved in the breakdown of sieve-element proteins to invalidate plant defense or to increase the availability of organic N compounds. Salivary polyphenoloxidases, peroxidases and oxidoreductases were suggested to detoxify, e.g., plant phenols. During the last years, an increasing number of salivary proteins have been categorized under the term 'effector'. Effectors may act in the suppression (C002 or MIF cytokine) or the induction (e.g., Mp10 or Mp 42) of plant defense, respectively. A remarkable component of watery saliva seems the protein GroEL that originates from Buchnera aphidicola, the obligate symbiont of aphids and probably reflects an excretory product that induces plant defense responses. Furthermore, chitin fragments in the saliva may trigger defense reactions (e.g., callose deposition). The functions of identified proteins and protein classes are discussed with regard to physical and chemical characteristics of apoplasmic and symplasmic plant compartments.
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Affiliation(s)
- Aart J. E. van Bel
- Institute of General Botany, Justus-Liebig-UniversityGiessen, Germany
- *Correspondence: Aart J. E. van Bel,
| | - Torsten Will
- Institute of Phytopathology, Justus-Liebig-UniversityGiessen, Germany
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius-Kühn InstituteQuedlinburg, Germany
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Haasl RJ, Payseur BA. Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication. Mol Ecol 2015. [PMID: 26224644 DOI: 10.1111/mec.13339] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genomewide scans for natural selection (GWSS) have become increasingly common over the last 15 years due to increased availability of genome-scale genetic data. Here, we report a representative survey of GWSS from 1999 to present and find that (i) between 1999 and 2009, 35 of 49 (71%) GWSS focused on human, while from 2010 to present, only 38 of 83 (46%) of GWSS focused on human, indicating increased focus on nonmodel organisms; (ii) the large majority of GWSS incorporate interpopulation or interspecific comparisons using, for example F(ST), cross-population extended haplotype homozygosity or the ratio of nonsynonymous to synonymous substitutions; (iii) most GWSS focus on detection of directional selection rather than other modes such as balancing selection; and (iv) in human GWSS, there is a clear shift after 2004 from microsatellite markers to dense SNP data. A survey of GWSS meant to identify loci positively selected in response to severe hypoxic conditions support an approach to GWSS in which a list of a priori candidate genes based on potential selective pressures are used to filter the list of significant hits a posteriori. We also discuss four frequently ignored determinants of genomic heterogeneity that complicate GWSS: mutation, recombination, selection and the genetic architecture of adaptive traits. We recommend that GWSS methodology should better incorporate aspects of genomewide heterogeneity using empirical estimates of relevant parameters and/or realistic, whole-chromosome simulations to improve interpretation of GWSS results. Finally, we argue that knowledge of potential selective agents improves interpretation of GWSS results and that new methods focused on correlations between environmental variables and genetic variation can help automate this approach.
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Affiliation(s)
- Ryan J Haasl
- Department of Biology, University of Wisconsin-Platteville, 1 University Plaza, Platteville, WI, 53818, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA
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Feng B, Lin X, Zheng K, Qian K, Chang Y, Du Y. Transcriptome and expression profiling analysis link patterns of gene expression to antennal responses in Spodoptera litura. BMC Genomics 2015; 16:269. [PMID: 25887537 PMCID: PMC4502548 DOI: 10.1186/s12864-015-1375-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/21/2015] [Indexed: 11/30/2022] Open
Abstract
Background The study of olfaction is key to understanding the interaction of
insects with their environment and provides opportunities to develop novel
tactics for control of pest species. Recent developments in transcriptomic
approaches enable the molecular basis of olfaction to be studied even in species
with limited genomic information. Here we use transcriptome and expression
profiling analysis to characterize the antennal transcriptome of the noctuid
moth and polyphagous pest Spodoptera
litura. Results We identify 74 candidate genes involved in odor detection and
recognition, encoding 26 ORs, 21 OBPs, 18 CSPs and 9 IRs. We examine their
expression levels in both sexes and seek evidence for their function by relating
their expression with levels of EAG response in male and female antennae to 58
host and non-host plant volatiles and sex pheromone components. The majority of
olfactory genes showed sex-biased expression, usually male-biased in ORs. A link
between OR gene expression and antennal responses to odors was evident, a third
of the compounds tested evoking a sex-biased response, in every case also
male-biased. Two candidate pheromone receptors, OR14 and OR23 were especially
strongly expressed and male-biased and we suggest that these may respond to the
two female sex pheromone components of S.
litura, Z9E11-14:OAc and Z9E12-14:OAc, which evoked strongly
male-biased EAG responses. Conclusions Our results provide the molecular basis for elucidating the
olfactory profile of moths and the sexual divergence of their behavior and could
enable the targeting of particular genes, and behaviors for pest
management. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1375-x) contains supplementary material, which is available to authorized
users.
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Affiliation(s)
- Bo Feng
- Institute of Health and Environmental Ecology, Wenzhou Medical University, University Town, Wenzhou, 325035, China.
| | - Xinda Lin
- College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, 310018, China.
| | - Kaidi Zheng
- Institute of Health and Environmental Ecology, Wenzhou Medical University, University Town, Wenzhou, 325035, China.
| | - Kai Qian
- Institute of Health and Environmental Ecology, Wenzhou Medical University, University Town, Wenzhou, 325035, China.
| | - Yongchang Chang
- Division of Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, AZ, 85013, USA.
| | - Yongjun Du
- Institute of Health and Environmental Ecology, Wenzhou Medical University, University Town, Wenzhou, 325035, China.
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Simon JC, d'Alencon E, Guy E, Jacquin-Joly E, Jaquiery J, Nouhaud P, Peccoud J, Sugio A, Streiff R. Genomics of adaptation to host-plants in herbivorous insects. Brief Funct Genomics 2015; 14:413-23. [DOI: 10.1093/bfgp/elv015] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Gauthier JP, Outreman Y, Mieuzet L, Simon JC. Bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16S ribosomal DNA. PLoS One 2015; 10:e0120664. [PMID: 25807173 PMCID: PMC4373712 DOI: 10.1371/journal.pone.0120664] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/05/2015] [Indexed: 02/01/2023] Open
Abstract
Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was underestimated due to the possible loss of environmental or transient taxa.
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Affiliation(s)
- Jean-Pierre Gauthier
- INRA, UMR 1349 IGEPP "Institut de Génétique, Environnement et Protection des Plantes", 35653, Le Rheu, France
| | - Yannick Outreman
- Agrocampus Ouest, UMR 1349 IGEPP "Institut de Génétique, Environnement et Protection des Plantes", 35042, Rennes, France
| | - Lucie Mieuzet
- INRA, UMR 1349 IGEPP "Institut de Génétique, Environnement et Protection des Plantes", 35653, Le Rheu, France
| | - Jean-Christophe Simon
- Agrocampus Ouest, UMR 1349 IGEPP "Institut de Génétique, Environnement et Protection des Plantes", 35042, Rennes, France
- * E-mail:
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38
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Bruce TJA. Interplay between insects and plants: dynamic and complex interactions that have coevolved over millions of years but act in milliseconds. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:455-65. [PMID: 25271259 DOI: 10.1093/jxb/eru391] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In an environment with changing availability and quality of host plants, phytophagous insects are under selection pressure to find quality hosts. They need to maximize their fitness by locating suitable plants and avoiding unsuitable ones. Thus, they have evolved a finely tuned sensory system, for detection of host cues, and a nervous system, capable of integrating inputs from sensory neurons with a high level of spatio-temporal resolution. Insect responses to cues are not fixed but depend on the context in which they are perceived, the physiological state of the insect, and prior learning experiences. However, there are examples of insects making 'mistakes' and being attracted to poor quality hosts. While insects have evolved ways of finding hosts, plants have been under selection pressure to do precisely the opposite and evade detection or defend themselves when attacked. Once on the plant, insect-associated molecules may trigger or suppress defence depending on whether the plant or the insect is ahead in evolutionary terms. Plant volatile emission is influenced by defence responses induced by insect feeding or oviposition which can attract natural enemies but repel herbivores. Conversely, plant reproductive fitness is increased by attraction of pollinators. Interactions can be altered by other organisms associated with the plant such as other insects, plant pathogens, or mycorrhizal fungi. Plant phenotype is plastic and can be changed by epigenetic factors in adaptation to periods of biotic stress. Space and time play crucial roles in influencing the outcome of interactions between insects and plants.
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Molecular Adaptations of Aphid Biotypes in Overcoming Host-Plant Resistance. SHORT VIEWS ON INSECT GENOMICS AND PROTEOMICS 2015. [DOI: 10.1007/978-3-319-24235-4_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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40
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Jaquiéry J, Stoeckel S, Larose C, Nouhaud P, Rispe C, Mieuzet L, Bonhomme J, Mahéo F, Legeai F, Gauthier JP, Prunier-Leterme N, Tagu D, Simon JC. Genetic control of contagious asexuality in the pea aphid. PLoS Genet 2014; 10:e1004838. [PMID: 25473828 PMCID: PMC4256089 DOI: 10.1371/journal.pgen.1004838] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 10/17/2014] [Indexed: 11/18/2022] Open
Abstract
Although evolutionary transitions from sexual to asexual reproduction are frequent in eukaryotes, the genetic bases of such shifts toward asexuality remain largely unknown. We addressed this issue in an aphid species where both sexual and obligate asexual lineages coexist in natural populations. These sexual and asexual lineages may occasionally interbreed because some asexual lineages maintain a residual production of males potentially able to mate with the females produced by sexual lineages. Hence, this species is an ideal model to study the genetic basis of the loss of sexual reproduction with quantitative genetic and population genomic approaches. Our analysis of the co-segregation of ∼ 300 molecular markers and reproductive phenotype in experimental crosses pinpointed an X-linked region controlling obligate asexuality, this state of character being recessive. A population genetic analysis (>400-marker genome scan) on wild sexual and asexual genotypes from geographically distant populations under divergent selection for reproductive strategies detected a strong signature of divergent selection in the genomic region identified by the experimental crosses. These population genetic data confirm the implication of the candidate region in the control of reproductive mode in wild populations originating from 700 km apart. Patterns of genetic differentiation along chromosomes suggest bidirectional gene flow between populations with distinct reproductive modes, supporting contagious asexuality as a prevailing route to permanent parthenogenesis in pea aphids. This genetic system provides new insights into the mechanisms of coexistence of sexual and asexual aphid lineages.
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Affiliation(s)
- Julie Jaquiéry
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France
| | - Solenn Stoeckel
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France
| | - Chloé Larose
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France
| | - Pierre Nouhaud
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France
| | - Claude Rispe
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France
| | - Lucie Mieuzet
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France
| | - Joël Bonhomme
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France
| | - Frédérique Mahéo
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France
| | - Fabrice Legeai
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France
- INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Campus de Beaulieu, Rennes, France
| | - Jean-Pierre Gauthier
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France
| | - Nathalie Prunier-Leterme
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France
| | - Denis Tagu
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France
| | - Jean-Christophe Simon
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France
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41
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Peccoud J, de la Huerta M, Bonhomme J, Laurence C, Outreman Y, Smadja CM, Simon JC. Widespread host-dependent hybrid unfitness in the pea aphid species complex. Evolution 2014; 68:2983-95. [PMID: 24957707 DOI: 10.1111/evo.12478] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/06/2014] [Indexed: 02/02/2023]
Abstract
Linking adaptive divergence to hybrid unfitness is necessary to understand the ecological factors contributing to reproductive isolation and speciation. To date, this link has been demonstrated in few model systems, most of which encompass ecotypes that occupy relatively early stages in the speciation process. Here we extend these studies by assessing how host-plant adaptation conditions hybrid fitness in the pea aphid, Acyrthosiphon pisum. We made crosses between and within five pea aphid biotypes adapted to different host plants and representing various stages of divergence within the complex. Performance of F1 hybrids and nonhybrids was assessed on a "universal" host that is favorable to all pea aphid biotypes in laboratory conditions. Although hybrids performed equally well as nonhybrids on the universal host, their performance was much lower than nonhybrids on the natural hosts of their parental populations. Hence, hybrids, rather than being intrinsically deficient, are maladapted to their parents' hosts. Interestingly, the impact of this maladaptation was stronger in certain hybrids from crosses involving the most divergent biotype, suggesting that host-dependent postzygotic isolation has continued to evolve late in divergence. Even though host-independent deficiencies are not excluded, hybrid maladaptation to parental hosts supports the hypothesis of ecological speciation in this complex.
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Affiliation(s)
- Jean Peccoud
- Institut National de la Recherche Agronomique INRA, Institut de Génétique, Environnement et Protection des Plantes (UMR 1349 IGEPP), Domaine de La Motte, BP, 35327, 35653 le Rheu Cedex, France
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Duvaux L, Geissmann Q, Gharbi K, Zhou JJ, Ferrari J, Smadja CM, Butlin RK. Dynamics of copy number variation in host races of the pea aphid. Mol Biol Evol 2014; 32:63-80. [PMID: 25234705 PMCID: PMC4271520 DOI: 10.1093/molbev/msu266] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Copy number variation (CNV) makes a major contribution to overall genetic variation and is suspected to play an important role in adaptation. However, aside from a few model species, the extent of CNV in natural populations has seldom been investigated. Here, we report on CNV in the pea aphid Acyrthosiphon pisum, a powerful system for studying the genetic architecture of host-plant adaptation and speciation thanks to multiple host races forming a continuum of genetic divergence. Recent studies have highlighted the potential importance of chemosensory genes, including the gustatory and olfactory receptor gene families (Gr and Or, respectively), in the process of host race formation. We used targeted resequencing to achieve a very high depth of coverage, and thereby revealed the extent of CNV of 434 genes, including 150 chemosensory genes, in 104 individuals distributed across eight host races of the pea aphid. We found that CNV was widespread in our global sample, with a significantly higher occurrence in multigene families, especially in Ors. We also observed a decrease in the gene probability of being completely duplicated or deleted (CDD) with increase in coding sequence length. Genes with CDD variants were usually more polymorphic for copy number, especially in the P450 gene family where toxin resistance may be related to gene dosage. We found that Gr were overrepresented among genes discriminating host races, as were CDD genes and pseudogenes. Our observations shed new light on CNV dynamics and are consistent with CNV playing a role in both local adaptation and speciation.
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Affiliation(s)
- Ludovic Duvaux
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Quentin Geissmann
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | - Jing-Jiang Zhou
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Julia Ferrari
- Department of Biology, University of York, York, United Kingdom
| | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554), CNRS, IRD, Université Montpellier 2, Montpellier, France
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom Sven Lovén Centre for Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
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43
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Harrison RG, Larson EL. Hybridization, Introgression, and the Nature of Species Boundaries. J Hered 2014; 105 Suppl 1:795-809. [DOI: 10.1093/jhered/esu033] [Citation(s) in RCA: 418] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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44
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Demaeght P, Osborne EJ, Odman-Naresh J, Grbić M, Nauen R, Merzendorfer H, Clark RM, Van Leeuwen T. High resolution genetic mapping uncovers chitin synthase-1 as the target-site of the structurally diverse mite growth inhibitors clofentezine, hexythiazox and etoxazole in Tetranychus urticae. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 51:52-61. [PMID: 24859419 PMCID: PMC4124130 DOI: 10.1016/j.ibmb.2014.05.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/09/2014] [Accepted: 05/10/2014] [Indexed: 05/09/2023]
Abstract
The acaricides clofentezine, hexythiazox and etoxazole are commonly referred to as 'mite growth inhibitors', and clofentezine and hexythiazox have been used successfully for the integrated control of plant mite pests for decades. Although they are still important today, their mode of action has remained elusive. Recently, a mutation in chitin synthase 1 (CHS1) was linked to etoxazole resistance. In this study, we identified and investigated a Tetranychus urticae strain (HexR) harboring recessive, monogenic resistance to each of hexythiazox, clofentezine, and etoxazole. To elucidate if there is a common genetic basis for the observed cross-resistance, we adapted a previously developed bulk segregant analysis method to map with high resolution a single, shared resistance locus for all three compounds. This finding indicates that the underlying molecular basis for resistance to all three compounds is identical. This locus is centered on the CHS1 gene, and as supported by additional genetic and biochemical studies, a non-synonymous variant (I1017F) in CHS1 associates with resistance to each of the tested acaricides in HexR. Our findings thus demonstrate a shared molecular mode of action for the chemically diverse mite growth inhibitors clofentezine, hexythiazox and etoxazole as inhibitors of an essential, non-catalytic activity of CHS1. Given the previously documented cross-resistance between clofentezine, hexythiazox and the benzyolphenylurea (BPU) compounds flufenoxuron and cycloxuron, CHS1 should be also considered as a potential target-site of insecticidal BPUs.
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Affiliation(s)
- Peter Demaeght
- Department of Crop Protection, Faculty of Bioscience Engineering, Coupure Links 653, Ghent University, B-9000 Ghent, Belgium
| | - Edward J Osborne
- Department of Biology, University of Utah, Salt Lake City, 257 South 1400 East, Utah 84112, USA
| | - Jothini Odman-Naresh
- Department of Biology/Chemistry, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Miodrag Grbić
- Department of Biology, The University of Western Ontario, 1151 Richmond St., London N6A 5B7, Canada; Instituto de Ciencias de la Vid y el Vino, 26006 Logroño, Spain
| | - Ralf Nauen
- R&D, Pest Control Biology, Bayer CropScience, Alfred Nobel Str. 50, D-40789 Monheim, Germany
| | - Hans Merzendorfer
- Department of Biology/Chemistry, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Richard M Clark
- Department of Biology, University of Utah, Salt Lake City, 257 South 1400 East, Utah 84112, USA; Center for Cell and Genome Science, University of Utah, Salt Lake City, 257 South 1400 East, Utah 84112, USA
| | - Thomas Van Leeuwen
- Department of Crop Protection, Faculty of Bioscience Engineering, Coupure Links 653, Ghent University, B-9000 Ghent, Belgium; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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Nouhaud P, Peccoud J, Mahéo F, Mieuzet L, Jaquiéry J, Simon JC. Genomic regions repeatedly involved in divergence among plant-specialized pea aphid biotypes. J Evol Biol 2014; 27:2013-20. [PMID: 24953130 DOI: 10.1111/jeb.12441] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 04/10/2014] [Accepted: 05/19/2014] [Indexed: 01/28/2023]
Abstract
Understanding the genetic bases of biological diversification is a long-standing goal in evolutionary biology. Here, we investigate whether replicated cases of adaptive divergence involve the same genomic regions in the pea aphid, Acyrthosiphon pisum, a large complex of genetically differentiated biotypes, each specialized on different species of legumes. A previous study identified genomic regions putatively involved in host-plant adaptation and/or reproductive isolation by performing a hierarchical genome scan in three biotypes. This led to the identification of 11 F(ST) outliers among 390 polymorphic microsatellite markers. In this study, the outlier status of these 11 loci was assessed in eight biotypes specialized on other host plants. Four of the 11 previously identified outliers showed greater genetic differentiation among these additional biotypes than expected under the null hypothesis of neutral evolution (α < 0.01). Whether these hotspots of genomic divergence result from adaptive events, intrinsic barriers or reduced recombination is discussed.
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Affiliation(s)
- P Nouhaud
- INRA, UMR 1349 IGEPP, Le Rheu, France
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Proestou DA, Flight P, Champlin D, Nacci D. Targeted approach to identify genetic loci associated with evolved dioxin tolerance in Atlantic killifish (Fundulus heteroclitus). BMC Evol Biol 2014; 14:7. [PMID: 24422627 PMCID: PMC4029433 DOI: 10.1186/1471-2148-14-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 12/30/2013] [Indexed: 11/10/2022] Open
Abstract
Background The most toxic aromatic hydrocarbon pollutants are categorized as dioxin-like compounds (DLCs) to which extreme tolerance has evolved independently and contemporaneously in (at least) four populations of Atlantic killifish (Fundulus heteroclitus). Surprisingly, the magnitude and phenotype of DLC tolerance is similar among these killifish populations that have adapted to varied, but highly aromatic hydrocarbon-contaminated urban/industrialized estuaries of the US Atlantic coast. Multiple tolerant and neighboring sensitive killifish populations were compared with the expectation that genetic loci associated with DLC tolerance would be revealed. Results Since the aryl hydrocarbon receptor (AHR) pathway partly or fully mediates DLC toxicity in vertebrates, single nucleotide polymorphisms (SNPs) from 42 genes associated with the AHR pathway were identified to serve as targeted markers. Wild fish (N = 36/37) from four highly tolerant killifish populations and four nearby sensitive populations were genotyped using 59 SNP markers. Similar to other killifish population genetic analyses, strong genetic differentiation among populations was detected, consistent with isolation by distance models. When DLC-sensitive populations were pooled and compared to pooled DLC-tolerant populations, multi-locus analyses did not distinguish the two groups. However, pairwise comparisons of nearby tolerant and sensitive populations revealed high differentiation among sensitive and tolerant populations at these specific loci: AHR 1 and 2, cathepsin Z, the cytochrome P450s (CYP1A and 3A30), and the NADH dehydrogenase subunits. In addition, significant shifts in minor allele frequency were observed at AHR2 and CYP1A loci across most sensitive/tolerant pairs, but only AHR2 exhibited shifts in the same direction across all pairs. Conclusions The observed differences in allelic composition at the AHR2 and CYP1A SNP loci were identified as significant among paired sensitive/tolerant populations of Atlantic killifish with multiple statistical tests. The genetic patterns reported here lend support to the argument that AHR2 and CYP1A play a role in the adaptive response to extreme DLC contamination. Additional functional assays are required to isolate the exact mechanism of DLC tolerance.
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Affiliation(s)
- Dina A Proestou
- US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, 27 Tarzwell Drive, Narragansett, RI 02882, USA.
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Feder JL, Flaxman SM, Egan SP, Comeault AA, Nosil P. Geographic Mode of Speciation and Genomic Divergence. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135825] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jeffrey L. Feder
- Department of Biological Sciences,
- Environmental Change Initiative, and
- Advanced Diagnostics and Therapeutics, University of Notre Dame, Notre Dame, Indiana 46556; ,
| | - Samuel M. Flaxman
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309;
| | - Scott P. Egan
- Department of Biological Sciences,
- Advanced Diagnostics and Therapeutics, University of Notre Dame, Notre Dame, Indiana 46556; ,
| | - Aaron A. Comeault
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S102TN, United Kingdom; ,
| | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S102TN, United Kingdom; ,
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Mullen SP, Shaw KL. Insect speciation rules: unifying concepts in speciation research. ANNUAL REVIEW OF ENTOMOLOGY 2013; 59:339-361. [PMID: 24160421 DOI: 10.1146/annurev-ento-120710-100621] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The study of speciation is concerned with understanding the connection between causes of divergent evolution and the origin and maintenance of barriers to gene exchange between incipient species. Although the field has historically focused either on examples of recent divergence and its causes or on the genetic basis of reproductive isolation between already divergent species, current efforts seek to unify these two approaches. Here we integrate these perspectives through a discussion of recent progress in several insect speciation model systems. We focus on the evolution of speciation phenotypes in each system (i.e., those phenotypes causally involved in reducing gene flow between incipient species), drawing an explicit connection between cause and effect (process and pattern). We emphasize emerging insights into the genomic architecture of speciation as well as timely areas for future research.
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Affiliation(s)
- Sean P Mullen
- Department of Biology, Boston University, Boston, Massachusetts 02215;
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Is ecological speciation a major trend in aphids? Insights from a molecular phylogeny of the conifer-feeding genus Cinara. Front Zool 2013; 10:56. [PMID: 24044736 PMCID: PMC3848992 DOI: 10.1186/1742-9994-10-56] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 09/13/2013] [Indexed: 12/13/2022] Open
Abstract
Introduction In the past decade ecological speciation has been recognized as having an important role in the diversification of plant-feeding insects. Aphids are host-specialised phytophagous insects that mate on their host plants and, as such, they are prone to experience reproductive isolation linked with host plant association that could ultimately lead to species formation. The generality of such a scenario remains to be tested through macroevolutionary studies. To explore the prevalence of host-driven speciation in the diversification of the aphid genus Cinara and to investigate alternative modes of speciation, we reconstructed a phylogeny of this genus based on mitochondrial, nuclear and Buchnera aphidicola DNA sequence fragments and applied a DNA-based method of species delimitation. Using a recent software (PhyloType), we explored evolutionary transitions in host-plant genera, feeding sites and geographic distributions in the diversification of Cinara and investigated how transitions in these characters have accompanied speciation events. Results The diversification of Cinara has been constrained by host fidelity to conifer genera sometimes followed by sequential colonization onto different host species and by feeding-site specialisation. Nevertheless, our analyses suggest that, at the most, only half of the speciation events were accompanied by ecological niche shifts. The contribution of geographical isolation in the speciation process is clearly apparent in the occurrence of species from two continents in the same clades in relatively terminal positions in our phylogeny. Furthermore, in agreement with predictions from scenarios in which geographic isolation accounts for speciation events, geographic overlap between species increased significantly with time elapsed since their separation. Conclusions The history of Cinara offers a different perspective on the mode of speciation of aphids than that provided by classic models such as the pea aphid. In this genus of aphids, the role of climate and landscape history has probably been as important as host-plant specialisation in having shaped present-day diversity.
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50
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Hansen AK, Moran NA. The impact of microbial symbionts on host plant utilization by herbivorous insects. Mol Ecol 2013; 23:1473-1496. [PMID: 23952067 DOI: 10.1111/mec.12421] [Citation(s) in RCA: 281] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/02/2013] [Accepted: 06/12/2013] [Indexed: 01/18/2023]
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