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Molloy B, Shin DS, Long J, Pellegrin C, Senatori B, Vieira P, Thorpe PJ, Damm A, Ahmad M, Vermeulen K, Derevnina L, Wei S, Sperling A, Reyes Estévez E, Bruty S, de Souza VHM, Kranse OP, Maier T, Baum T, Eves-van den Akker S. The origin, deployment, and evolution of a plant-parasitic nematode effectorome. PLoS Pathog 2024; 20:e1012395. [PMID: 39074142 PMCID: PMC11309470 DOI: 10.1371/journal.ppat.1012395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 08/08/2024] [Accepted: 07/05/2024] [Indexed: 07/31/2024] Open
Abstract
Plant-parasitic nematodes constrain global food security. During parasitism, they secrete effectors into the host plant from two types of pharyngeal gland cells. These effectors elicit profound changes in host biology to suppress immunity and establish a unique feeding organ from which the nematode draws nutrition. Despite the importance of effectors in nematode parasitism, there has been no comprehensive identification and characterisation of the effector repertoire of any plant-parasitic nematode. To address this, we advance techniques for gland cell isolation and transcriptional analysis to define a stringent annotation of putative effectors for the cyst nematode Heterodera schachtii at three key life-stages. We define 717 effector gene loci: 269 "known" high-confidence homologs of plant-parasitic nematode effectors, and 448 "novel" effectors with high gland cell expression. In doing so we define the most comprehensive "effectorome" of a plant-parasitic nematode to date. Using this effector definition, we provide the first systems-level understanding of the origin, deployment and evolution of a plant-parasitic nematode effectorome. The robust identification of the effector repertoire of a plant-parasitic nematode will underpin our understanding of nematode pathology, and hence, inform strategies for crop protection.
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Affiliation(s)
- Beth Molloy
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Dio S. Shin
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan Long
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Clement Pellegrin
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Beatrice Senatori
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Paulo Vieira
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture—Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Peter J. Thorpe
- The Data Analysis Group, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Anika Damm
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Mariam Ahmad
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Kerry Vermeulen
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Lida Derevnina
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Siyuan Wei
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alexis Sperling
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Estefany Reyes Estévez
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Samuel Bruty
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Victor Hugo Moura de Souza
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Olaf Prosper Kranse
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Tom Maier
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Thomas Baum
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, Iowa, United States of America
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Talbi N, Blekemolen MC, Janevska S, Zendler D, van Tilbeurgh H, Fudal I, Takken FLW. Facilitation of Symplastic Effector Protein Mobility by Paired Effectors Is Conserved in Different Classes of Fungal Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:304-314. [PMID: 37782126 DOI: 10.1094/mpmi-07-23-0103-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
It has been discovered that plant pathogens produce effectors that spread via plasmodesmata (PD) to allow modulation of host processes in distal uninfected cells. Fusarium oxysporum f. sp. lycopersici (Fol) facilitates effector translocation by expansion of the size-exclusion limit of PD using the Six5/Avr2 effector pair. How other fungal pathogens manipulate PD is unknown. We recently reported that many fungal pathogens belonging to different families carry effector pairs that resemble the SIX5/AVR2 gene pair from Fol. Here, we performed structural predictions of three of these effector pairs from Leptosphaeria maculans (Lm) and tested their ability to manipulate PD and to complement the virulence defect of a Fol SIX5 knockout mutant. We show that the AvrLm10A homologs are structurally related to FolSix5 and localize at PD when they are expressed with their paired effectors. Furthermore, these effectors were found to complement FolSix5 function in cell-to-cell mobility assays and in fungal virulence. We conclude that distantly related fungal species rely on structurally related paired effector proteins to manipulate PD and facilitate effector mobility. The wide distribution of these effector pairs implies Six5-mediated effector translocation to be a conserved propensity among fungal plant pathogens. [Formula: see text] Copyright © 2024 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)
- Nacera Talbi
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Mila C Blekemolen
- Molecular Plant Pathology, Swammerdam Institute of Life Science (SILS), University of Amsterdam, Amsterdam, the Netherlands
| | - Slavica Janevska
- Molecular Plant Pathology, Swammerdam Institute of Life Science (SILS), University of Amsterdam, Amsterdam, the Netherlands
| | - Daniel Zendler
- Molecular Plant Pathology, Swammerdam Institute of Life Science (SILS), University of Amsterdam, Amsterdam, the Netherlands
| | - Herman van Tilbeurgh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Frank L W Takken
- Molecular Plant Pathology, Swammerdam Institute of Life Science (SILS), University of Amsterdam, Amsterdam, the Netherlands
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Molloy B, Baum T, Eves-van den Akker S. Unlocking the development- and physiology-altering 'effector toolbox' of plant-parasitic nematodes. Trends Parasitol 2023; 39:732-738. [PMID: 37438213 DOI: 10.1016/j.pt.2023.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023]
Abstract
Plant parasites take advantage of host developmental plasticity to elicit profound developmental and physiological changes. In the case of plant-parasitic nematodes (PPNs), these changes can result in the development of new plant organs. Despite the importance of the development- and physiology-altering abilities of these parasites in pathology, research has historically focused on their abilities to suppress immunity. We argue that, given the dramatic changes involved in feeding site establishment, it is entirely possible that development- and physiology-altering abilities of PPNs may, in fact, dominate effector repertoires - highlighting the need for novel high-throughput screens for development- and physiology-altering 'tools'. Uncovering this portion of the nematode 'toolbox' can enable biotechnology, enhance crop protection, and shed light on fundamental host biology itself.
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Affiliation(s)
- Beth Molloy
- Department of Plant Sciences - Crop Science Centre, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Thomas Baum
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA, USA
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4
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Kumar A, Fitoussi N, Sanadhya P, Sichov N, Bucki P, Bornstein M, Belausuv E, Brown Miyara S. Two Candidate Meloidogyne javanica Effector Genes, MjShKT and MjPUT3: A Functional Investigation of Their Roles in Regulating Nematode Parasitism. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:79-94. [PMID: 36324054 DOI: 10.1094/mpmi-10-22-0212-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
During parasitism, root-knot nematode Meloidogyne spp. inject molecules termed effectors that have multifunctional roles in construction and maintenance of nematode feeding sites. As an outcome of transcriptomic analysis of Meloidogyne javanica, we identified and characterized two differentially expressed genes encoding the predicted proteins MjShKT, carrying a Stichodactyla toxin (ShKT) domain, and MjPUT3, carrying a ground-like domain, both expressed during nematode parasitism of the tomato plant. Fluorescence in-situ hybridization revealed expression of MjShKT and MjPUT3 in the dorsal esophageal glands, suggesting their injection into host cells. MjShKT expression was upregulated during the parasitic life stages, to a maximum at the mature female stage, whereas MjPUT3 expression increased in third- to fourth-stage juveniles. Subcellular in-planta localization of MjShKT and MjPUT3 using a fused fluorescence marker indicated MjShKT co-occurrence with the endoplasmic reticulum, the perinuclear endoplasmatic reticulum, and the Golgi organelle markers, while MjPUT3 localized, to some extent, within the endoplasmatic reticulum and was clearly observed within the nucleoplasm. MjShKT inhibited programmed cell death induced by overexpression of MAPKKKα and Gpa2/RBP-1. Overexpression of MjShKT in tomato hairy roots allowed an increase in nematode reproduction, as indicated by the high number of eggs produced on roots overexpressing MjShKT. Roots overexpressing MjPUT3 were characterized by enhanced root growth, with no effect on nematode development on those roots. Investigation of the two candidate effectors suggested that MjShKT is mainly involved in manipulating the plant effector-triggered immune response toward establishment and maintenance of active feeding sites, whereas MjPUT3 might modulate roots morphology in favor of nematode fitness in the host roots. [Formula: see text] Copyright © 2023 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)
- Anil Kumar
- Department of Entomology, Nematology and Chemistry units, Agricultural Research Organization (ARO), Volcani Center, Bet Dagan 50250, Israel
| | - Nathalia Fitoussi
- Department of Entomology, Nematology and Chemistry units, Agricultural Research Organization (ARO), Volcani Center, Bet Dagan 50250, Israel
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Payal Sanadhya
- Department of Entomology, Nematology and Chemistry units, Agricultural Research Organization (ARO), Volcani Center, Bet Dagan 50250, Israel
| | - Natalia Sichov
- Department of Entomology, Nematology and Chemistry units, Agricultural Research Organization (ARO), Volcani Center, Bet Dagan 50250, Israel
| | - Patricia Bucki
- Department of Entomology, Nematology and Chemistry units, Agricultural Research Organization (ARO), Volcani Center, Bet Dagan 50250, Israel
| | - Menachem Bornstein
- Department of Plant Pathology and Weed Research, ARO, Volcani Center, Bet Dagan 50250, Israel
| | - Eduard Belausuv
- Department of Plant Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
| | - Sigal Brown Miyara
- Department of Entomology, Nematology and Chemistry units, Agricultural Research Organization (ARO), Volcani Center, Bet Dagan 50250, Israel
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Streptomyces hydrogenans strain DH-16 alleviates negative impact of Meloidogyne incognita stress by modifying physio-biochemical attributes in Solanum lycopersicum plants. Sci Rep 2022; 12:15214. [PMID: 36076057 PMCID: PMC9458671 DOI: 10.1038/s41598-022-19636-0] [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: 11/19/2021] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
The current study assessed the nematicidal and plant growth promoting potential of metabolites produced by Streptomyces hydrogenans strain DH-16 on morphological and physiological activities in 60 days old Solanum lycopersicum plants grown under Meloidogyne incognita stress. M. incognita infestation altered the levels of various photosynthetic pigments, various stress markers, enzymatic and non-enzymatic antioxidants in S. lycopersicum plants grown under in-vivo conditions. However, treatment with culture cells, supernatant and extract produced by S. hydrogenans strain DH-16 significantly reduced the number of galls in M. incognita infested plants when compared with untreated M. incognita infected plants. Moreover, the culture cells/ supernatant/ extract remarkably lowered the levels of stress markers (Hydrogen peroxide and Malondialdehyde) in infected plants and enhanced the activities of non-enzymatic antioxidants (glutathione, tocopherol) and enzymatic antioxidants (Catalase, Superoxide dismutase, Ascorbate peroxidase, Guaiacol peroxidase, Gluatathione-S-transferase and Polyphenol oxidase) in metabolites treated M. incognita infected plants. The enhanced level of different photosynthetic attributes were also evaluated by studying gas exchange parameters and different plant pigments. Moreover, an increment in the content of phenolic compounds such as total phenols, anthocyanin and flavonoids were also reflected in treated and nematode infested plants. The present study also evaluated the microscopic analysis depicting cell viability, nuclear damage and hydrogen peroxide localization in differently treated plants. The outcome of the present study therefore endorses the efficacy of DH-16 as a potential biocontrol agent that help plants in mitigating M. incognita stress.
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Rutter WB, Franco J, Gleason C. Rooting Out the Mechanisms of Root-Knot Nematode-Plant Interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:43-76. [PMID: 35316614 DOI: 10.1146/annurev-phyto-021621-120943] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Root-knot nematodes (RKNs; Meloidogyne spp.) engage in complex parasitic interactions with many different host plants around the world, initiating elaborate feeding sites and disrupting host root architecture. Although RKNs have been the focus of research for many decades, new molecular tools have provided useful insights into the biological mechanisms these pests use to infect and manipulate their hosts. From identifying host defense mechanisms underlying resistance to RKNs to characterizing nematode effectors that alter host cellular functions, the past decade of research has significantly expanded our understanding of RKN-plant interactions, and the increasing number of quality parasite and host genomes promises to enhance future research efforts into RKNs. In this review, we have highlighted recent discoveries, summarized the current understanding within the field, and provided links to new and useful resources for researchers. Our goal is to offer insights and tools to support the study of molecular RKN-plant interactions.
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Affiliation(s)
- William B Rutter
- US Vegetable Laboratory, USDA Agricultural Research Service, Charleston, South Carolina, USA
| | - Jessica Franco
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA;
| | - Cynthia Gleason
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA;
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Eves-van den Akker S. Plant-nematode interactions. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102035. [PMID: 33784578 DOI: 10.1016/j.pbi.2021.102035] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/05/2021] [Accepted: 02/23/2021] [Indexed: 05/27/2023]
Abstract
Plant-parasitic nematodes threaten food security in the developed and developing world. This review looks at the field through a wide lens, aiming to capture a breadth of recent landmark achievements that have changed our understanding of plant-nematode interactions in particular, and plant pathology in general. It recognises the importance of expanding existing paradigms in plant-pathology to encompass plant-nematode interactions and, at the same time, celebrates achievements that build on the uniqueness of the system. It highlights emerging areas of plant nematology. Finally, it argues that the accelerated progress of recent years is prophetic, and that cumulative advances in our understanding, coupled with technological advances in genetic engineering of plants and nematodes, promise to lift perennial constraints on the field and thereby further expedite progress.
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Kranse O, Beasley H, Adams S, Pires-daSilva A, Bell C, Lilley CJ, Urwin PE, Bird D, Miska E, Smant G, Gheysen G, Jones J, Viney M, Abad P, Maier TR, Baum TJ, Siddique S, Williamson V, Akay A, Eves-van den Akker S. Toward genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles. G3-GENES GENOMES GENETICS 2021; 11:6135037. [PMID: 33585878 PMCID: PMC8022973 DOI: 10.1093/g3journal/jkaa058] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/30/2020] [Indexed: 12/16/2022]
Abstract
Plant-parasitic nematodes are a continuing threat to food security, causing an estimated 100 billion USD in crop losses each year. The most problematic are the obligate sedentary endoparasites (primarily root knot nematodes and cyst nematodes). Progress in understanding their biology is held back by a lack of tools for functional genetics: forward genetics is largely restricted to studies of natural variation in populations and reverse genetics is entirely reliant on RNA interference. There is an expectation that the development of functional genetic tools would accelerate the progress of research on plant-parasitic nematodes, and hence the development of novel control solutions. Here, we develop some of the foundational biology required to deliver a functional genetic tool kit in plant-parasitic nematodes. We characterize the gonads of male Heterodera schachtii and Meloidogyne hapla in the context of spermatogenesis. We test and optimize various methods for the delivery, expression, and/or detection of exogenous nucleic acids in plant-parasitic nematodes. We demonstrate that delivery of macromolecules to cyst and root knot nematode male germlines is difficult, but possible. Similarly, we demonstrate the delivery of oligonucleotides to root knot nematode gametes. Finally, we develop a transient expression system in plant-parasitic nematodes by demonstrating the delivery and expression of exogenous mRNA encoding various reporter genes throughout the body of H. schachtii juveniles using lipofectamine-based transfection. We anticipate these developments to be independently useful, will expedite the development of genetic modification tools for plant-parasitic nematodes, and ultimately catalyze research on a group of nematodes that threaten global food security.
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Affiliation(s)
- Olaf Kranse
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Helen Beasley
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Sally Adams
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Christopher Bell
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Catherine J Lilley
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Peter E Urwin
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David Bird
- Entomology and Plant Pathology, NC State University, Raleigh, NC 27695-7613, USA
| | - Eric Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, UK
| | - Geert Smant
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Godelieve Gheysen
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - John Jones
- Cell & Molecular Sciences Department, The James Hutton Institute, Dundee, DD2 5DA, UK.,School of Biology, Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - Mark Viney
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Pierre Abad
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Thomas R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Shahid Siddique
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Valerie Williamson
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Alper Akay
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Genome Expression Dynamics Reveal the Parasitism Regulatory Landscape of the Root-Knot Nematode Meloidogyne incognita and a Promoter Motif Associated with Effector Genes. Genes (Basel) 2021; 12:genes12050771. [PMID: 34070210 PMCID: PMC8158474 DOI: 10.3390/genes12050771] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 12/21/2022] Open
Abstract
Root-knot nematodes (genus Meloidogyne) are the major contributor to crop losses caused by nematodes. These nematodes secrete effector proteins into the plant, derived from two sets of pharyngeal gland cells, to manipulate host physiology and immunity. Successful completion of the life cycle, involving successive molts from egg to adult, covers morphologically and functionally distinct stages and will require precise control of gene expression, including effector genes. The details of how root-knot nematodes regulate transcription remain sparse. Here, we report a life stage-specific transcriptome of Meloidogyne incognita. Combined with an available annotated genome, we explore the spatio-temporal regulation of gene expression. We reveal gene expression clusters and predicted functions that accompany the major developmental transitions. Focusing on effectors, we identify a putative cis-regulatory motif associated with expression in the dorsal glands, providing an insight into effector regulation. We combine the presence of this motif with several other criteria to predict a novel set of putative dorsal gland effectors. Finally, we show this motif, and thereby its utility, is broadly conserved across the Meloidogyne genus, and we name it Mel-DOG. Taken together, we provide the first genome-wide analysis of spatio-temporal gene expression in a root-knot nematode and identify a new set of candidate effector genes that will guide future functional analyses.
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10
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Price JA, Coyne D, Blok VC, Jones JT. Potato cyst nematodes Globodera rostochiensis and G. pallida. MOLECULAR PLANT PATHOLOGY 2021; 22:495-507. [PMID: 33709540 PMCID: PMC8035638 DOI: 10.1111/mpp.13047] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 05/12/2023]
Abstract
TAXONOMY Phylum Nematoda; class Chromadorea; order Rhabditida; suborder Tylenchina; infraorder Tylenchomorpha; superfamily Tylenchoidea; family Heteroderidae; subfamily Heteroderinae; Genus Globodera. BIOLOGY Potato cyst nematodes (PCN) are biotrophic, sedentary endoparasitic nematodes. Invasive (second) stage juveniles (J2) hatch from eggs in response to the presence of host root exudates and subsequently locate and invade the host. The nematodes induce the formation of a large, multinucleate syncytium in host roots, formed by fusion of up to 300 root cell protoplasts. The nematodes rely on this single syncytium for the nutrients required to develop through a further three moults to the adult male or female stage. This extended period of biotrophy-between 4 and 6 weeks in total-is almost unparalleled in plant-pathogen interactions. Females remain at the root while adult males revert to the vermiform body plan of the J2 and leave the root to locate and fertilize the female nematodes. The female body forms a cyst that contains the next generation of eggs. HOST RANGE The host range of PCN is limited to plants of the Solanaceae family. While the most economically important hosts are potato (Solanum tuberosum), tomato (Solanum lycopersicum), and aubergine (Solanum melongena), over 170 species of Solanaceae are thought to be potential hosts for PCN (Sullivan et al., 2007). DISEASE SYMPTOMS Symptoms are similar to those associated with nutrient deficiency, such as stunted growth, yellowing of leaves and reduced yields. This absence of specific symptoms reduces awareness of the disease among growers. DISEASE CONTROL Resistance genes (where available in suitable cultivars), application of nematicides, crop rotation. Great effort is put into reducing the spread of PCN through quarantine measures and use of certified seed stocks. USEFUL WEBSITES Genomic information for PCN is accessible through WormBase ParaSite.
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Affiliation(s)
- James A. Price
- School of BiologyBiomedical Sciences Research ComplexUniversity of St AndrewsSt AndrewsUK
- Cell & Molecular Sciences DepartmentThe James Hutton InstituteDundeeUK
| | - Danny Coyne
- International Institute of Tropical Agriculture (IITA)NairobiKenya
| | - Vivian C. Blok
- Cell & Molecular Sciences DepartmentThe James Hutton InstituteDundeeUK
| | - John T. Jones
- School of BiologyBiomedical Sciences Research ComplexUniversity of St AndrewsSt AndrewsUK
- Cell & Molecular Sciences DepartmentThe James Hutton InstituteDundeeUK
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11
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Zheng Q, Putker V, Goverse A. Molecular and Cellular Mechanisms Involved in Host-Specific Resistance to Cyst Nematodes in Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:641582. [PMID: 33767723 PMCID: PMC7986850 DOI: 10.3389/fpls.2021.641582] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/16/2021] [Indexed: 05/17/2023]
Abstract
Cyst nematodes are able to infect a wide range of crop species and are regarded as a major threat in crop production. In response to invasion of cyst nematodes, plants activate their innate immune system to defend themselves by conferring basal and host-specific defense responses depending on the plant genotype. Basal defense is dependent on the detection of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs), while host-specific defense mainly relies on the activation of canonical and non-canonical resistance (R) genes or quantitative trait loci (QTL). Currently, application of R genes and QTLs in crop species is a major approach to control cyst nematode in crop cultivation. However, emerging virulent cyst nematode field populations are threatening crop production due to host genetic selection by the application of a limited set of resistance genes in current crop cultivars. To counteract this problem, increased knowledge about the mechanisms involved in host-specific resistance mediated by R genes and QTLs to cyst nematodes is indispensable to improve their efficient and sustainable use in field crops. Despite the identification of an increasing number of resistance traits to cyst nematodes in various crops, the underlying genes and defense mechanisms are often unknown. In the last decade, indebt studies on the functioning of a number of cyst nematode R genes and QTLs have revealed novel insights in how plants respond to cyst nematode infection by the activation of host-specific defense responses. This review presents current knowledge of molecular and cellular mechanisms involved in the recognition of cyst nematodes, the activation of defense signaling and resistance response types mediated by R genes or QTLs. Finally, future directions for research are proposed to develop management strategies to better control cyst nematodes in crop cultivation.
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Affiliation(s)
- Qi Zheng
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Vera Putker
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
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12
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Favery B, Dubreuil G, Chen MS, Giron D, Abad P. Gall-Inducing Parasites: Convergent and Conserved Strategies of Plant Manipulation by Insects and Nematodes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2020; 58:1-22. [PMID: 32853101 DOI: 10.1146/annurev-phyto-010820-012722] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Gall-inducing insects and nematodes engage in sophisticated interactions with their host plants. These parasites can induce major morphological and physiological changes in host roots, leaves, and other tissues. Sedentary endoparasitic nematodes, root-knot and cyst nematodes in particular, as well as gall-inducing and leaf-mining insects, manipulate plant development to form unique organs that provide them with food from feeding cells. Sometimes, infected tissues may undergo a developmental switch resulting in the formation of aberrant and spectacular structures (clubs or galls). We describe here the complex interactions between these plant-reprogramming sedentary endoparasites and their infected hosts, focusing on similarities between strategies of plant manipulation. We highlight progress in our understanding of the host plant response to infection and focus on the nematode and insect molecules secreted in planta. We suggest thatlooking at similarities may identify convergent and conserved strategies and shed light on the promise they hold for the development of new management strategies in agriculture and forestry.
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Affiliation(s)
- Bruno Favery
- INRAE, CNRS, Université Côte d'Azur, ISA, F-06600 Sophia-Antipolis, France;
| | - Géraldine Dubreuil
- Institut de Recherche sur la Biologie de l'Insecte, CNRS, Université de Tours, UMR 7261, 37200 Tours, France;
| | - Ming-Shun Chen
- USDA-ARS and Department of Entomology, Kansas State University, Manhattan, Kansas 66506, USA
| | - David Giron
- Institut de Recherche sur la Biologie de l'Insecte, CNRS, Université de Tours, UMR 7261, 37200 Tours, France;
| | - Pierre Abad
- INRAE, CNRS, Université Côte d'Azur, ISA, F-06600 Sophia-Antipolis, France;
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13
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Pokhare SS, Thorpe P, Hedley P, Morris J, Habash SS, Elashry A, Eves-van den Akker S, Grundler FMW, Jones JT. Signatures of adaptation to a monocot host in the plant-parasitic cyst nematode Heterodera sacchari. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1263-1274. [PMID: 32623778 DOI: 10.1111/tpj.14910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/18/2020] [Indexed: 05/03/2023]
Abstract
Interactions between plant-parasitic nematodes and their hosts are mediated by effectors, i.e. secreted proteins that manipulate the plant to the benefit of the pathogen. To understand the role of effectors in host adaptation in nematodes, we analysed the transcriptome of Heterodera sacchari, a cyst nematode parasite of rice (Oryza sativa) and sugarcane (Saccharum officinarum). A multi-gene phylogenetic analysis showed that H. sacchari and the cereal cyst nematode Heterodera avenae share a common evolutionary origin and that they evolved to parasitise monocot plants from a common dicot-parasitic ancestor. We compared the effector repertoires of H. sacchari with those of the dicot parasites Heterodera glycines and Globodera rostochiensis to understand the consequences of this transition. While, in general, effector repertoires are similar between the species, comparing effectors and non-effectors of H. sacchari and G. rostochiensis shows that effectors have accumulated more mutations than non-effectors. Although most effectors show conserved spatiotemporal expression profiles and likely function, some H. sacchari effectors are adapted to monocots. This is exemplified by the plant-peptide hormone mimics, the CLAVATA3/EMBRYO SURROUNDING REGION-like (CLE) effectors. Peptide hormones encoded by H. sacchari CLE effectors are more similar to those from rice than those from other plants, or those from other plant-parasitic nematodes. We experimentally validated the functional significance of these observations by demonstrating that CLE peptides encoded by H. sacchari induce a short root phenotype in rice, whereas those from a related dicot parasite do not. These data provide a functional example of effector evolution that co-occurred with the transition from a dicot-parasitic to a monocot-parasitic lifestyle.
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Affiliation(s)
- Somnath S Pokhare
- Department of Molecular Phytomedicine, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, 53115, Germany
- Crop Protection Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Peter Thorpe
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TZ, UK
| | - Pete Hedley
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Jennifer Morris
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Samer S Habash
- Department of Molecular Phytomedicine, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, 53115, Germany
| | - Abdelnaser Elashry
- Department of Molecular Phytomedicine, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, 53115, Germany
| | | | - Florian M W Grundler
- Department of Molecular Phytomedicine, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, 53115, Germany
| | - John T Jones
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9TZ, UK
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14
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Khanna K, Sharma A, Ohri P, Bhardwaj R, Abd Allah EF, Hashem A, Ahmad P. Impact of Plant Growth Promoting Rhizobacteria in the Orchestration of Lycopersicon esculentum Mill. Resistance to Plant Parasitic Nematodes: A Metabolomic Approach to Evaluate Defense Responses Under Field Conditions. Biomolecules 2019; 9:E676. [PMID: 31683675 PMCID: PMC6920908 DOI: 10.3390/biom9110676] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/21/2019] [Accepted: 10/25/2019] [Indexed: 01/25/2023] Open
Abstract
The present study deals with biological control of Meloidogyne incognita in 45-days old Lycopersicon esculentum, inoculated with Pseudomonas aeruginosa(M1) and Burkholderia gladioli (M2). The improved plant growth and biomass of nematode infested Plant growth promoting rhizobacteria (PGPR) inoculated plants was observed. Remarkable reduction in the numbers of second stage juvenile (J2s), root galls was recorded after treatment of microbes relative to experimental controls. Moreover, the lowered activities of oxidative stress markers (H2O2 (hydrogen peroxide), O2- (superoxide anion), malondialdehyde (MDA)) was estimated in plants after rhizobacterial supplementation. Higher activities of enzymatic (SOD (Superoxide dismutase), POD (Guaiacol peroxidase), CAT (Catalase), GPOX (Glutathione peroxidase), APOX (Ascorbate peroxidase), GST (Glutathione-S-transferase), GR (Glutathione reductase), DHAR (Dehydroascorbate reductase), PPO (Polyphenol oxidase)) and non-enzymatic (glutathione, ascorbic acid, tocopherol) antioxidants were further determined in nematode infected plants following the addition of bacterial strains. The upregulation of photosynthetic activities were depicted by evaluating plant pigments and gas exchange attributes. An increase in the levels of phenolic compounds (total phenols, flavonoids, anthocyanins), osmoprotectants (total osmolytes, carbohydrates, reducing sugars, trehalose, proline, glycine betaine, free amino acids) and organic acids (fumaric, succinic, citric, malic acid) were reflected in infected plants, showing further enhancement after application of biocontrol agents. The study revealed the understanding of plant metabolism, along with the initiative to commercially exploit the biocontrol agents as an alternative to chemical nematicides in infected fields for sustainable agriculture.
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Affiliation(s)
- Kanika Khanna
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India.
| | - Anket Sharma
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India.
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Puja Ohri
- Department of Zoology, Guru Nanak Dev University, Amritsar 143005, India.
| | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India.
| | - Elsayed F Abd Allah
- Department of Plant Production, Faculty of Food & Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia.
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P. O. Box. 2460, Riyadh11451, Saudi Arabia.
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza 12511, Egypt.
| | - Parvaiz Ahmad
- Botany and Microbiology Department, College of Science, King Saud University, P. O. Box. 2460, Riyadh11451, Saudi Arabia.
- Department of Botany, S.P. College, Srinagar, Jammu andKashmir190001, India.
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15
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Transcriptome analysis of Globodera pallida from the susceptible host Solanum tuberosum or the resistant plant Solanum sisymbriifolium. Sci Rep 2019; 9:13256. [PMID: 31519937 PMCID: PMC6744408 DOI: 10.1038/s41598-019-49725-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/30/2019] [Indexed: 12/15/2022] Open
Abstract
A transcriptome analysis of G. pallida juveniles collected from S. tuberosum or S. sisymbriifolium 24 h post infestation was performed to provide insights into the parasitic process of this nematode. A total of 41 G. pallida genes were found to be significantly differentially expressed when parasitizing the two plant species. Among this set, 12 were overexpressed when G. pallida was parasitizing S. tuberosum and 29 were overexpressed when parasitizing S. sisymbriifolium. Out of the 12 genes, three code for secretory proteins; one is homologous to effector gene Rbp-4, the second is an uncharacterized protein with a signal peptide sequence, and the third is an ortholog of a Globodera rostochiensis effector belonging to the 1106 effector family. Other overexpressed genes from G. pallida when parasitizing S. tuberosum were either unknown, associated with a stress or defense response, or associated with sex differentiation. Effector genes namely Eng-1, Cathepsin S-like cysteine protease, cellulase, and two unknown genes with secretory characteristics were over expressed when G. pallida was parasitizing S. sisymbriifolium relative to expression from S. tuberosum. Our findings provide insight into gene regulation of G. pallida while infecting either the trap crop S. sisymbriifolium or the susceptible host, S. tuberosum.
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16
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Vieira P, Gleason C. Plant-parasitic nematode effectors - insights into their diversity and new tools for their identification. CURRENT OPINION IN PLANT BIOLOGY 2019; 50:37-43. [PMID: 30921686 DOI: 10.1016/j.pbi.2019.02.007] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/19/2019] [Accepted: 02/22/2019] [Indexed: 05/20/2023]
Abstract
Plant-parasitic nematodes (PPNs) are a large group of obligate biotrophic pathogens that secrete molecules, called effectors, involved in parasitism. The majority of work in molecular phytonematology has focused on the root-knot and cyst nematodes, which are both sedentary endoparasitic nematodes. More recently, inexpensive sequencing technology has facilitated effector searches in PPNs with different parasitic lifestyles. Work in different PPN species suggests that effectors are diverse, and selection pressure from plant hosts has contributed to the presence of large, expanded effector gene families. The identification of promoter elements/motifs preceding effector gene sequences suggests that promoter analysis can computationally predict new putative effectors. However, until a method of genetic transformation is available for PPNs, work on characterizing effectors will be hindered.
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Affiliation(s)
- Paulo Vieira
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, United States
| | - Cynthia Gleason
- Dept. of Plant Pathology, Washington State University, Pullman, WA 99164, United States.
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17
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Ibrahim HMM, Ahmad EM, Martínez-Medina A, Aly MAM. Effective approaches to study the plant-root knot nematode interaction. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:332-342. [PMID: 31207494 DOI: 10.1016/j.plaphy.2019.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/26/2019] [Accepted: 06/08/2019] [Indexed: 05/24/2023]
Abstract
Plant-parasitic nematodes cause major agricultural losses worldwide. Examining the molecular mechanisms underlying plant-nematode interactions and how plants respond to different invading pathogens is attracting major attention to reduce the expanding gap between agricultural production and the needs of the growing world population. This review summarizes the most recent developments in plant-nematode interactions and the diverse approaches used to improve plant resistance against root knot nematode (RKN). We will emphasize the recent rapid advances in genome sequencing technologies, small interfering RNA techniques (RNAi) and targeted genome editing which are contributing to the significant progress in understanding the plant-nematode interaction mechanisms. Also, molecular approaches to improve plant resistance against nematodes are considered.
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Affiliation(s)
- Heba M M Ibrahim
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt.
| | - Esraa M Ahmad
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Ainhoa Martínez-Medina
- Molecular Interaction Ecology, German Centre for Integrative Biodiversity Research, Leipzig, Germany
| | - Mohammed A M Aly
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
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18
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Mejias J, Truong NM, Abad P, Favery B, Quentin M. Plant Proteins and Processes Targeted by Parasitic Nematode Effectors. FRONTIERS IN PLANT SCIENCE 2019; 10:970. [PMID: 31417587 PMCID: PMC6682612 DOI: 10.3389/fpls.2019.00970] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/11/2019] [Indexed: 05/17/2023]
Abstract
Sedentary endoparasitic nematodes, such as root-knot nematodes (RKN; Meloidogyne spp.) and cyst nematodes (CN; Heterodera spp. and Globodera spp.) cause considerable damage to agricultural crops. RKN and CN spend most of their life cycle in plant roots, in which they induce the formation of multinucleate hypertrophied feeding cells, called "giant cells" and "syncytia," respectively. The giant cells result from nuclear divisions of vascular cells without cytokinesis. They are surrounded by small dividing cells and they form a new organ within the root known as a root knot or gall. CN infection leads to the fusion of several root cells into a unique syncytium. These dramatically modified host cells act as metabolic sinks from which the nematode withdraws nutrients throughout its life, and they are thus essential for nematode development. Both RKN and CN secrete effector proteins that are synthesized in the oesophageal glands and delivered to the appropriate cell in the host plant via a syringe-like stylet, triggering the ontogenesis of the feeding structures. Within the plant cell or in the apoplast, effectors associate with specific host proteins, enabling them to hijack important processes for cell morphogenesis and physiology or immunity. Here, we review recent findings on the identification and functional characterization of plant targets of RKN and CN effectors. A better understanding of the molecular determinants of these biotrophic relationships would enable us to improve the yields of crops infected with parasitic nematodes and to expand our comprehension of root development.
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Affiliation(s)
| | | | | | | | - Michaël Quentin
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut Sophia Agrobiotech, Université Côte d’Azur, Sophia Antipolis, France
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19
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Sabeh M, Lord E, Grenier É, St-Arnaud M, Mimee B. What determines host specificity in hyperspecialized plant parasitic nematodes? BMC Genomics 2019; 20:457. [PMID: 31170914 PMCID: PMC6555003 DOI: 10.1186/s12864-019-5853-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/28/2019] [Indexed: 12/21/2022] Open
Abstract
Background In hyperspecialized parasites, the ability to grow on a particular host relies on specific virulence factors called effectors. These excreted proteins are involved in the molecular mechanisms of parasitism and distinguish virulent pathogens from non-virulent related species. The potato cyst nematodes (PCN) Globodera rostochiensis and G. pallida are major plant-parasitic nematodes developing on numerous solanaceous species including potato. Their close relatives, G. tabacum and G. mexicana are stimulated by potato root diffusate but unable to establish a feeding site on this plant host. Results RNA sequencing was used to characterize transcriptomic differences among these four Globodera species and to identify genes associated with host specificity. We identified seven transcripts that were unique to PCN species, including a protein involved in ubiquitination. We also found 545 genes that were differentially expressed between PCN and non-PCN species, including 78 genes coding for effector proteins, which represent more than a 6-fold enrichment compared to the whole transcriptome. Gene polymorphism analysis identified 359 homozygous non-synonymous variants showing a strong evidence for selection in PCN species. Conclusions Overall, we demonstrated that the determinant of host specificity resides in the regulation of essential effector gene expression that could be under the control of a single or of very few regulatory genes. Such genes are therefore promising targets for the development of novel and more sustainable resistances against potato cyst nematodes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5853-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Sabeh
- St-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, Quebec, Canada.,Biodiversity Center, Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, Montreal, Quebec, Canada
| | - Etienne Lord
- St-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, Quebec, Canada
| | - Éric Grenier
- INRA, UMR1349 IGEPP (Institute of Genetics, Environment and Plant Protection), F-35653, Le Rheu, France
| | - Marc St-Arnaud
- Biodiversity Center, Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, Montreal, Quebec, Canada
| | - Benjamin Mimee
- St-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, Quebec, Canada.
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20
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Espada M, Eves-van den Akker S, Maier T, Vijayapalani P, Baum T, Mota M, Jones JT. STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus. BMC Genomics 2018; 19:553. [PMID: 30053797 PMCID: PMC6062891 DOI: 10.1186/s12864-018-4908-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/29/2018] [Indexed: 11/10/2022] Open
Abstract
Background Plant-parasitic nematodes cause severe damage to a wide range of crop and forest species worldwide. The migratory endoparasitic nematode, Bursaphelenchus xylophilus, (pinewood nematode) is a quarantine pathogen that infects pine trees and has a hugely detrimental economic impact on the forestry industry. Under certain environmental conditions large areas of infected trees can be destroyed, leading to damage on an ecological scale. The interactions of B. xylophilus with plants are mediated by secreted effector proteins produced in the pharyngeal gland cells. Identification of effectors is important to understand mechanisms of parasitism and to develop new control measures for the pathogens. Results Using an approach pioneered in cyst nematodes, we have analysed the promoter regions of a small panel of previously validated pharyngeal gland cell effectors from B. xylophilus to identify an associated putative regulatory promoter motif: STATAWAARS. The presence of STATAWAARS in the promoter region of an uncharacterized gene is a predictor that the corresponding gene encodes a putatively secreted protein, consistent with effector function. Furthermore, we are able to experimentally validate that a subset of STATAWAARS-containing genes are specifically expressed in the pharyngeal glands. Finally, we independently validate the association of STATAWAARS with tissue-specific expression by directly sequencing the mRNA of pharyngeal gland cells. We combine a series of criteria, including STATAWAARS predictions and abundance in the gland cell transcriptome, to generate a comprehensive effector repertoire for B. xylophilus. The genes highlighted by this approach include many previously described effectors and a series of novel “pioneer” effectors. Conclusions We provide a major scientific advance in the area of effector regulation. We identify a novel promoter motif (STATAWAARS) associated with expression in the pharyngeal gland cells. Our data, coupled with those from previous studies, suggest that lineage-specific promoter motifs are a theme of effector regulation in the phylum Nematoda. Electronic supplementary material The online version of this article (10.1186/s12864-018-4908-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Margarida Espada
- NemaLab, ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554, Évora, Portugal.,Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - Tom Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, 50011, USA
| | | | - Thomas Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, 50011, USA
| | - Manuel Mota
- NemaLab, ICAAM - Departamento de Biologia, Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554, Évora, Portugal
| | - John T Jones
- Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK. .,School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9TZ, UK.
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21
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Lilley CJ, Maqbool A, Wu D, Yusup HB, Jones LM, Birch PRJ, Banfield MJ, Urwin PE, Eves-van den Akker S. Effector gene birth in plant parasitic nematodes: Neofunctionalization of a housekeeping glutathione synthetase gene. PLoS Genet 2018; 14:e1007310. [PMID: 29641602 PMCID: PMC5919673 DOI: 10.1371/journal.pgen.1007310] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 04/26/2018] [Accepted: 03/16/2018] [Indexed: 11/24/2022] Open
Abstract
Plant pathogens and parasites are a major threat to global food security. Plant parasitism has arisen four times independently within the phylum Nematoda, resulting in at least one parasite of every major food crop in the world. Some species within the most economically important order (Tylenchida) secrete proteins termed effectors into their host during infection to re-programme host development and immunity. The precise detail of how nematodes evolve new effectors is not clear. Here we reconstruct the evolutionary history of a novel effector gene family. We show that during the evolution of plant parasitism in the Tylenchida, the housekeeping glutathione synthetase (GS) gene was extensively replicated. New GS paralogues acquired multiple dorsal gland promoter elements, altered spatial expression to the secretory dorsal gland, altered temporal expression to primarily parasitic stages, and gained a signal peptide for secretion. The gene products are delivered into the host plant cell during infection, giving rise to "GS-like effectors". Remarkably, by solving the structure of GS-like effectors we show that during this process they have also diversified in biochemical activity, and likely represent the founding members of a novel class of GS-like enzyme. Our results demonstrate the re-purposing of an endogenous housekeeping gene to form a family of effectors with modified functions. We anticipate that our discovery will be a blueprint to understand the evolution of other plant-parasitic nematode effectors, and the foundation to uncover a novel enzymatic function.
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Affiliation(s)
- Catherine J. Lilley
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Abbas Maqbool
- Dept. of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Duqing Wu
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Hazijah B. Yusup
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Laura M. Jones
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Paul R. J. Birch
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mark J. Banfield
- Dept. of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Peter E. Urwin
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sebastian Eves-van den Akker
- Dept. of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
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22
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Eoche-Bosy D, Gautier M, Esquibet M, Legeai F, Bretaudeau A, Bouchez O, Fournet S, Grenier E, Montarry J. Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida. Mol Ecol 2017; 26:4700-4711. [PMID: 28734070 DOI: 10.1111/mec.14240] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 12/30/2022]
Abstract
Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaVvrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole-genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a)virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability.
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Affiliation(s)
- D Eoche-Bosy
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - M Gautier
- CBGP, INRA, IRD, CIRAD, Montpellier SupAgro, Montferrier-sur-Lez, France.,IBC, Montpellier, France
| | - M Esquibet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - F Legeai
- IGEPP, BIPAA, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France.,IRISA, GenScale, INRIA, Rennes, France
| | - A Bretaudeau
- IGEPP, BIPAA, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France.,IRISA, GenOuest COre Facility, INRIA, Rennes, France
| | - O Bouchez
- GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France.,GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - S Fournet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - E Grenier
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - J Montarry
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
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23
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Kikuchi T, Eves-van den Akker S, Jones JT. Genome Evolution of Plant-Parasitic Nematodes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:333-354. [PMID: 28590877 DOI: 10.1146/annurev-phyto-080516-035434] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Plant parasitism has evolved independently on at least four separate occasions in the phylum Nematoda. The application of next-generation sequencing (NGS) to plant-parasitic nematodes has allowed a wide range of genome- or transcriptome-level comparisons, and these have identified genome adaptations that enable parasitism of plants. Current genome data suggest that horizontal gene transfer, gene family expansions, evolution of new genes that mediate interactions with the host, and parasitism-specific gene regulation are important adaptations that allow nematodes to parasitize plants. Sequencing of a larger number of nematode genomes, including plant parasites that show different modes of parasitism or that have evolved in currently unsampled clades, and using free-living taxa as comparators would allow more detailed analysis and a better understanding of the organization of key genes within the genomes. This would facilitate a more complete understanding of the way in which parasitism has shaped the genomes of plant-parasitic nematodes.
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Affiliation(s)
- Taisei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan;
| | - Sebastian Eves-van den Akker
- Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
- Department of Biological Chemistry, The John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - John T Jones
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom
- School of Biology, University of St. Andrews, North Haugh, St. Andrews, KY16 9TZ, United Kingdom
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24
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Zhang M, Coaker G. Harnessing Effector-Triggered Immunity for Durable Disease Resistance. PHYTOPATHOLOGY 2017; 107:912-919. [PMID: 28430023 PMCID: PMC5810938 DOI: 10.1094/phyto-03-17-0086-rvw] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Genetic control of plant diseases has traditionally included the deployment of single immune receptors with nucleotide-binding leucine-rich repeat (NLR) domain architecture. These NLRs recognize corresponding pathogen effector proteins inside plant cells, resulting in effector-triggered immunity (ETI). Although ETI triggers robust resistance, deployment of single NLRs can be rapidly overcome by pathogen populations within a single or a few growing seasons. In order to generate more durable disease resistance against devastating plant pathogens, a multitiered strategy that incorporates stacked NLRs combined with other sources of disease resistance is necessary. New genetic and genomic technologies have enabled advancements in identifying conserved pathogen effectors, isolating NLR repertoires from diverse plants, and editing plant genomes to enhance resistance. Significant advancements have also been made in understanding plant immune perception at the receptor level, which has promise for engineering new sources of resistance. Here, we discuss how to utilize recent scientific advancements in a multilayered strategy for developing more durable disease resistance.
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Affiliation(s)
- Meixiang Zhang
- First and second authors: Department of Plant Pathology, University of California, Davis 95616; and first author: Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Gitta Coaker
- First and second authors: Department of Plant Pathology, University of California, Davis 95616; and first author: Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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