1
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Hill R, McMullan M. Recombination triggers fungal crop disease. Nat Ecol Evol 2023; 7:1961-1962. [PMID: 37945943 DOI: 10.1038/s41559-023-02132-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
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2
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Rahnama M, Condon B, Ascari JP, Dupuis JR, Del Ponte EM, Pedley KF, Martinez S, Valent B, Farman ML. Recent co-evolution of two pandemic plant diseases in a multi-hybrid swarm. Nat Ecol Evol 2023; 7:2055-2066. [PMID: 37945944 PMCID: PMC10697843 DOI: 10.1038/s41559-023-02237-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 09/28/2023] [Indexed: 11/12/2023]
Abstract
Most plant pathogens exhibit host specificity but when former barriers to infection break down, new diseases can rapidly emerge. For a number of fungal diseases, there is increasing evidence that hybridization plays a major role in driving host jumps. However, the relative contributions of existing variation versus new mutations in adapting to new host(s) is unclear. Here we reconstruct the evolutionary history of two recently emerged populations of the fungus Pyricularia oryzae that are responsible for two new plant diseases: wheat blast and grey leaf spot of ryegrasses. We provide evidence that wheat blast/grey leaf spot evolved through two distinct mating episodes: the first occurred ~60 years ago, when a fungal individual adapted to Eleusine mated with another individual from Urochloa. Then, about 10 years later, a single progeny from this cross underwent a series of matings with a small number of individuals from three additional host-specialized populations. These matings introduced non-functional alleles of two key host-specificity factors, whose recombination in a multi-hybrid swarm probably facilitated the host jump. We show that very few mutations have arisen since the founding event and a majority are private to individual isolates. Thus, adaptation to the wheat or Lolium hosts appears to have been instantaneous, and driven entirely by selection on repartitioned standing variation, with no obvious role for newly formed mutations.
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Affiliation(s)
- Mostafa Rahnama
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
- Department of Biology, Tennesse Tech University, Cookeville, TN, USA
| | - Bradford Condon
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| | - João P Ascari
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - Julian R Dupuis
- Department of Entomology S-225 Agricultural Science Center, University of Kentucky, Lexington, KY, USA
| | - Emerson M Del Ponte
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - Kerry F Pedley
- USDA/ARS/Foreign Disease Weed Science Research Unit, Fort Detrick, Frederick, MD, USA
| | - Sebastián Martinez
- Laboratorio de Patología Vegetal, Instituto Nacional de Investigación Agropecuaria, Treinta y Tres, Uruguay
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Mark L Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA.
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3
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Gu B, Parkes T, Rabanal F, Smith C, Lu FH, McKenzie N, Dong H, Weigel D, Jones JDG, Cevik V, Bevan MW. The integrated LIM-peptidase domain of the CSA1-CHS3/DAR4 paired immune receptor detects changes in DA1 peptidase inhibitors in Arabidopsis. Cell Host Microbe 2023; 31:949-961.e5. [PMID: 37167970 DOI: 10.1016/j.chom.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 03/09/2023] [Accepted: 04/06/2023] [Indexed: 05/13/2023]
Abstract
White blister rust, caused by the oomycete Albugo candida, is a widespread disease of Brassica crops. The Brassica relative Arabidopsis thaliana uses the paired immune receptor complex CSA1-CHS3/DAR4 to resist Albugo infection. The CHS3/DAR4 sensor NLR, which functions together with its partner, the helper NLR CSA1, carries an integrated domain (ID) with homology to DA1 peptidases. Using domain swaps with several DA1 homologs, we show that the LIM-peptidase domain of the family member CHS3/DAR4 functions as an integrated decoy for the family member DAR3, which interacts with and inhibits the peptidase activities of the three closely related peptidases DA1, DAR1, and DAR2. Albugo infection rapidly lowers DAR3 levels and activates DA1 peptidase activity, thereby promoting endoreduplication of host tissues to support pathogen growth. We propose that the paired immune receptor CSA1-CHS3/DAR4 detects the actions of a putative Albugo effector that reduces DAR3 levels, resulting in defense activation.
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Affiliation(s)
- Benguo Gu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Toby Parkes
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Fernando Rabanal
- Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Caroline Smith
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Fu-Hao Lu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Neil McKenzie
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hui Dong
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Detlef Weigel
- Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.
| | - Volkan Cevik
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath BA2 7AY, UK.
| | - Michael W Bevan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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4
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Rai P, Prasad L, Rai PK. Fungal effectors versus defense-related genes of B. juncea and the status of resistant transgenics against fungal pathogens. FRONTIERS IN PLANT SCIENCE 2023; 14:1139009. [PMID: 37360735 PMCID: PMC10285668 DOI: 10.3389/fpls.2023.1139009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 05/09/2023] [Indexed: 06/28/2023]
Abstract
Oilseed brassica has become instrumental in securing global food and nutritional security. B. juncea, colloquially known as Indian mustard, is cultivated across tropics and subtropics including Indian subcontinent. The production of Indian mustard is severely hampered by fungal pathogens which necessitates human interventions. Chemicals are often resorted to as they are quick and effective, but due to their economic and ecological unsustainability, there is a need to explore their alternatives. The B. juncea-fungal pathosystem is quite diverse as it covers broad-host range necrotrophs (Sclerotinia sclerotiorum), narrow-host range necrotrophs (Alternaria brassicae and A. brassicicola) and biotrophic oomycetes (Albugo candida and Hyaloperonospora brassica). Plants ward off fungal pathogens through two-step resistance mechanism; PTI which involves recognition of elicitors and ETI where the resistance gene (R gene) interacts with the fungal effectors. The hormonal signalling is also found to play a vital role in defense as the JA/ET pathway is initiated at the time of necrotroph infection and SA pathway is induced when the biotrophs attack plants. The review discuss the prevalence of fungal pathogens of Indian mustard and the studies conducted on effectoromics. It covers both pathogenicity conferring genes and host-specific toxins (HSTs) that can be used for a variety of purposes such as identifying cognate R genes, understanding pathogenicity and virulence mechanisms, and establishing the phylogeny of fungal pathogens. It further encompasses the studies on identifying resistant sources and characterisation of R genes/quantitative trait loci and defense-related genes identified in Brassicaceae and unrelated species which, upon introgression or overexpression, confer resistance. Finally, the studies conducted on developing resistant transgenics in Brassicaceae have been covered in which chitinase and glucanase genes are mostly used. The knowledge gained from this review can further be used for imparting resistance against major fungal pathogens.
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Affiliation(s)
- Prajjwal Rai
- Division of Plant Pathology, Indian Agriculture Research Institute, New Delhi, India
| | - Laxman Prasad
- Division of Plant Pathology, Indian Agriculture Research Institute, New Delhi, India
| | - Pramod Kumar Rai
- Division of Plant Pathology, Directorate of Rapeseed-Mustard Research, Bharatpur, India
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5
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Breen S, McLellan H, Birch PRJ, Gilroy EM. Tuning the Wavelength: Manipulation of Light Signaling to Control Plant Defense. Int J Mol Sci 2023; 24:ijms24043803. [PMID: 36835216 PMCID: PMC9958957 DOI: 10.3390/ijms24043803] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
The growth-defense trade-off in plants is a phenomenon whereby plants must balance the allocation of their resources between developmental growth and defense against attack by pests and pathogens. Consequently, there are a series of points where growth signaling can negatively regulate defenses and where defense signaling can inhibit growth. Light perception by various photoreceptors has a major role in the control of growth and thus many points where it can influence defense. Plant pathogens secrete effector proteins to manipulate defense signaling in their hosts. Evidence is emerging that some of these effectors target light signaling pathways. Several effectors from different kingdoms of life have converged on key chloroplast processes to take advantage of regulatory crosstalk. Moreover, plant pathogens also perceive and react to light in complex ways to regulate their own growth, development, and virulence. Recent work has shown that varying light wavelengths may provide a novel way of controlling or preventing disease outbreaks in plants.
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Affiliation(s)
- Susan Breen
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK
| | - Hazel McLellan
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK
| | - Paul R. J. Birch
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK
| | - Eleanor M. Gilroy
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK
- Correspondence: ; Tel.: +44-1382568827
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6
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Redkar A, Cevik V, Bailey K, Zhao H, Kim DS, Zou Z, Furzer OJ, Fairhead S, Borhan MH, Holub EB, Jones JDG. The Arabidopsis WRR4A and WRR4B paralogous NLR proteins both confer recognition of multiple Albugo candida effectors. THE NEW PHYTOLOGIST 2023; 237:532-547. [PMID: 35838065 PMCID: PMC10087428 DOI: 10.1111/nph.18378] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/05/2022] [Indexed: 05/26/2023]
Abstract
The oomycete Albugo candida causes white blister rust, an important disease of Brassica crops. Distinct races of A. candida are defined by their capacity to infect different host plant species. Each A. candida race encodes secreted proteins with a CX2 CX5 G ('CCG') motif that are polymorphic and show presence/absence variation, and are therefore candidate effectors. The White Rust Resistance 4 (WRR4) locus in Arabidopsis thaliana accession Col-0 contains three genes that encode intracellular nucleotide-binding domain leucine-rich repeat immune receptors. The Col-0 alleles of WRR4A and WRR4B confer resistance to multiple A. candida races, although both WRR4A and WRR4B can be overcome by the Col-0-virulent race 4 isolate AcEx1. Comparison of CCG candidate effectors in avirulent and virulent races, and transient co-expression of CCG effectors from four A. candida races in Nicotiana sp. or A. thaliana, revealed CCG effectors that trigger WRR4A- or WRR4B-dependent hypersensitive responses. We found eight WRR4A-recognised CCGs and four WRR4B-recognised CCGs, the first recognised proteins from A. candida for which the cognate immune receptors in A. thaliana are known. This multiple recognition capacity potentially explains the broad-spectrum resistance to several A. candida races conferred by WRR4 paralogues. We further show that of five tested CCGs, three confer enhanced disease susceptibility when expressed in planta, consistent with A. candida CCG proteins being effectors.
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Affiliation(s)
- Amey Redkar
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- Department of BotanySavitribai Phule Pune UniversityGaneshkhindPune411007India
| | - Volkan Cevik
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- The Milner Centre for Evolution, Department of Biology and BiochemistryUniversity of BathBathBA2 7AYUK
| | - Kate Bailey
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
| | - He Zhao
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
| | - Dae Sung Kim
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- Present address:
State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei UniversityWuhan430062China
| | - Zhou Zou
- The Milner Centre for Evolution, Department of Biology and BiochemistryUniversity of BathBathBA2 7AYUK
| | - Oliver J. Furzer
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- Department of BiologyUniversity of North CarolinaChapel HillNC27599USA
| | - Sebastian Fairhead
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- School of Life SciencesWarwick Crop Centre, University of WarwickWellesbourneCV35 9EFUK
| | - M. Hossein Borhan
- Agriculture and Agri‐Food Canada107 Science PlaceSaskatoonSKS7N 0X2Canada
| | - Eric B. Holub
- School of Life SciencesWarwick Crop Centre, University of WarwickWellesbourneCV35 9EFUK
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7
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Chatterjee A, Nirwan S, Mohapatra S, Sharma P, Agnihotri A, Shrivastava N. Biochemical aspects of pathogenic variability in white rust infected Indian mustard. Mycologia 2022; 114:757-768. [PMID: 35648633 DOI: 10.1080/00275514.2022.2060007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
White rust caused by Albugo candida, an oomycete pathogen, is a devastating disease of Brassica juncea (Indian mustard) worldwide. There is a need to screen virulent white rust isolates to challenge the developed white rust-resistant B. juncea cultivars to screen their resistance potential. The current study explores pathogenic and biochemical response of Indian mustard to white rust isolates collected from three different geographic locations of India. The observations refine our understanding of the disease severity in India. Disease progression and biochemical responses were studied in the cotyledonary as well as true leaf stage of the B. juncea cultivar Varuna at different time points. The biochemical findings highlight the fluctuation of significant biochemical parameters such as total proteins, sugars, and phenols, superoxide dismutase, and hydrogen peroxide during the A. candida infection in B. juncea.
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Affiliation(s)
- Anupriya Chatterjee
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
| | - Shradha Nirwan
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
| | - Swati Mohapatra
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
| | - Pankaj Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201303, India
| | - Abha Agnihotri
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
| | - Neeraj Shrivastava
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
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8
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Hamelin RC, Bilodeau GJ, Heinzelmann R, Hrywkiw K, Capron A, Dort E, Dale AL, Giroux E, Kus S, Carleson NC, Grünwald NJ, Feau N. Genomic biosurveillance detects a sexual hybrid in the sudden oak death pathogen. Commun Biol 2022; 5:477. [PMID: 35589982 PMCID: PMC9120034 DOI: 10.1038/s42003-022-03394-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 04/21/2022] [Indexed: 11/24/2022] Open
Abstract
Invasive exotic pathogens pose a threat to trees and forest ecosystems worldwide, hampering the provision of essential ecosystem services such as carbon sequestration and water purification. Hybridization is a major evolutionary force that can drive the emergence of pathogens. Phytophthora ramorum, an emergent pathogen that causes the sudden oak and larch death, spreads as reproductively isolated divergent clonal lineages. We use a genomic biosurveillance approach by sequencing genomes of P. ramorum from survey and inspection samples and report the discovery of variants of P. ramorum that are the result of hybridization via sexual recombination between North American and European lineages. We show that these hybrids are viable, can infect a host and produce spores for long-term survival and propagation. Genome sequencing revealed genotypic combinations at 54,515 single nucleotide polymorphism loci not present in parental lineages. More than 6,000 of those genotypes are predicted to have a functional impact in genes associated with host infection, including effectors, carbohydrate-active enzymes and proteases. We also observed post-meiotic mitotic recombination that could generate additional genotypic and phenotypic variation and contribute to homoploid hybrid speciation. Our study highlights the importance of plant pathogen biosurveillance to detect variants, including hybrids, and inform management and control. Genome sequencing of isolates of the pathogen responsible for sudden oak death in the United States and sudden larch death in Europe reveal hybridisation between European and American lineages.
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Affiliation(s)
- Richard C Hamelin
- The Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada.
| | | | - Renate Heinzelmann
- The Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Kelly Hrywkiw
- The Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Arnaud Capron
- The Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Erika Dort
- The Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Angela L Dale
- New Construction Materials, FPInnovations, Vancouver, BC, Canada
| | - Emilie Giroux
- Ottawa Plant Laboratory, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Stacey Kus
- New Construction Materials, FPInnovations, Vancouver, BC, Canada
| | - Nick C Carleson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Niklaus J Grünwald
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.,Horticultural Crops Research Unit, USDA ARS, Corvallis, OR, USA
| | - Nicolas Feau
- The Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada.
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9
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Broders K, Iriarte-Broders G, Bergstrom GC, Byamukama E, Chilvers M, Cruz C, Dalla-Lana F, Duray Z, Malvick D, Mueller D, Paul P, Plewa D, Raid R, Robertson AE, Salgado-Salazar C, Smith D, Telenko D, VanEtten K, Kleczewski NM. Phyllachora species infecting maize and other grass species in the Americas represents a complex of closely related species. Ecol Evol 2022; 12:e8832. [PMID: 35494500 PMCID: PMC9036037 DOI: 10.1002/ece3.8832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/07/2022] [Accepted: 03/31/2022] [Indexed: 11/09/2022] Open
Abstract
The genus Phyllachora contains numerous obligate fungal parasites that produce raised, melanized structures called stromata on their plant hosts referred to as tar spot. Members of this genus are known to infect many grass species but generally do not cause significant damage or defoliation, with the exception of P. maydis which has emerged as an important pathogen of maize throughout the Americas, but the origin of this pathogen remains unknown. To date, species designations for Phyllachora have been based on host associations and morphology, and most species are assumed to be host specific. We assessed the sequence diversity of 186 single stroma isolates collected from 16 hosts representing 15 countries. Samples included both herbarium and contemporary strains that covered a temporal range from 1905 to 2019. These 186 isolates were grouped into five distinct species with strong bootstrap support. We found three closely related, but genetically distinct groups of Phyllachora are capable of infecting maize in the United States, we refer to these as the P. maydis species complex. Based on herbarium specimens, we hypothesize that these three groups in the P. maydis species complex originated from Central America, Mexico, and the Caribbean. Although two of these groups were only found on maize, the third and largest group contained contemporary strains found on maize and other grass hosts, as well as herbarium specimens from maize and other grasses that include 10 species of Phyllachora. The herbarium specimens were previously identified based on morphology and host association. This work represents the first attempt at molecular characterization of Phyllachora species infecting grass hosts and indicates some Phyllachora species can infect a broad range of host species and there may be significant synonymy in the Phyllachora genus.
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Affiliation(s)
- Kirk Broders
- Agricultural Research Service National Center for Agricultural Utilization Research Mycotoxin Prevention and Applied Microbiology Research Unit. 1815 N. University USDA Peoria Illinois USA
| | - Gloria Iriarte-Broders
- Agricultural Research Service National Center for Agricultural Utilization Research Mycotoxin Prevention and Applied Microbiology Research Unit. 1815 N. University USDA Peoria Illinois USA.,Independent Data Analyst Dunlap Illinois USA
| | - Gary C Bergstrom
- Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca New York USA
| | - Emmanuel Byamukama
- Department of Agronomy, Horticulture, and Plant Science South Dakota State University Brookings South Dakota USA
| | - Martin Chilvers
- Department of Plant, Soil, and Microbial Sciences Michigan State University East Lansing Michigan USA
| | - Christian Cruz
- Department of Botany and Plant Pathology Purdue University West Lafayette Indiana USA
| | - Felipe Dalla-Lana
- Department of Plant Pathology and Environmental Microbiology Southeast Agricultural Research & Extension Center Pennsylvania State University Manheim Pennsylvania USA
| | - Zachary Duray
- Department of Crop Sciences University of Illinois Urbana Illinois USA
| | - Dean Malvick
- Department of Plant Pathology University of Minnesota St Paul Minnesota USA
| | - Daren Mueller
- Department of Plant Pathology and Microbiology Iowa State University Ames Iowa USA
| | - Pierce Paul
- Department of Plant Pathology Wooster The Ohio State University Ohio USA
| | - Diane Plewa
- Department of Crop Sciences University of Illinois Urbana Illinois USA
| | - Richard Raid
- Department of Plant Pathology University of Florida Gainesville Florida USA
| | - Alison E Robertson
- Department of Plant Pathology and Microbiology Iowa State University Ames Iowa USA
| | - Catalina Salgado-Salazar
- Agricultural Research Service, Mycology and Nematology Genetic Diversity, and Biology Laboratory USDA Beltsville Maryland USA
| | - Damon Smith
- Department of Plant Pathology University of Wisconsin-Madison Madison Wisconsin USA
| | - Darcy Telenko
- Department of Plant Pathology and Environmental Microbiology Southeast Agricultural Research & Extension Center Pennsylvania State University Manheim Pennsylvania USA
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10
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Skiadas P, Klein J, Quiroz Monnens T, Elberse J, de Jonge R, Van den Ackerveken G, Seidl MF. Sexual reproduction contributes to the evolution of resistance breaking isolates of the spinach pathogen Peronospora effusa. Environ Microbiol 2022; 24:1622-1637. [PMID: 35191594 PMCID: PMC9304176 DOI: 10.1111/1462-2920.15944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
Peronospora effusa causes downy mildew, the economically most important disease of cultivated spinach worldwide. To date, 19 P. effusa races have been denominated based on their capacity to break spinach resistances, but their genetic diversity and the evolutionary processes that contribute to race emergence are unknown. Here, we performed the first systematic analysis of P. effusa races showing that those emerge by both asexual and sexual reproduction. Specifically, we studied the diversity of 26 P. effusa isolates from 16 denominated races based on mitochondrial and nuclear comparative genomics. Mitochondrial genomes based on long‐read sequencing coupled with diversity assessment based on short‐read sequencing uncovered two mitochondrial haplogroups, each with distinct genome organization. Nuclear genome‐wide comparisons of the 26 isolates revealed that 10 isolates from six races could clearly be divided into three asexually evolving groups, in concordance with their mitochondrial phylogeny. The remaining isolates showed signals of reticulated evolution and discordance between nuclear and mitochondrial phylogenies, suggesting that these evolved through sexual reproduction. Increased understanding of this pathogen's reproductive modes will provide the framework for future studies into the molecular mechanisms underlying race emergence and into the P. effusa‐spinach interaction, thus assisting in sustainable production of spinach through knowledge‐driven resistance breeding.
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Affiliation(s)
- Petros Skiadas
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584, CH, Utrecht, The Netherlands.,Plant-Microbe Interactions, Utrecht University, Padualaan 8 3584 CH, Utrecht, The Netherlands
| | - Joël Klein
- Plant-Microbe Interactions, Utrecht University, Padualaan 8 3584 CH, Utrecht, The Netherlands
| | - Thomas Quiroz Monnens
- Plant-Microbe Interactions, Utrecht University, Padualaan 8 3584 CH, Utrecht, The Netherlands
| | - Joyce Elberse
- Plant-Microbe Interactions, Utrecht University, Padualaan 8 3584 CH, Utrecht, The Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Utrecht University, Padualaan 8 3584 CH, Utrecht, The Netherlands
| | | | - Michael F Seidl
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584, CH, Utrecht, The Netherlands
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11
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Furzer OJ, Cevik V, Fairhead S, Bailey K, Redkar A, Schudoma C, MacLean D, Holub EB, Jones JDG. An Improved Assembly of the Albugo candida Ac2V Genome Reveals the Expansion of the "CCG" Class of Effectors. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:39-48. [PMID: 34546764 DOI: 10.1094/mpmi-04-21-0075-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We resequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB genome assembly is 10% larger and more contiguous compared with a previous version. Our annotation of the new assembly, aided by RNA-sequencing information, revealed a 175% expansion (40 to 110) in the CHxC effector class, which we redefined as "CCG" based on motif analysis. This class of effectors consist of arrays of phylogenetically related paralogs residing in gene sparse regions, and shows signatures of positive selection and presence/absence polymorphism. This work provides a resource that allows the dissection of the genomic components underlying A. candida adaptation and, particularly, the role of CCG effectors in virulence and avirulence on different hosts.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Oliver J Furzer
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Volkan Cevik
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Kate Bailey
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Amey Redkar
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
- Department of Genetics, University of Córdoba, Córdoba 14071, Spain
| | - Christian Schudoma
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Dan MacLean
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Eric B Holub
- University of Warwick, School of Life Sciences, Warwick Crop Centre, Wellesbourne, CV35 9EF, United Kingdom
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
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12
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Sullam KE, Musa T. Ecological Dynamics and Microbial Treatments against Oomycete Plant Pathogens. PLANTS 2021; 10:plants10122697. [PMID: 34961168 PMCID: PMC8707103 DOI: 10.3390/plants10122697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/16/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022]
Abstract
In this review, we explore how ecological concepts may help assist with applying microbial biocontrol agents to oomycete pathogens. Oomycetes cause a variety of agricultural diseases, including potato late blight, apple replant diseases, and downy mildew of grapevine, which also can lead to significant economic damage in their respective crops. The use of microbial biocontrol agents is increasingly gaining interest due to pressure from governments and society to reduce chemical plant protection products. The success of a biocontrol agent is dependent on many ecological processes, including the establishment on the host, persistence in the environment, and expression of traits that may be dependent on the microbiome. This review examines recent literature and trends in research that incorporate ecological aspects, especially microbiome, host, and environmental interactions, into biological control development and applications. We explore ecological factors that may influence microbial biocontrol agents’ efficacy and discuss key research avenues forward.
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13
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Castel B, Fairhead S, Furzer OJ, Redkar A, Wang S, Cevik V, Holub EB, Jones JDG. Evolutionary trade-offs at the Arabidopsis WRR4A resistance locus underpin alternate Albugo candida race recognition specificities. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1490-1502. [PMID: 34181787 DOI: 10.1111/tpj.15396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
The oomycete Albugo candida causes white rust of Brassicaceae, including vegetable and oilseed crops, and wild relatives such as Arabidopsis thaliana. Novel White Rust Resistance (WRR) genes from Arabidopsis enable new insights into plant/parasite co-evolution. WRR4A from Arabidopsis accession Columbia (Col-0) provides resistance to many but not all white rust races, and encodes a nucleotide-binding, leucine-rich repeat immune receptor. Col-0 WRR4A resistance is broken by AcEx1, an isolate of A. candida. We identified an allele of WRR4A in Arabidopsis accession Øystese-0 (Oy-0) and other accessions that confers full resistance to AcEx1. WRR4AOy-0 carries a C-terminal extension required for recognition of AcEx1, but reduces recognition of several effectors recognized by the WRR4ACol-0 allele. WRR4AOy-0 confers full resistance to AcEx1 when expressed in the oilseed crop Camelina sativa.
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Affiliation(s)
- Baptiste Castel
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Warwick Crop Centre, School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, United Kingdom
| | - Oliver J Furzer
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Amey Redkar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Department of Genetics, University of Cordoba, 14071, Cordoba, Spain
| | - Shanshan Wang
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
| | - Volkan Cevik
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, BA2 7AY, Bath, United Kingdom
| | - Eric B Holub
- Warwick Crop Centre, School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, United Kingdom
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
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14
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Cho CH, Jang S, Choi BY, Hong D, Choi DS, Choi S, Kim H, Han SK, Kim S, Kim M, Palmgren M, Sohn KH, Yoon HS, Lee Y. Phylogenetic analysis of ABCG subfamily proteins in plants: functional clustering and coevolution with ABCGs of pathogens. PHYSIOLOGIA PLANTARUM 2021; 172:1422-1438. [PMID: 31828796 PMCID: PMC8359288 DOI: 10.1111/ppl.13052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/19/2019] [Indexed: 05/02/2023]
Abstract
ABCG subfamily proteins are highly enriched in terrestrial plants. Many of these proteins secrete secondary metabolites that repel or inhibit pathogens. To establish why the ABCG subfamily proteins proliferated extensively during evolution, we constructed phylogenetic trees from a broad range of eukaryotic organisms. ABCG proteins were massively duplicated in land plants and in oomycetes, a group of agronomically important plant pathogens, which prompted us to hypothesize that plant and pathogen ABCGs coevolved. Supporting this hypothesis, full-size ABCGs in host plants (Arabidopsis thaliana and Glycine max) and their pathogens (Hyaloperonospora arabidopsidis and Phytophthora sojae, respectively) had similar divergence times and patterns. Furthermore, generalist pathogens with broad ranges of host plants have diversified more ABCGs than their specialist counterparts. The hypothesis was further tested using an example pair of ABCGs that first diverged during multiplication in a host plant and its pathogen: AtABCG31 of A. thaliana and HpaP802307 of H. arabidopsidis. AtABCG31 expression was activated following infection with H. arabidopsidis, and disrupting AtABCG31 led to increased susceptibility to H. arabidopsidis. Together, our results suggest that ABCG genes in plants and their oomycete pathogens coevolved in an arms race, to extrude secondary metabolites involved in the plant's defense response against pathogens.
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Affiliation(s)
- Chung Hyun Cho
- Department of Biological SciencesSungkyunkwan UniversitySuwonKorea
| | - Sunghoon Jang
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
| | - Bae Young Choi
- Division of Integrative Bioscience and BiotechnologyPOSTECHPohang37673Korea
| | - Daewoong Hong
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
| | - Du Seok Choi
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
- Present address:
GreenBio Center, Corporate R&D, LG Chem, LtdSeoul07796Korea
| | - Sera Choi
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
| | - Haseong Kim
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
| | - Seong Kyu Han
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
| | - Sanguk Kim
- Division of Integrative Bioscience and BiotechnologyPOSTECHPohang37673Korea
| | - Min‐Sung Kim
- Division of Integrative Bioscience and BiotechnologyPOSTECHPohang37673Korea
| | - Michael Palmgren
- Department of Plant and Environmental ScienceUniversity of CopenhagenDK‐1871FrederiksbergDenmark
| | - Kee Hoon Sohn
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
- Division of Integrative Bioscience and BiotechnologyPOSTECHPohang37673Korea
| | - Hwan Su Yoon
- Department of Biological SciencesSungkyunkwan UniversitySuwonKorea
| | - Youngsook Lee
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
- Division of Integrative Bioscience and BiotechnologyPOSTECHPohang37673Korea
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15
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Sacristán S, Goss EM, Eves-van den Akker S. How Do Pathogens Evolve Novel Virulence Activities? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:576-586. [PMID: 33522842 DOI: 10.1094/mpmi-09-20-0258-ia] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article is part of the Top 10 Unanswered Questions in MPMI invited review series.We consider the state of knowledge on pathogen evolution of novel virulence activities, broadly defined as anything that increases pathogen fitness with the consequence of causing disease in either the qualitative or quantitative senses, including adaptation of pathogens to host immunity and physiology, host species, genotypes, or tissues, or the environment. The evolution of novel virulence activities as an adaptive trait is based on the selection exerted by hosts on variants that have been generated de novo or arrived from elsewhere. In addition, the biotic and abiotic environment a pathogen experiences beyond the host may influence pathogen virulence activities. We consider host-pathogen evolution, host range expansion, and external factors that can mediate pathogen evolution. We then discuss the mechanisms by which pathogens generate and recombine the genetic variation that leads to novel virulence activities, including DNA point mutation, transposable element activity, gene duplication and neofunctionalization, and genetic exchange. In summary, if there is an (epi)genetic mechanism that can create variation in the genome, it will be used by pathogens to evolve virulence factors. Our knowledge of virulence evolution has been biased by pathogen evolution in response to major gene resistance, leaving other virulence activities underexplored. Understanding the key driving forces that give rise to novel virulence activities and the integration of evolutionary concepts and methods with mechanistic research on plant-microbe interactions can help inform crop protection.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
| | - Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, U.S.A
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Van Oosterhout C. Mitigating the threat of emerging infectious diseases; a coevolutionary perspective. Virulence 2021; 12:1288-1295. [PMID: 33957064 PMCID: PMC8115449 DOI: 10.1080/21505594.2021.1920741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Cock Van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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17
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Anupriya C, Shradha N, Prasun B, Abha A, Pankaj S, Abdin MZ, Neeraj S. Genomic and Molecular Perspectives of Host-pathogen Interaction and Resistance Strategies against White Rust in Oilseed Mustard. Curr Genomics 2020; 21:179-193. [PMID: 33071612 PMCID: PMC7521032 DOI: 10.2174/1389202921999200508075410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/25/2020] [Accepted: 03/14/2020] [Indexed: 11/29/2022] Open
Abstract
Oilseed brassicas stand as the second most valuable source of vegetable oil and the third most traded one across the globe. However, the yield can be severely affected by infections caused by phytopathogens. White rust is a major oomycete disease of oilseed brassicas resulting in up to 60% yield loss globally. So far, success in the development of oomycete resistant Brassicas through conventional breeding has been limited. Hence, there is an imperative need to blend conventional and frontier biotechnological means to breed for improved crop protection and yield. This review provides a deep insight into the white rust disease and explains the oomycete-plant molecular events with special reference to Albugo candida describing the role of effector molecules, A. candida secretome, and disease response mechanism along with nucleotide-binding leucine-rich repeat receptor (NLR) signaling. Based on these facts, we further discussed the recent progress and future scopes of genomic approaches to transfer white rust resistance in the susceptible varieties of oilseed brassicas, while elucidating the role of resistance and susceptibility genes. Novel genomic technologies have been widely used in crop sustainability by deploying resistance in the host. Enrichment of NLR repertoire, over-expression of R genes, silencing of avirulent and disease susceptibility genes through RNA interference and CRSPR-Cas are technologies which have been successfully applied against pathogen-resistance mechanism. The article provides new insight into Albugo and Brassica genomics which could be useful for producing high yielding and WR resistant oilseed cultivars across the globe.
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Affiliation(s)
- Chatterjee Anupriya
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Nirwan Shradha
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Bandyopadhyay Prasun
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Agnihotri Abha
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Sharma Pankaj
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Malik Zainul Abdin
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Shrivastava Neeraj
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
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18
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Quilodrán CS, Tsoupas A, Currat M. The Spatial Signature of Introgression After a Biological Invasion With Hybridization. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.569620] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The accumulation of genome-wide molecular data has emphasized the important role of hybridization in the evolution of many organisms, which may carry introgressed genomic segments resulting from past admixture events with other taxa. Despite a number of examples of hybridization occurring during biological invasions, the resulting spatial patterns of genomic introgression remain poorly understood. Preliminary simulation studies have suggested a heterogeneous spatial level of introgression for invasive taxa after range expansion. We investigated in detail the robustness of this pattern and its persistence over time for both invasive and local organisms. Using spatially explicit simulations, we explored the spatial distribution of introgression across the area of colonization of an invasive taxon hybridizing with a local taxon. The general pattern for neutral loci supported by our results is an increasing introgression of local genes into the invasive taxon with the increase in the distance from the source of the invasion and a decreasing introgression of invasive genes into the local taxon. However, we also show there is some variation in this general trend depending on the scenario investigated. Spatial heterogeneity of introgression within a given taxon is thus an expected neutral pattern in structured populations after a biological invasion with a low to moderate amount of hybridization. We further show that this pattern is consistent with published empirical observations. Using additional simulations, we argue that the spatial pattern of Neanderthal introgression in modern humans, which has been documented to be higher in Asia than in Europe, can be explained by a model of hybridization with Neanderthals in Eurasia during the range expansion of modern humans from Africa. Our results support the view that weak hybridization during range expansion may explain spatially heterogeneous introgression patterns without the need to invoke selection.
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19
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Riaz S, Menéndez CM, Tenscher A, Pap D, Walker MA. Genetic mapping and survey of powdery mildew resistance in the wild Central Asian ancestor of cultivated grapevines in Central Asia. HORTICULTURE RESEARCH 2020; 7:104. [PMID: 32637132 PMCID: PMC7326912 DOI: 10.1038/s41438-020-0335-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 04/01/2020] [Accepted: 05/01/2020] [Indexed: 05/21/2023]
Abstract
Cultivated grapevines (Vitis vinifera) lack resistance to powdery mildew (PM) with few exceptions. Resistance to this pathogen within V. vinifera has been reported in earlier studies and identified as the Ren1 locus in two Central Asian table grape accessions. Other PM-resistant cultivated varieties and accessions of the wild ancestor V. vinifera subsp. sylvestris were soon identified raising questions regarding the origin of the resistance. In this study, F1 breeding populations were developed with a PM susceptible V. vinifera subsp. vinifera breeding line and a PM-resistant subsp. sylvestris accession. Genotyping was carried out with five Ren1 locus linked SSR markers. A PM resistance locus explaining up to 96% of the phenotypic variation was identified in the same genomic position, where the Ren1 locus was previously reported. New SSR marker alleles linked with the resistance locus were identified. We report results of PM resistance in multiple accessions of subsp. sylvestris collected as seed lots or cuttings from five countries in the Caucasus and Central Asia. A total of 20 females from 11 seed lots and 19 males from nine seed lots collected from Georgia, Armenia, and Azerbaijan were resistant to PM. Three male and one female plant collected as cuttings from Afghanistan and Iran were also resistant to PM. Allelic analysis of markers linked with the Ren1 locus in conjunction with disease evaluation data found a high diversity of allelic haplotypes, which are only possible via recombination events occurring over a long time period. Sequence analysis of two alleles of the SSR marker that cosegregates with the resistance found SNPs that were present in the wild progenitor and in cultivated forms. Variable levels of PM resistance among the tested accessions were also observed. These lines of evidence suggest that the powdery mildew fungus may have been present in Asia for a longer time than currently thought, giving the wild progenitor V. vinifera subsp. sylvestris time to coevolve with and develop resistance to this pathogen.
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Affiliation(s)
- Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Cristina M. Menéndez
- Instituto de Ciencias de la Vid y del Vino (ICVV), Universidad de La Rioja-CSIC-Gobierno de La Rioja, Carretera de Burgos Km, 6, Finca La Grajera, Logroño, La Rioja 26007 Spain
| | - Alan Tenscher
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Daniel Pap
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - M. Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
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20
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de Vries S, Stukenbrock EH, Rose LE. Rapid evolution in plant-microbe interactions - an evolutionary genomics perspective. THE NEW PHYTOLOGIST 2020; 226:1256-1262. [PMID: 31997351 DOI: 10.1111/nph.16458] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 01/13/2020] [Indexed: 05/22/2023]
Abstract
Access to greater genomic resolution through new sequencing technologies is transforming the field of plant pathology. As scientists embrace these new methods, some overarching patterns and observations come into focus. Evolutionary genomic studies are used to determine not only the origins of pathogen lineages and geographic patterns of genetic diversity, but also to discern how natural selection structures genetic variation across the genome. With greater and greater resolution, we can now pinpoint the targets of selection on a large scale. At multiple levels, crypsis and convergent evolution are evident. Host jumps and shifts may be more pervasive than once believed, and hybridization and horizontal gene transfer (HGT) likely play important roles in the emergence of genetic novelty.
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Affiliation(s)
- Sophie de Vries
- Institute of Population Genetics, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- The Botanical Institute, Christian-Albrechts University of Kiel, Am Botanischen Garden 9-11, 24118, Kiel, Germany
| | - Laura E Rose
- Institute of Population Genetics, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
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21
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Cotton JA, Durrant C, Franssen SU, Gelanew T, Hailu A, Mateus D, Sanders MJ, Berriman M, Volf P, Miles MA, Yeo M. Genomic analysis of natural intra-specific hybrids among Ethiopian isolates of Leishmania donovani. PLoS Negl Trop Dis 2020; 14:e0007143. [PMID: 32310945 PMCID: PMC7237039 DOI: 10.1371/journal.pntd.0007143] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/19/2020] [Accepted: 12/24/2019] [Indexed: 12/30/2022] Open
Abstract
Parasites of the genus Leishmania (Kinetoplastida: Trypanosomatidae) cause widespread and devastating human diseases. Visceral leishmaniasis due to Leishmania donovani is endemic in Ethiopia where it has also been responsible for major epidemics. The presence of hybrid genotypes has been widely reported in surveys of natural populations, genetic variation reported in a number of Leishmania species, and the extant capacity for genetic exchange demonstrated in laboratory experiments. However, patterns of recombination and the evolutionary history of admixture that produced these hybrid populations remain unclear. Here, we use whole-genome sequence data to investigate Ethiopian L. donovani isolates previously characterized as hybrids by microsatellite and multi-locus sequencing. To date there is only one previous study on a natural population of Leishmania hybrids based on whole-genome sequences. We propose that these hybrids originate from recombination between two different lineages of Ethiopian L. donovani occurring in the same region. Patterns of inheritance are more complex than previously reported with multiple, apparently independent, origins from similar parents that include backcrossing with parental types. Analysis indicates that hybrids are representative of at least three different histories. Furthermore, isolates were highly polysomic at the level of chromosomes with differences between parasites recovered from a recrudescent infection from a previously treated individual. The results demonstrate that recombination is a significant feature of natural populations and contributes to the growing body of data that shows how recombination, and gene flow, shape natural populations of Leishmania.
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Affiliation(s)
| | | | | | - Tesfaye Gelanew
- Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Asrat Hailu
- Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - David Mateus
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michael A. Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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22
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Feurtey A, Stevens DM, Stephan W, Stukenbrock EH. Interspecific Gene Exchange Introduces High Genetic Variability in Crop Pathogen. Genome Biol Evol 2020; 11:3095-3105. [PMID: 31603209 PMCID: PMC6836716 DOI: 10.1093/gbe/evz224] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2019] [Indexed: 12/27/2022] Open
Abstract
Genome analyses have revealed a profound role of hybridization and introgression in the evolution of many eukaryote lineages, including fungi. The impact of recurrent introgression on fungal evolution however remains elusive. Here, we analyzed signatures of introgression along the genome of the fungal wheat pathogen Zymoseptoria tritici. We applied a comparative population genomics approach, including genome data from five Zymoseptoria species, to characterize the distribution and composition of introgressed regions representing segments with an exceptional haplotype pattern. These regions are found throughout the genome, comprising 5% of the total genome and overlapping with > 1,000 predicted genes. We performed window-based phylogenetic analyses along the genome to distinguish regions which have a monophyletic or nonmonophyletic origin with Z. tritici sequences. A majority of nonmonophyletic windows overlap with the highly variable regions suggesting that these originate from introgression. We verified that incongruent gene genealogies do not result from incomplete lineage sorting by comparing the observed and expected length distribution of haplotype blocks resulting from incomplete lineage sorting. Although protein-coding genes are not enriched in these regions, we identify 18 that encode putative virulence determinants. Moreover, we find an enrichment of transposable elements in these regions implying that hybridization may contribute to the horizontal spread of transposable elements. We detected a similar pattern in the closely related species Zymoseptoria ardabiliae, suggesting that hybridization is widespread among these closely related grass pathogens. Overall, our results demonstrate a significant impact of recurrent hybridization on overall genome evolution of this important wheat pathogen.
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Affiliation(s)
- Alice Feurtey
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Botanical Institute, Christian-Albrechts University of Kiel, Germany
| | - Danielle M Stevens
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Botanical Institute, Christian-Albrechts University of Kiel, Germany.,Department of Plant Pathology, University of California, Davis
| | - Wolfgang Stephan
- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Botanical Institute, Christian-Albrechts University of Kiel, Germany
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23
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Thines M. An evolutionary framework for host shifts - jumping ships for survival. THE NEW PHYTOLOGIST 2019; 224:605-617. [PMID: 31381166 DOI: 10.1111/nph.16092] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
Host jumping is a process by which pathogens settle in new host groups. It is a cornerstone in the evolution of pathogens, as it leads to pathogen diversification. It is unsurprising that host jumping is observed in facultative pathogens, as they can reproduce even if they kill their hosts. However, host jumps were thought to be rare in obligate biotrophic pathogens, but molecular phylogenetics has revealed that the opposite is true. Here, I review some concepts and recent findings and present several hypotheses on the matter. In short, pathogens evolve and diversify via host jumps, followed by radiation, specialisation and speciation. Host jumps are facilitated by, for example, effector innovations, stress, compatible pathogens and physiological similarities. Host jumping, subsequent establishment, and speciation takes place rapidly - within centuries and millennia rather than over millions of years. If pathogens are unable to evolve into neutral or mutualistic interactions with their hosts, they will eventually be removed from the host population, despite balancing trade-offs. Thus, generally, plant pathogens only survive in the course of evolution if they jump hosts. This is also reflected by the diversity patterns observed in many genera of plant pathogens, where it leads to a mosaic pattern of host groups over time, in which the original host group becomes increasingly obscure.
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Affiliation(s)
- Marco Thines
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, D-60486, Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
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24
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Herlihy J, Ludwig NR, van den Ackerveken G, McDowell JM. Oomycetes Used in Arabidopsis Research. THE ARABIDOPSIS BOOK 2019; 17:e0188. [PMID: 33149730 PMCID: PMC7592078 DOI: 10.1199/tab.0188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Arabidopsis plants in their natural environment are susceptible to infection by oomycete pathogens, in particular to downy mildew and white rust diseases. These naturally occurring infectious agents have imposed evolutionary pressures on Arabidopsis populations and are therefore highly relevant for the study of host-pathogen co-evolution. In addition, the study of oomycete diseases, including infections caused by several Phytophthora species, has led to many scientific discoveries on Arabidopsis immunity and disease. Herein, we describe the major oomycete species used for experiments on Arabidopsis, and how these pathosystems have been used to provide significant insights into mechanistic and evolutionary aspects of plant-oomycete interactions. We also highlight understudied aspects of plant-oomycete interactions, as well as translational approaches, that can be productively addressed using the reference pathosystems described in this article.
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Affiliation(s)
- John Herlihy
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Nora R. Ludwig
- Plant–Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Guido van den Ackerveken
- Plant–Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - John M. McDowell
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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25
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Dussert Y, Mazet ID, Couture C, Gouzy J, Piron MC, Kuchly C, Bouchez O, Rispe C, Mestre P, Delmotte F. A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes. Genome Biol Evol 2019; 11:954-969. [PMID: 30847481 PMCID: PMC6660063 DOI: 10.1093/gbe/evz048] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2019] [Indexed: 02/06/2023] Open
Abstract
Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant–pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.
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Affiliation(s)
- Yann Dussert
- SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | | | - Carole Couture
- SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Jérôme Gouzy
- LIPM, INRA, Université de Toulouse, CNRS, Castanet-Tolosan, France
| | | | - Claire Kuchly
- US 1426 GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France
| | | | | | - Pere Mestre
- SVQV, INRA, Université de Strasbourg, Colmar, France
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26
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Evolutionary genomics of anthroponosis in Cryptosporidium. Nat Microbiol 2019; 4:826-836. [DOI: 10.1038/s41564-019-0377-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 01/18/2019] [Indexed: 01/19/2023]
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27
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Dussert Y, Mazet ID, Couture C, Gouzy J, Piron MC, Kuchly C, Bouchez O, Rispe C, Mestre P, Delmotte F. A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes. Genome Biol Evol 2019. [PMID: 30847481 DOI: 10.1101/350041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant-pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.
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Affiliation(s)
- Yann Dussert
- SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | | | - Carole Couture
- SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Jérôme Gouzy
- LIPM, INRA, Université de Toulouse, CNRS, Castanet-Tolosan, France
| | | | - Claire Kuchly
- US 1426 GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France
| | | | | | - Pere Mestre
- SVQV, INRA, Université de Strasbourg, Colmar, France
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28
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Jouet A, Saunders DGO, McMullan M, Ward B, Furzer O, Jupe F, Cevik V, Hein I, Thilliez GJA, Holub E, van Oosterhout C, Jones JDG. Albugo candida race diversity, ploidy and host-associated microbes revealed using DNA sequence capture on diseased plants in the field. THE NEW PHYTOLOGIST 2019; 221:1529-1543. [PMID: 30288750 DOI: 10.1111/nph.15417] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/20/2018] [Indexed: 05/28/2023]
Abstract
Physiological races of the oomycete Albugo candida are biotrophic pathogens of diverse plant species, primarily the Brassicaceae, and cause infections that suppress host immunity to other pathogens. However, A. candida race diversity and the consequences of host immunosuppression are poorly understood in the field. We report a method that enables sequencing of DNA of plant pathogens and plant-associated microbes directly from field samples (Pathogen Enrichment Sequencing: PenSeq). We apply this method to explore race diversity in A. candida and to detect A. candida-associated microbes in the field (91 A. candida-infected plants). We show with unprecedented resolution that each host plant species supports colonization by one of 17 distinct phylogenetic lineages, each with an unique repertoire of effector candidate alleles. These data reveal the crucial role of sexual and asexual reproduction, polyploidy and host domestication in A. candida specialization on distinct plant species. Our bait design also enabled phylogenetic assignment of DNA sequences from bacteria and fungi from plants in the field. This paper shows that targeted sequencing has a great potential for the study of pathogen populations while they are colonizing their hosts. This method could be applied to other microbes, especially to those that cannot be cultured.
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Affiliation(s)
- Agathe Jouet
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Mark McMullan
- The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Ben Ward
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
- The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Oliver Furzer
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- University of North Carolina, Chapel Hill, NC, 27599-2200, USA
| | - Florian Jupe
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- Plant Molecular and Cellular Biology Laboratory, Salk Institute, La Jolla, CA, 92037, USA
| | - Volkan Cevik
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Ingo Hein
- The James Hutton Institute, CMS, Dundee, DD2 5DA, UK
- Division of Plant Sciences at the James Hutton Institute, the University of Dundee, Dundee, DD2 5DA, UK
| | - Gaetan J A Thilliez
- The James Hutton Institute, CMS, Dundee, DD2 5DA, UK
- Quadram Institute Bioscience, Norwich Research Park, Colney Lane, NR4 7UH, Norwich, UK
| | - Eric Holub
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Warwick, CV35 9EF, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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29
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Transgressive segregation reveals mechanisms of Arabidopsis immunity to Brassica-infecting races of white rust ( Albugo candida). Proc Natl Acad Sci U S A 2019; 116:2767-2773. [PMID: 30692254 PMCID: PMC6377460 DOI: 10.1073/pnas.1812911116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Most plants resist most plant pathogens. Barley resists wheat-infecting powdery mildew races (and vice versa), and both barley and wheat resist potato late blight. Such “nonhost” resistance could result because the pathogen fails to suppress defense or triggers innate immunity due to failure to evade detection. Albugo candida causes white rust on most Brassicaceae, and we investigated Arabidopsis NHR to Brassica-infecting races. Transgressive segregation for resistance in Arabidopsis recombinant inbred lines revealed genes encoding nucleotide-binding, leucine-rich repeat (NLR) immune receptors. Some of these NLR-encoding genes confer resistance to white rust in Brassica sp. This genetic method thus provides a route to reveal resistance genes for crops, widening the pool from which such genes might be obtained. Arabidopsis thaliana accessions are universally resistant at the adult leaf stage to white rust (Albugo candida) races that infect the crop species Brassica juncea and Brassica oleracea. We used transgressive segregation in recombinant inbred lines to test if this apparent species-wide (nonhost) resistance in A. thaliana is due to natural pyramiding of multiple Resistance (R) genes. We screened 593 inbred lines from an Arabidopsis multiparent advanced generation intercross (MAGIC) mapping population, derived from 19 resistant parental accessions, and identified two transgressive segregants that are susceptible to the pathogen. These were crossed to each MAGIC parent, and analysis of resulting F2 progeny followed by positional cloning showed that resistance to an isolate of A. candida race 2 (Ac2V) can be explained in each accession by at least one of four genes encoding nucleotide-binding, leucine-rich repeat (NLR) immune receptors. An additional gene was identified that confers resistance to an isolate of A. candida race 9 (AcBoT) that infects B. oleracea. Thus, effector-triggered immunity conferred by distinct NLR-encoding genes in multiple A. thaliana accessions provides species-wide resistance to these crop pathogens.
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30
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McMullan M, Rafiqi M, Kaithakottil G, Clavijo BJ, Bilham L, Orton E, Percival-Alwyn L, Ward BJ, Edwards A, Saunders DGO, Garcia Accinelli G, Wright J, Verweij W, Koutsovoulos G, Yoshida K, Hosoya T, Williamson L, Jennings P, Ioos R, Husson C, Hietala AM, Vivian-Smith A, Solheim H, MaClean D, Fosker C, Hall N, Brown JKM, Swarbreck D, Blaxter M, Downie JA, Clark MD. The ash dieback invasion of Europe was founded by two genetically divergent individuals. Nat Ecol Evol 2018; 2:1000-1008. [PMID: 29686237 PMCID: PMC5969572 DOI: 10.1038/s41559-018-0548-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 03/27/2018] [Indexed: 11/22/2022]
Abstract
Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H. fraxineus, although a minority (~5%) have partial resistance to dieback. Here, we assemble and annotate a H. fraxineus draft genome which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan, reveals a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H. fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.
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Affiliation(s)
- Mark McMullan
- The Earlham Institute, Norwich Research Park, Norwich, UK.
| | | | | | | | | | | | | | - Ben J Ward
- The Earlham Institute, Norwich Research Park, Norwich, UK
| | - Anne Edwards
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | | | - Walter Verweij
- The Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Kentaro Yoshida
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.,Graduate school of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Tsuyoshi Hosoya
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | | | | | - Renaud Ioos
- ANSES Laboratoire de la Santé des Végétaux, Malzéville, France
| | | | - Ari M Hietala
- Norwegian Institute of Bioeconomy Research, Ås, Norway
| | | | | | - Dan MaClean
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | | | - Neil Hall
- The Earlham Institute, Norwich Research Park, Norwich, UK
| | | | | | - Mark Blaxter
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK.,Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Matthew D Clark
- The Earlham Institute, Norwich Research Park, Norwich, UK. .,Department of Life Sciences, Natural History Museum, London, UK.
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31
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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32
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Hacquard S, Spaepen S, Garrido-Oter R, Schulze-Lefert P. Interplay Between Innate Immunity and the Plant Microbiota. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:565-589. [PMID: 28645232 DOI: 10.1146/annurev-phyto-080516-035623] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer of this system is also engaged in cooperative plant-microbe interactions and influences host colonization by beneficial microbial communities. This immune layer involves sensing of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) that initiate quantitative immune responses to control host-microbial load, whereas diversification of MAMPs and PRRs emerges as a mechanism that locally sculpts microbial assemblages in plant populations. This suggests a more complex microbial management role of the innate immune system for controlled accommodation of beneficial microbes and in pathogen elimination. The finding that similar molecular strategies are deployed by symbionts and pathogens to dampen immune responses is consistent with this hypothesis but implies different selective pressures on the immune system due to contrasting outcomes on plant fitness. The reciprocal interplay between microbiota and the immune system likely plays a critical role in shaping beneficial plant-microbiota combinations and maintaining microbial homeostasis.
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Affiliation(s)
- Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Stijn Spaepen
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Ruben Garrido-Oter
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
- Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
- Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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33
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Kroll S, Agler MT, Kemen E. Genomic dissection of host-microbe and microbe-microbe interactions for advanced plant breeding. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:71-78. [PMID: 28235716 DOI: 10.1016/j.pbi.2017.01.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 05/23/2023]
Abstract
Agriculture faces many emerging challenges to sustainability, including limited nutrient resources, losses from diseases caused by current and emerging pathogens and environmental degradation. Microorganisms have great importance for plant growth and performance, including the potential to increase yields, nutrient uptake and pathogen resistance. An urgent need is therefore to understand and engineer plants and their associated microbial communities. Recent massive genomic sequencing of host plants and associated microbes offers resources to identify novel mechanisms of communal assembly mediated by the host. For example, host-microbe and microbe-microbe interactions are involved in niche formation, thereby contributing to colonization. By leveraging genomic resources, genetic traits underlying those mechanisms will become important resources to design plants selecting and hosting beneficial microbial communities.
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Affiliation(s)
- Samuel Kroll
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Matthew T Agler
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Eric Kemen
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany.
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34
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Prince DC, Rallapalli G, Xu D, Schoonbeek HJ, Çevik V, Asai S, Kemen E, Cruz-Mireles N, Kemen A, Belhaj K, Schornack S, Kamoun S, Holub EB, Halkier BA, Jones JDG. Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana. BMC Biol 2017; 15:20. [PMID: 28320402 PMCID: PMC5358052 DOI: 10.1186/s12915-017-0360-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/22/2017] [Indexed: 02/04/2023] Open
Abstract
Background Plants are exposed to diverse pathogens and pests, yet most plants are resistant to most plant pathogens. Non-host resistance describes the ability of all members of a plant species to successfully prevent colonization by any given member of a pathogen species. White blister rust caused by Albugo species can overcome non-host resistance and enable secondary infection and reproduction of usually non-virulent pathogens, including the potato late blight pathogen Phytophthora infestans on Arabidopsis thaliana. However, the molecular basis of host defense suppression in this complex plant–microbe interaction is unclear. Here, we investigate specific defense mechanisms in Arabidopsis that are suppressed by Albugo infection. Results Gene expression profiling revealed that two species of Albugo upregulate genes associated with tryptophan-derived antimicrobial metabolites in Arabidopsis. Albugo laibachii-infected tissue has altered levels of these metabolites, with lower indol-3-yl methylglucosinolate and higher camalexin accumulation than uninfected tissue. We investigated the contribution of these Albugo-imposed phenotypes to suppression of non-host resistance to P. infestans. Absence of tryptophan-derived antimicrobial compounds enables P. infestans colonization of Arabidopsis, although to a lesser extent than Albugo-infected tissue. A. laibachii also suppresses a subset of genes regulated by salicylic acid; however, salicylic acid plays only a minor role in non-host resistance to P. infestans. Conclusions Albugo sp. alter tryptophan-derived metabolites and suppress elements of the responses to salicylic acid in Arabidopsis. Albugo sp. imposed alterations in tryptophan-derived metabolites may play a role in Arabidopsis non-host resistance to P. infestans. Understanding the basis of non-host resistance to pathogens such as P. infestans could assist in development of strategies to elevate food security. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0360-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David C Prince
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Ghanasyam Rallapalli
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Deyang Xu
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 40 Thorvaldsensvej, DK-1871, Frederiksberg C, Denmark
| | - Henk-Jan Schoonbeek
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Volkan Çevik
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Shuta Asai
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Plant Immunity Research Group, Center for Sustainable Resource Science, RIKEN Yokohama Institute, Yokohama, Japan
| | - Eric Kemen
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Neftaly Cruz-Mireles
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Ariane Kemen
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Khaoula Belhaj
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sebastian Schornack
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Eric B Holub
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne, UK
| | - Barbara A Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 40 Thorvaldsensvej, DK-1871, Frederiksberg C, Denmark
| | - Jonathan D G Jones
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DRG, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson ACC, van Oosterhout C, Swarbreck D, Hogenhout SA. Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biol 2017; 18:27. [PMID: 28190401 PMCID: PMC5304397 DOI: 10.1186/s13059-016-1145-3] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/22/2016] [Indexed: 12/04/2022] Open
Abstract
Background The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species. Results To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes. Conclusions Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1145-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas C Mathers
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Yazhou Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | | | - Fabrice Legeai
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Sam T Mugford
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Patrice Baa-Puyoulet
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Anthony Bretaudeau
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | | | - Stefano Colella
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France.,Present Address: INRA, UMR1342 IRD-CIRAD-INRA-SupAgro-Université de Montpellier, Laboratoire des Symbioses Tropicales et Méditéranéennes, Campus International de Baillarguet, TA-A82/J, F-34398, Montpellier cedex 5, France
| | - Olivier Collin
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thomas Derrien
- CNRS, UMR 6290, Institut de Génétique et Developpement de Rennes, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, 35000, Rennes, France
| | - Honglin Feng
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Toni Gabaldón
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Anna Jordan
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Irene Julca
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Graeme J Kettles
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Rothamsted Research, Harpenden, Hertforshire, ALF5 2JQ, UK
| | - Krissana Kowitwanich
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: J. R. Simplot Company, Boise, ID, USA
| | - Dominique Lavenier
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Paolo Lenzi
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Alson H. Smith Jr. Agriculture and Extension Center, Virginia Tech, Winchester, 22602, VA, USA
| | - Sara Lopez-Gomollon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Present address: Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Damian Loska
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Daniel Mapleson
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Florian Maumus
- The International Aphid Genomics Consortium, Miami, USA.,Unité de Recherche Génomique-Info (URGI), INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Simon Moxon
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Daniel R G Price
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.,Present address: Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Akiko Sugio
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Manuella van Munster
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Marilyne Uzest
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Darren Waite
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Georg Jander
- The International Aphid Genomics Consortium, Miami, USA.,Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
| | - Denis Tagu
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Alex C C Wilson
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Cock van Oosterhout
- The International Aphid Genomics Consortium, Miami, USA.,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Saskia A Hogenhout
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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36
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Badet T, Peyraud R, Mbengue M, Navaud O, Derbyshire M, Oliver RP, Barbacci A, Raffaele S. Codon optimization underpins generalist parasitism in fungi. eLife 2017; 6:e22472. [PMID: 28157073 PMCID: PMC5315462 DOI: 10.7554/elife.22472] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/28/2017] [Indexed: 01/04/2023] Open
Abstract
The range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet, the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasites. We found that the longer proteins encoded by broad host range fungi likely increase natural selection on codon optimization in these species. Accordingly, codon optimization correlates with host range across the fungal kingdom. At the species level, biased patterns of synonymous substitutions underpin increased codon optimization in a generalist but not a specialist fungal pathogen. Virulence genes were consistently enriched in highly codon-optimized genes of generalist but not specialist species. We conclude that codon optimization is related to the capacity of parasites to colonize multiple hosts. Our results link genome evolution and translational regulation to the long-term persistence of generalist parasitism.
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Affiliation(s)
- Thomas Badet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Remi Peyraud
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Malick Mbengue
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Olivier Navaud
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Mark Derbyshire
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - Richard P Oliver
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - Adelin Barbacci
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Sylvain Raffaele
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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37
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Stam R, Scheikl D, Tellier A. The wild tomato species Solanum chilense shows variation in pathogen resistance between geographically distinct populations. PeerJ 2017; 5:e2910. [PMID: 28133579 PMCID: PMC5248578 DOI: 10.7717/peerj.2910] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/08/2016] [Indexed: 12/13/2022] Open
Abstract
Wild tomatoes are a valuable source of disease resistance germplasm for tomato (Solanum lycopersicum) breeders. Many species are known to possess a certain degree of resistance against certain pathogens; however, evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense, both differences in habitat and within species genetic diversity are very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense. We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens (Alternaria solani, Phytophthora infestans and a Fusarium sp.) and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense, resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved.
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Affiliation(s)
- Remco Stam
- Section of Population Genetics, Technical University of Munich, Freising, Germany
| | - Daniela Scheikl
- Section of Population Genetics, Technical University of Munich, Freising, Germany
| | - Aurélien Tellier
- Section of Population Genetics, Technical University of Munich, Freising, Germany
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38
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Belhaj K, Cano LM, Prince DC, Kemen A, Yoshida K, Dagdas YF, Etherington GJ, Schoonbeek H, van Esse HP, Jones JD, Kamoun S, Schornack S. Arabidopsis late blight: infection of a nonhost plant by Albugo laibachii enables full colonization by Phytophthora infestans. Cell Microbiol 2017; 19:e12628. [PMID: 27302335 PMCID: PMC5215655 DOI: 10.1111/cmi.12628] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 04/15/2016] [Accepted: 05/30/2016] [Indexed: 01/20/2023]
Abstract
The oomycete pathogen Phytophthora infestans causes potato late blight, and as a potato and tomato specialist pathogen, is seemingly poorly adapted to infect plants outside the Solanaceae. Here, we report the unexpected finding that P. infestans can infect Arabidopsis thaliana when another oomycete pathogen, Albugo laibachii, has colonized the host plant. The behaviour and speed of P. infestans infection in Arabidopsis pre-infected with A. laibachii resemble P. infestans infection of susceptible potato plants. Transcriptional profiling of P. infestans genes during infection revealed a significant overlap in the sets of secreted-protein genes that are induced in P. infestans upon colonization of potato and susceptible Arabidopsis, suggesting major similarities in P. infestans gene expression dynamics on the two plant species. Furthermore, we found haustoria of A. laibachii and P. infestans within the same Arabidopsis cells. This Arabidopsis-A. laibachii-P. infestans tripartite interaction opens up various possibilities to dissect the molecular mechanisms of P. infestans infection and the processes occurring in co-infected Arabidopsis cells.
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Affiliation(s)
- Khaoula Belhaj
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
| | - Liliana M. Cano
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
- University of FloridaDepartment of Plant Pathology, Indian River Research and Education CenterFort PierceUSA
| | - David C. Prince
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
- School of Biological SciencesUniversity of East AngliaNorwichUnited Kingdom
| | - Ariane Kemen
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
- Max Planck Institute for Plant Breeding ResearchCologneGermany
| | - Kentaro Yoshida
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
- Organization of Advanced Science and TechnologyKobe UniversityKobeHyogoJapan
| | - Yasin F. Dagdas
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
| | - Graham J. Etherington
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
- The Genome Analysis CentreNorwich Research ParkNorwichUnited Kingdom
| | - Henk‐jan Schoonbeek
- John Innes CentreDepartment of Crop Genetics, Norwich Research ParkNorwichUnited Kingdom
| | | | | | - Sophien Kamoun
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
| | - Sebastian Schornack
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
- Sainsbury LaboratoryUniversity of CambridgeCambridgeUnited Kingdom
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39
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Interspecific hybridization impacts host range and pathogenicity of filamentous microbes. Curr Opin Microbiol 2016; 32:7-13. [DOI: 10.1016/j.mib.2016.04.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/30/2016] [Accepted: 04/08/2016] [Indexed: 11/24/2022]
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40
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Ruhe J, Agler MT, Placzek A, Kramer K, Finkemeier I, Kemen EM. Obligate Biotroph Pathogens of the Genus Albugo Are Better Adapted to Active Host Defense Compared to Niche Competitors. FRONTIERS IN PLANT SCIENCE 2016; 7:820. [PMID: 27379119 PMCID: PMC4913113 DOI: 10.3389/fpls.2016.00820] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/25/2016] [Indexed: 05/23/2023]
Abstract
Recent research suggested that plants behave differently under combined versus single abiotic and biotic stress conditions in controlled environments. While this work has provided a glimpse into how plants might behave under complex natural conditions, it also highlights the need for field experiments using established model systems. In nature, diverse microbes colonize the phyllosphere of Arabidopsis thaliana, including the obligate biotroph oomycete genus Albugo, causal agent of the common disease white rust. Biotrophic, as well as hemibiotrophic plant pathogens are characterized by efficient suppression of host defense responses. Lab experiments have even shown that Albugo sp. can suppress non-host resistance, thereby enabling otherwise avirulent pathogen growth. We asked how a pathogen that is vitally dependent on a living host can compete in nature for limited niche space while paradoxically enabling colonization of its host plant for competitors? To address this question, we used a proteomics approach to identify differences and similarities between lab and field samples of Albugo sp.-infected and -uninfected A. thaliana plants. We could identify highly similar apoplastic proteomic profiles in both infected and uninfected plants. In wild plants, however, a broad range of defense-related proteins were detected in the apoplast regardless of infection status, while no or low levels of defense-related proteins were detected in lab samples. These results indicate that Albugo sp. do not strongly affect immune responses and leave distinct branches of the immune signaling network intact. To validate our findings and to get mechanistic insights, we tested a panel of A. thaliana mutant plants with induced or compromised immunity for susceptibility to different biotrophic pathogens. Our findings suggest that the biotroph pathogen Albugo selectively interferes with host defense under different environmental and competitive pressures to maintain its ecological niche dominance. Adaptation to host immune responses while maintaining a partially active host immunity seems advantageous against competitors. We suggest a model for future research that considers not only host-microbe but in addition microbe-microbe and microbe-host environment factors.
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Affiliation(s)
- Jonas Ruhe
- Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Matthew T. Agler
- Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Katharina Kramer
- Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Iris Finkemeier
- Max Planck Institute for Plant Breeding ResearchCologne, Germany
- Institute of Plant Biology and Biotechnology, University of MuensterMünster, Germany
| | - Eric M. Kemen
- Max Planck Institute for Plant Breeding ResearchCologne, Germany
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41
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Chappell TM, Rausher MD. Evolution of host range in Coleosporium ipomoeae, a plant pathogen with multiple hosts. Proc Natl Acad Sci U S A 2016; 113:5346-51. [PMID: 27114547 PMCID: PMC4868424 DOI: 10.1073/pnas.1522997113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plants and their pathogens coevolve locally. Previous investigations of one host-one pathogen systems have demonstrated that natural selection favors pathogen genotypes that are virulent on a broad range of host genotypes. In the present study, we examine a system consisting of one pathogen species that infects three host species in the morning glory genus Ipomoea. We show that many pathogen genotypes can infect two or three of the host species when tested on plants from nonlocal communities. By contrast, pathogen genotypes are highly host-specific, infecting only one host species, when tested on host species from the local community. This pattern indicates that within-community evolution narrows the host breadth of pathogen genotypes. Possible evolutionary mechanisms include direct selection for narrow host breadth due to costs of virulence and evolution of ipomoea resistance in the host species.
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Affiliation(s)
| | - Mark D Rausher
- Department of Biology, Duke University, Durham, NC 27708
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42
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Buckley J, Kilbride E, Cevik V, Vicente JG, Holub EB, Mable BK. R-gene variation across Arabidopsis lyrata subspecies: effects of population structure, selection and mating system. BMC Evol Biol 2016; 16:93. [PMID: 27150007 PMCID: PMC4858910 DOI: 10.1186/s12862-016-0665-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/23/2016] [Indexed: 11/10/2022] Open
Abstract
Background Examining allelic variation of R-genes in closely related perennial species of Arabidopsis thaliana is critical to understanding how population structure and ecology interact with selection to shape the evolution of innate immunity in plants. We finely sampled natural populations of Arabidopsis lyrata from the Great Lakes region of North America (A. l. lyrata) and broadly sampled six European countries (A. l. petraea) to investigate allelic variation of two R-genes (RPM1 and WRR4) and neutral genetic markers (Restriction Associated DNA sequences and microsatellites) in relation to mating system, phylogeographic structure and subspecies divergence. Results Fine-scale sampling of populations revealed strong effects of mating system and population structure on patterns of polymorphism for both neutral loci and R-genes, with no strong evidence for selection. Broad geographic sampling revealed evidence of balancing selection maintaining polymorphism in R-genes, with elevated heterozygosity and diversity compared to neutral expectations and sharing of alleles among diverged subspecies. Codon-based tests detected both positive and purifying selection for both R-genes, as commonly found for animal immune genes. Conclusions Our results highlight that combining fine and broad-scale sampling strategies can reveal the multiple factors influencing polymorphism and divergence at potentially adaptive genes such as R-genes. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0665-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James Buckley
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK. .,Current address: Center for Adaptation to a Changing Environment, ETH Zurich, Zurich, 8092, Switzerland.
| | - Elizabeth Kilbride
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Volkan Cevik
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, CV359EF, UK.,Current address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR47UH, UK
| | - Joana G Vicente
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, CV359EF, UK
| | - Eric B Holub
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, CV359EF, UK
| | - Barbara K Mable
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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43
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Svensson O, Smith A, García-Alonso J, van Oosterhout C. Hybridization generates a hopeful monster: a hermaphroditic selfing cichlid. ROYAL SOCIETY OPEN SCIENCE 2016; 3:150684. [PMID: 27069660 PMCID: PMC4821271 DOI: 10.1098/rsos.150684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/18/2016] [Indexed: 06/05/2023]
Abstract
Compared with other phylogenetic groups, self-fertilization (selfing) is exceedingly rare in vertebrates and is known to occur only in one small clade of fishes. Here we report observing one F1-hybrid individual that developed into a functional hermaphrodite after crossing two closely-related sexually reproducing species of cichlids. Microsatellite alleles segregated consistent with selfing and Mendelian inheritance and we could rule out different modes of parthenogenesis including automixis. We discuss why selfing is not more commonly observed in vertebrates in nature, and the role of hybridization in the evolution of novel traits.
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Affiliation(s)
- Ola Svensson
- School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, UK
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, Gothenburg 405 30, Sweden
| | - Alan Smith
- School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, UK
| | - Javier García-Alonso
- School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, UK
- Biodiversity Group, Centro Universitario Regional Este, Universidad de la República, Maldonado 20000, Uruguay
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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44
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Stukenbrock EH. The Role of Hybridization in the Evolution and Emergence of New Fungal Plant Pathogens. PHYTOPATHOLOGY 2016; 106:104-12. [PMID: 26824768 DOI: 10.1094/phyto-08-15-0184-rvw] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Hybridization in fungi has recently been recognized as a major force in the generation of new fungal plant pathogens. These include the grass pathogen Zymoseptoria pseudotritici and the powdery mildew pathogen Blumeria graminis triticale of triticale. Hybridization also plays an important role in the transfer of genetic material between species. This process is termed introgressive hybridization and involves extensive backcrossing between hybrid and the parental species. Introgressive hybridization has contributed substantially to the successful spread of plant pathogens such as Ophiostoma ulmi and O. novo-ulmi, the causal agents of Dutch elm disease, and other tree pathogens such as the rust pathogen Melampsora. Hybridization occurs more readily between species that have previously not coexisted, so-called allopatric species. Reproductive barriers between allopatric species are likely to be more permissive allowing interspecific mating to occur. The bringing together of allopatric species of plant pathogens by global agricultural trade consequently increases the potential for hybridization between pathogen species. In light of global environmental changes, agricultural development, and the facilitated long-distance spread of fungal plant pathogens, hybridization should be considered an important mechanism whereby new pathogens may emerge. Recent studies have gained insight into the genetics and biology of fungal hybrids. Here I summarize current knowledge about hybrid speciation and introgressive hybridization. I propose that future studies will benefit greatly from the availability of large genome data sets and that genome data provide a powerful resource in combination with experimental approaches for analyses of hybrid species.
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Affiliation(s)
- Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 9-11, 24118 Kiel, Germany and Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
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Agler MT, Ruhe J, Kroll S, Morhenn C, Kim ST, Weigel D, Kemen EM. Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation. PLoS Biol 2016; 14:e1002352. [PMID: 26788878 PMCID: PMC4720289 DOI: 10.1371/journal.pbio.1002352] [Citation(s) in RCA: 619] [Impact Index Per Article: 77.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/08/2015] [Indexed: 12/15/2022] Open
Abstract
Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe–microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe–microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial “hubs,” are strongly interconnected and have a severe effect on communities. By documenting these microbe–microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on “hub” microbes, which, via microbe–microbe interactions, transmit the effects to the microbial community. We analyzed two “hub” microbes (the obligate biotrophic oomycete pathogen Albugo and the basidiomycete yeast fungus Dioszegia) more closely. Albugo had strong effects on epiphytic and endophytic bacterial colonization. Specifically, alpha diversity decreased and beta diversity stabilized in the presence of Albugo infection, whereas they otherwise varied between plants. Dioszegia, on the other hand, provided evidence for direct hub interaction with phyllosphere bacteria. The identification of microbial “hubs” and their importance in phyllosphere microbiome structuring has crucial implications for plant–pathogen and microbe–microbe research and opens new entry points for ecosystem management and future targeted biocontrol. The revelation that effects can cascade through communities via “hub” microbes is important to understand community structure perturbations in parallel fields including human microbiomes and bioprocesses. In particular, parallels to human microbiome “keystone” pathogens and microbes open new avenues of interdisciplinary research that promise to better our understanding of functions of host-associated microbiomes. Microbial interactions between kingdoms are responsible for significant microbiome variation on the surface of plants. Highly connected microbes are most important, amplifying abiotic and host factors to cause large perturbations in the structure of microbial communities. Under natural conditions, plant growth and behavior strongly depend on associated microbial communities called the microbiome. Much research has been performed to evaluate how the environment and plant genes help to determine the structure of the microbiome. Here, we show that interactions between microorganisms on plants can be responsible for large portions of observed microbial community structures on leaves. Importantly, particular microbes, termed “hub microbes” due to their central position in a microbial network, are disproportionally important in shaping microbial communities on plant hosts. We discovered fungal and oomycete hub microbes that act by suppressing the growth and diversity of other microbes—even across kingdoms—and several candidate bacterial hubs, which largely positively control the abundance of other bacteria. We also showed that factors impacting the microbial community—such as plant genotype—are strongest if they affect colonization of a hub microbe because the hub in turn affects colonization by many other microbes. Our results further suggest that hub microbes interact directly or via the microbial community. Hub microbes are thus promising targets for better understanding the effects of host genomic engineering and for future work in controlling disease-associated and beneficial host-associated microbial communities.
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Affiliation(s)
- Matthew T. Agler
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jonas Ruhe
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Samuel Kroll
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Sang-Tae Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eric M. Kemen
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- * E-mail:
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Tollenaere C, Susi H, Laine AL. Evolutionary and Epidemiological Implications of Multiple Infection in Plants. TRENDS IN PLANT SCIENCE 2016; 21:80-90. [PMID: 26651920 DOI: 10.1016/j.tplants.2015.10.014] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 10/02/2015] [Accepted: 10/20/2015] [Indexed: 05/04/2023]
Abstract
Recent methodological advances have uncovered tremendous microbial diversity cohabiting in the same host plant, and many of these microbes cause disease. In this review we highlight how the presence of other pathogen species, or other pathogen genotypes, within a plant can affect key components of host-pathogen interactions: (i) within-plant virulence and pathogen accumulation, through direct and host-mediated mechanisms; (ii) evolutionary trajectories of pathogen populations, through virulence evolution, generation of novel genetic combinations, and maintenance of genetic diversity; and (iii) disease dynamics, with multiple infection likely to render epidemics more devastating. The major future challenges are to couple a community ecology approach with a molecular investigation of the mechanisms operating under coinfection and to evaluate the evolution and effectiveness of resistance within a coinfection framework.
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Affiliation(s)
- Charlotte Tollenaere
- Interactions Plantes-Microorganismes et Environnement (IPME), Institut de Recherches pour le Développement (IRD) - Cirad - Université de Montpellier, 34394 Montpellier, France; Laboratoire Mixte International Patho-Bios, IRD-INERA (Institut de l'Environnement et de Recherches Agricoles), BP171, Bobo-Dioulasso, Burkina Faso
| | - Hanna Susi
- Metapopulation Research Centre, Department of Biosciences, PO Box 65 (Viikinkaari 1), FI-00014 University of Helsinki, Helsinki, Finland
| | - Anna-Liisa Laine
- Metapopulation Research Centre, Department of Biosciences, PO Box 65 (Viikinkaari 1), FI-00014 University of Helsinki, Helsinki, Finland.
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Ward BJ, van Oosterhout C. HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data. Mol Ecol Resour 2015; 16:534-9. [PMID: 26394708 DOI: 10.1111/1755-0998.12469] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 09/09/2015] [Accepted: 09/16/2015] [Indexed: 11/29/2022]
Abstract
HYBRIDCHECK is a software package to visualize the recombination signal in large DNA sequence data set, and it can be used to analyse recombination, genetic introgression, hybridization and horizontal gene transfer. It can scan large (multiple kb) contigs and whole-genome sequences of three or more individuals. HYBRIDCHECK is written in the r software for OS X, Linux and Windows operating systems, and it has a simple graphical user interface. In addition, the r code can be readily incorporated in scripts and analysis pipelines. HYBRIDCHECK implements several ABBA-BABA tests and visualizes the effects of hybridization and the resulting mosaic-like genome structure in high-density graphics. The package also reports the following: (i) the breakpoint positions, (ii) the number of mutations in each introgressed block, (iii) the probability that the identified region is not caused by recombination and (iv) the estimated age of each recombination event. The divergence times between the donor and recombinant sequence are calculated using a JC, K80, F81, HKY or GTR correction, and the dating algorithm is exceedingly fast. By estimating the coalescence time of introgressed blocks, it is possible to distinguish between hybridization and incomplete lineage sorting. HYBRIDCHECK is libré software and it and its manual are free to download from http://ward9250.github.io/HybridCheck/.
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Affiliation(s)
- Ben J Ward
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, Norwich, NR4 7TJ, UK
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Jouet A, McMullan M, van Oosterhout C. The effects of recombination, mutation and selection on the evolution of the Rp1 resistance genes in grasses. Mol Ecol 2015; 24:3077-92. [PMID: 25907026 DOI: 10.1111/mec.13213] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 03/25/2015] [Accepted: 04/09/2015] [Indexed: 01/30/2023]
Abstract
Plant immune genes, or resistance genes, are involved in a co-evolutionary arms race with a diverse range of pathogens. In agronomically important grasses, such R genes have been extensively studied because of their role in pathogen resistance and in the breeding of resistant cultivars. In this study, we evaluate the importance of recombination, mutation and selection on the evolution of the R gene complex Rp1 of Sorghum, Triticum, Brachypodium, Oryza and Zea. Analyses show that recombination is widespread, and we detected 73 independent instances of sequence exchange, involving on average 1567 of 4692 nucleotides analysed (33.4%). We were able to date 24 interspecific recombination events and found that four occurred postspeciation, which suggests that genetic introgression took place between different grass species. Other interspecific events seemed to have been maintained over long evolutionary time, suggesting the presence of balancing selection. Significant positive selection (i.e. a relative excess of nonsynonymous substitutions (dN /dS >1)) was detected in 17-95 codons (0.42-2.02%). Recombination was significantly associated with areas with high levels of polymorphism but not with an elevated dN /dS ratio. Finally, phylogenetic analyses show that recombination results in a general overestimation of the divergence time (mean = 14.3%) and an alteration of the gene tree topology if the tree is not calibrated. Given that the statistical power to detect recombination is determined by the level of polymorphism of the amplicon as well as the number of sequences analysed, it is likely that many studies have underestimated the importance of recombination relative to the mutation rate.
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Affiliation(s)
- Agathe Jouet
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mark McMullan
- The Genome Analysis Center, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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