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Bali S, Gleason C. Unveiling the Diversity: Plant Parasitic Nematode Effectors and Their Plant Interaction Partners. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:179-189. [PMID: 37870371 DOI: 10.1094/mpmi-09-23-0124-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: 10/24/2023]
Abstract
Root-knot and cyst nematodes are two groups of plant parasitic nematodes that cause the majority of crop losses in agriculture. As a result, these nematodes are the focus of most nematode effector research. Root-knot and cyst nematode effectors are defined as secreted molecules, typically proteins, with crucial roles in nematode parasitism. There are likely hundreds of secreted effector molecules exuded through the nematode stylet into the plant. The current research has shown that nematode effectors can target a variety of host proteins and have impacts that include the suppression of plant immune responses and the manipulation of host hormone signaling. The discovery of effectors that localize to the nucleus indicates that the nematodes can directly modulate host gene expression for cellular reprogramming during feeding site formation. In addition, plant peptide mimicry by some nematode effectors highlights the sophisticated strategies the nematodes employ to manipulate host processes. Here we describe research on the interactions between nematode effectors and host proteins that will provide insights into the molecular mechanisms underpinning plant-nematode interactions. By identifying the host proteins and pathways that are targeted by root-knot and cyst nematode effectors, scientists can gain a better understanding of how nematodes establish feeding sites and subvert plant immune responses. Such information will be invaluable for future engineering of nematode-resistant crops, ultimately fostering advancements in agricultural practices and crop protection. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.
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Affiliation(s)
- Sapinder Bali
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
| | - Cynthia Gleason
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
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2
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Dayi M. Evolution of parasitism genes in the plant parasitic nematodes. Sci Rep 2024; 14:3733. [PMID: 38355886 PMCID: PMC10866927 DOI: 10.1038/s41598-024-54330-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 02/11/2024] [Indexed: 02/16/2024] Open
Abstract
The plant-parasitic nematodes are considered as one of the most destructive pests, from which the migratory and sedentary endoparasitic plant parasitic nematodes infect more than 4000 plant species and cause over $100 billion crop losses annually worldwide. These nematodes use multiple strategies to infect their host and to establish a successful parasitism inside the host such as cell-wall degradation enzymes, inhibition of host defense proteins, and molecular mimicry. In the present study, the main parasitism-associated gene families were identified and compared between the migratory and sedentary endoparasitic nematodes. The results showed that the migratory and sedentary endoparasitic nematodes share a core conserved parasitism mechanism established throughout the evolution of parasitism. However, genes involved in pectin degradation and hydrolase activity are rapidly evolving in the migratory endoparasitic nematodes. Additionally, cell-wall degrading enzymes such as GH45 cellulases and pectate lyase and peptidase and peptidase inhibitors were expanded in the migratory endoparasitic nematodes. The molecular mimicry mechanism was another key finding that differs between the endoparasitic and sedentary parasitic nematodes. The PL22 gene family, which is believed to play a significant role in the molecular mechanisms of nematode parasitism, has been found to be present exclusively in migratory endoparasitic nematodes. Phylogenetic analysis has suggested that it was de novo born in these nematodes. This discovery sheds new light on the molecular evolution of these parasites and has significant implications for our understanding of their biology and pathogenicity. This study contributes to our understanding of core parasitism mechanisms conserved throughout the nematodes and provides unique clues on the evolution of parasitism and the direction shaped by the host.
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Affiliation(s)
- Mehmet Dayi
- Forestry Vocational School, Düzce University, Konuralp Campus, 81620, Düzce, Turkey.
- Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562, Japan.
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3
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Dhiman V, Biswas S, Shekhawat RS, Sadhukhan A, Yadav P. In silico characterization of five novel disease-resistance proteins in Oryza sativa sp. japonica against bacterial leaf blight and rice blast diseases. 3 Biotech 2024; 14:48. [PMID: 38268986 PMCID: PMC10803709 DOI: 10.1007/s13205-023-03893-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/16/2023] [Indexed: 01/26/2024] Open
Abstract
In the current study, gene network analysis revealed five novel disease-resistance proteins against bacterial leaf blight (BB) and rice blast (RB) diseases caused by Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (M. oryzae), respectively. In silico modeling, refinement, and model quality assessment were performed to predict the best structures of these five proteins and submitted to ModelArchive for future use. An in-silico annotation indicated that the five proteins functioned in signal transduction pathways as kinases, phospholipases, transcription factors, and DNA-modifying enzymes. The proteins were localized in the nucleus and plasma membrane. Phylogenetic analysis showed the evolutionary relation of the five proteins with disease-resistance proteins (XA21, OsTRX1, PLD, and HKD-motif-containing proteins). This indicates similar disease-resistant properties between five unknown proteins and their evolutionary-related proteins. Furthermore, gene expression profiling of these proteins using public microarray data showed their differential expression under Xoo and M. oryzae infection. This study provides an insight into developing disease-resistant rice varieties by predicting novel candidate resistance proteins, which will assist rice breeders in improving crop yield to address future food security through molecular breeding and biotechnology. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03893-5.
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Affiliation(s)
- Vedikaa Dhiman
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, 342030 Rajasthan India
| | - Soham Biswas
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana India
| | - Rajveer Singh Shekhawat
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, 342030 Rajasthan India
| | - Ayan Sadhukhan
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, 342030 Rajasthan India
| | - Pankaj Yadav
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, 342030 Rajasthan India
- School of Artificial Intelligence and Data Science, Indian Institute of Technology, Jodhpur, Rajasthan India
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Chen S, Tran TTT, Yeh AYC, Yang H, Chen J, Yang Y, Wang X. The Globodera rostochiensis Gr29D09 Effector with a Role in Defense Suppression Targets the Potato Hexokinase 1 Protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:25-35. [PMID: 37717227 DOI: 10.1094/mpmi-07-23-0095-r] [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: 09/19/2023]
Abstract
The potato cyst nematode (Globodera rostochiensis) is an obligate root pathogen of potatoes. G. rostochiensis encodes several highly expanded effector gene families, including the Gr4D06 family; however, little is known about the function of this effector family. We cloned four 29D09 genes from G. rostochiensis (named Gr29D09v1/v2/v3/v4) that share high sequence similarity and are homologous to the Hg29D09 and Hg4D06 effector genes from the soybean cyst nematode (Heterodera glycines). Phylogenetic analysis revealed that Gr29D09 genes belong to a subgroup of the Gr4D06 family. We showed that Gr29D09 genes are expressed exclusively within the nematode's dorsal gland cell and are dramatically upregulated in parasitic stages, indicating involvement of Gr29D09 effectors in nematode parasitism. Transgenic potato lines overexpressing Gr29D09 variants showed increased susceptibility to G. rostochiensis. Transient expression assays in Nicotiana benthamiana demonstrated that Gr29D09v3 could suppress reactive oxygen species (ROS) production and defense gene expression induced by flg22 and cell death mediated by immune receptors. These results suggest a critical role of Gr29D09 effectors in defense suppression. The use of affinity purification coupled with nanoliquid chromatography-tandem mass spectrometry identified potato hexokinase 1 (StHXK1) as a candidate target of Gr29D09. The Gr29D09-StHXK1 interaction was further confirmed using in planta protein-protein interaction assays. Plant HXKs have been implicated in defense regulation against pathogen infection. Interestingly, we found that StHXK1 could enhance flg22-induced ROS production, consistent with a positive role of plant HXKs in defense. Altogether, our results suggest that targeting StHXK1 by Gr29D09 effectors may impair the positive function of StHXK1 in plant immunity, thereby aiding nematode parasitism. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Shiyan Chen
- School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Tien Thi Thuy Tran
- School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Athena Yi-Chun Yeh
- School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Huijun Yang
- Robert W. Holley Center for Agriculture and Health, U.S. Department of Agriculture, Agricultural Research Service, Ithaca, NY, U.S.A
| | - Jiansong Chen
- School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Yong Yang
- Robert W. Holley Center for Agriculture and Health, U.S. Department of Agriculture, Agricultural Research Service, Ithaca, NY, U.S.A
| | - Xiaohong Wang
- School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
- Robert W. Holley Center for Agriculture and Health, U.S. Department of Agriculture, Agricultural Research Service, Ithaca, NY, U.S.A
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Matuszkiewicz M, Sobczak M. Syncytium Induced by Plant-Parasitic Nematodes. Results Probl Cell Differ 2024; 71:371-403. [PMID: 37996687 DOI: 10.1007/978-3-031-37936-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Plant-parasitic nematodes from the genera Globodera, Heterodera (cyst-forming nematodes), and Meloidogyne (root-knot nematodes) are notorious and serious pests of crops. They cause tremendous economic losses between US $80 and 358 billion a year. Nematodes infect the roots of plants and induce the formation of specialised feeding structures (syncytium and giant cells, respectively) that nourish juveniles and adults of the nematodes. The specialised secretory glands enable nematodes to synthesise and secrete effectors that facilitate migration through root tissues and alter the morphogenetic programme of host cells. The formation of feeding sites is associated with the suppression of plant defence responses and deep reprogramming of the development and metabolism of plant cells.In this chapter, we focus on syncytia induced by the sedentary cyst-forming nematodes and provide an overview of ultrastructural changes that occur in the host roots during syncytium formation in conjunction with the most important molecular changes during compatible and incompatible plant responses to infection with nematodes.
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Affiliation(s)
- Mateusz Matuszkiewicz
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences (WULS-SGGW), Warsaw, Poland.
| | - Mirosław Sobczak
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences (WULS-SGGW), Warsaw, Poland
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van Steenbrugge JJM, van den Elsen S, Holterman M, Lozano‐Torres J, Putker V, Thorpe P, Goverse A, Sterken M, Smant G, Helder J. Comparative genomics among cyst nematodes reveals distinct evolutionary histories among effector families and an irregular distribution of effector-associated promoter motifs. Mol Ecol 2023; 32:1515-1529. [PMID: 35560992 PMCID: PMC10946958 DOI: 10.1111/mec.16505] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/26/2022] [Accepted: 05/04/2022] [Indexed: 11/30/2022]
Abstract
Potato cyst nematodes (PCNs), an umbrella term used for two species, Globodera pallida and G. rostochiensis, belong worldwide to the most harmful pathogens of potato. Pathotype-specific host plant resistances are essential for PCN control. However, the poor delineation of G. pallida pathotypes has hampered the efficient use of available host plant resistances. Long-read sequencing technology allowed us to generate a new reference genome of G. pallida population D383 and, as compared to the current reference, the new genome assembly is 42 times less fragmented. For comparison of diversification patterns of six effector families between G. pallida and G. rostochiensis, an additional reference genome was generated for an outgroup, the beet cyst nematode Heterodera schachtii (IRS population). Large evolutionary contrasts in effector family topologies were observed. While VAPs (venom allergen-like proteins) diversified before the split between the three cyst nematode species, the families GLAND5 and GLAND13 only expanded in PCNs after their separation from the genus Heterodera. Although DNA motifs in the promoter regions thought to be involved in the orchestration of effector expression ("DOG boxes") were present in all three cyst nematode species, their presence is not a necessity for dorsal gland-produced effectors. Notably, DOG box dosage was only loosely correlated with the expression level of individual effector variants. Comparison of the G. pallida genome with those of two other cyst nematodes underlined the fundamental differences in evolutionary history between effector families. Resequencing of PCN populations with different virulence characteristics will allow for the linking of these characteristics to the composition of the effector repertoire as well as for the mapping of PCN diversification patterns resulting from extreme anthropogenic range expansion.
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Affiliation(s)
| | - Sven van den Elsen
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
| | - Martijn Holterman
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
- SolyntaWageningenThe Netherlands
| | | | - Vera Putker
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
| | - Peter Thorpe
- School of Medicine, Medical & Biological SciencesUniversity of St. AndrewsSt AndrewsUK
| | - Aska Goverse
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
| | - Mark G. Sterken
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
| | - Geert Smant
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
| | - Johannes Helder
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
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7
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Verma A, Lin M, Smith D, Walker JC, Hewezi T, Davis EL, Hussey RS, Baum TJ, Mitchum MG. A novel sugar beet cyst nematode effector 2D01 targets the Arabidopsis HAESA receptor-like kinase. MOLECULAR PLANT PATHOLOGY 2022; 23:1765-1782. [PMID: 36069343 PMCID: PMC9644282 DOI: 10.1111/mpp.13263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Plant-parasitic cyst nematodes use a stylet to deliver effector proteins produced in oesophageal gland cells into root cells to cause disease in plants. These effectors are deployed to modulate plant defence responses and developmental programmes for the formation of a specialized feeding site called a syncytium. The Hg2D01 effector gene, coding for a novel 185-amino-acid secreted protein, was previously shown to be up-regulated in the dorsal gland of parasitic juveniles of the soybean cyst nematode Heterodera glycines, but its function has remained unknown. Genome analyses revealed that Hg2D01 belongs to a highly diversified effector gene family in the genomes of H. glycines and the sugar beet cyst nematode Heterodera schachtii. For functional studies using the model Arabidopsis thaliana-H. schachtii pathosystem, we cloned the orthologous Hs2D01 sequence from H. schachtii. We demonstrate that Hs2D01 is a cytoplasmic effector that interacts with the intracellular kinase domain of HAESA (HAE), a cell surface-associated leucine-rich repeat (LRR) receptor-like kinase (RLK) involved in signalling the activation of cell wall-remodelling enzymes important for cell separation during abscission and lateral root emergence. Furthermore, we show that AtHAE is expressed in the syncytium and, therefore, could serve as a viable host target for Hs2D01. Infective juveniles effectively penetrated the roots of HAE and HAESA-LIKE2 (HSL2) double mutant plants; however, fewer nematodes developed on the roots, consistent with a role for this receptor family in nematode infection. Taken together, our results suggest that the Hs2D01-AtHAE interaction may play an important role in sugar beet cyst nematode parasitism.
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Affiliation(s)
- Anju Verma
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaAthensGeorgiaUSA
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
| | - Marriam Lin
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
- Boyle Frederickson Intellectual Property LawMilwaukeeWisconsinUSA
| | - Dante Smith
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
- Conagra Brands, Inc., Corporate Microbiology, Research and DevelopmentOmahaNebraskaUSA
| | - John C. Walker
- Division of Biological SciencesUniversity of MissouriColumbiaMissouriUSA
| | - Tarek Hewezi
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Eric L. Davis
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Richard S. Hussey
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaAthensGeorgiaUSA
| | - Thomas J. Baum
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Melissa G. Mitchum
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaAthensGeorgiaUSA
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
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8
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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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9
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Goverse A, Mitchum MG. At the molecular plant-nematode interface: New players and emerging paradigms. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102225. [PMID: 35537283 DOI: 10.1016/j.pbi.2022.102225] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/24/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Plant-parasitic nematodes (PPNs) secrete an array of molecules that can lead to their detection by or promote infection of their hosts. However, the function of these molecules in plant cells is often unknown or limited to phenotypic observations. Similarly, how plant cells detect and/or respond to these molecules is still poorly understood. Here, we highlight recent advances in mechanistic insights into the molecular dialogue between PPNs and plants at the cellular level. New discoveries reveal a) the essential roles of extra- and intracellular plant receptors in PPN perception and the manipulation of host immune- or developmental pathways during infection and b) how PPNs target such receptors to manipulate their hosts. Finally, the plant secretory pathway has emerged as a critical player in PPN peptide delivery, feeding site formation and non-canonical resistance.
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Affiliation(s)
- Aska Goverse
- Laboratory of Nematology, Dept of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands.
| | - Melissa G Mitchum
- Department of Plant Pathology and Institute of Plant Breeding, Genetics & Genomics, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA
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10
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Zhao G, Wang J, Chen X, Sha H, Liu X, Han Y, Qiu G, Zhang F, Fang J. OsASHL1 and OsASHL2, two members of the COMPASS-like complex, control floral transition and plant development in rice. J Genet Genomics 2022; 49:870-880. [DOI: 10.1016/j.jgg.2022.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/14/2022] [Accepted: 02/20/2022] [Indexed: 11/26/2022]
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11
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Handayani ND, Lestari P, van As W, Holterman M, van den Elsen S, Dikin A, Bert W, Helder J, Van Steenbrugge JJM. Genomic Reconstruction of the Introduction and Diversification of Golden Potato Cyst Nematode Populations in Indonesia. PHYTOPATHOLOGY 2022; 112:396-403. [PMID: 34129357 DOI: 10.1094/phyto-04-21-0150-r] [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: 06/12/2023]
Abstract
Potato cyst nematodes (PCNs), the umbrella term for Globodera rostochiensis and G. pallida, coevolved with their Solanaceous hosts in the Andean Mountain region. From there, PCN proliferated worldwide to virtually all potato production areas. PCN is a major factor limiting the potato production in Indonesia. In our survey, only G. rostochiensis was found. Fourteen field populations were collected on Java and Sumatra, and unique variants were called by mapping resequencing data on a G. rostochiensis reference genome. A phylogenetic tree based on 1.4 million unique variants showed a genotypic separation between the outgroup, a Scottish Ro1 population, and all Indonesian populations. This separation was comparable in size with the genotypic distinction between the Javanese and the Sumatran PCN populations. Next, variants within PCN effector gene families SPRYSEC, 1106, 4D06, and venom allergen-like protein (VAL) that all interfere with the host innate immune system were compared. Distinct selective pressures acted on these effector families; while SPRYSECs (4,341 single-nucleotide polymorphisms [SNPs]/insertions or deletions of bases [indels]) behaved like neutral genes, the phylogenetic trees of 1106, 4D06, and VAL proteins (235, 790, and 150 SNPs/indels, respectively) showed deviating topologies. Our data suggest that PCN was introduced on Java not too long after the introduction of potato in the middle of the eighteenth century. Soon thereafter, the pathogen established on Sumatra and started to diversify independently. This scenario was corroborated by diversification patterns of the effector families 1106, 4D06, and VAL. Our data demonstrate how genome resequencing data from a nonindigenous pathogen can be used to reconstruct the introduction and diversification process.
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Affiliation(s)
- Nurul Dwi Handayani
- Indonesian Agricultural Quarantine Agency, Ministry of Agriculture, Ragunan, Jakarta 12550, Indonesia
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
- Nematology Research Unit, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Prabowo Lestari
- Indonesian Agricultural Quarantine Agency, Ministry of Agriculture, Ragunan, Jakarta 12550, Indonesia
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
- Nematology Research Unit, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Wouter van As
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Martijn Holterman
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
- Solynta, 6703 HA Wageningen, The Netherlands
| | - Sven van den Elsen
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Antarjo Dikin
- Directorate General of Estate Crops, Ministry of Agriculture, Ragunan, Jakarta 12550, Indonesia
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Johannes Helder
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
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12
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van Steenbrugge JJM, van den Elsen S, Holterman M, Sterken MG, Thorpe P, Goverse A, Smant G, Helder J. Comparative genomics of two inbred lines of the potato cyst nematode Globodera rostochiensis reveals disparate effector family-specific diversification patterns. BMC Genomics 2021; 22:611. [PMID: 34380421 PMCID: PMC8359618 DOI: 10.1186/s12864-021-07914-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Potato cyst nematodes belong to the most harmful pathogens in potato, and durable management of these parasites largely depends on host-plant resistances. These resistances are pathotype specific. The current Globodera rostochiensis pathotype scheme that defines five pathotypes (Ro1 - Ro5) is both fundamentally and practically of limited value. Hence, resistant potato varieties are used worldwide in a poorly informed manner. RESULTS We generated two novel reference genomes of G. rostochiensis inbred lines derived from a Ro1 and a Ro5 population. These genome sequences comprise 173 and 189 scaffolds respectively, marking a ≈ 24-fold reduction in fragmentation as compared to the current reference genome. We provide copy number variations for 19 effector families. Four dorsal gland effector families were investigated in more detail. SPRYSECs, known to be implicated in plant defence suppression, constitute by far the most diversified family studied herein with 60 and 99 variants in Ro1 and Ro5 distributed over 18 and 26 scaffolds. In contrast, CLEs, effectors involved in feeding site induction, show strong physical clustering. The 10 and 16 variants cluster on respectively 2 and 1 scaffolds. Given that pathotypes are defined by their effectoromes, we pinpoint the disparate nature of the contributing effector families in terms of sequence diversification and loss and gain of variants. CONCLUSIONS Two novel reference genomes allow for nearly complete inventories of effector diversification and physical organisation within and between pathotypes. Combined with insights we provide on effector family-specific diversification patterns, this constitutes a basis for an effectorome-based virulence scheme for this notorious pathogen.
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Affiliation(s)
| | - Sven van den Elsen
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Martijn Holterman
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands.,Solynta, Dreijenlaan 2, 6703 HA, Wageningen, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Peter Thorpe
- School of Medicine, Medical & Biological Sciences, University of St. Andrews, North Haugh, St Andrews, United Kingdom
| | - Aska Goverse
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Geert Smant
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Johannes Helder
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
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13
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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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14
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The Genomic Impact of Selection for Virulence against Resistance in the Potato Cyst Nematode, Globodera pallida. Genes (Basel) 2020; 11:genes11121429. [PMID: 33260722 PMCID: PMC7760817 DOI: 10.3390/genes11121429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 11/17/2022] Open
Abstract
Although the use of natural resistance is the most effective management approach against the potato cyst nematode (PCN) Globodera pallida, the existence of pathotypes with different virulence characteristics constitutes a constraint towards this goal. Two resistance sources, GpaV (from Solanum vernei) and H3 from S. tuberosum ssp. andigena CPC2802 (from the Commonwealth Potato Collection) are widely used in potato breeding programmes in European potato industry. However, the use of resistant cultivars may drive strong selection towards virulence, which allows the increase in frequency of virulent alleles in the population and therefore, the emergence of highly virulent nematode lineages. This study aimed to identify Avirulence (Avr) genes in G. pallida populations selected for virulence on the above resistance sources, and the genomic impact of selection processes on the nematode. The selection drive in the populations was found to be specific to their genetic background. At the genomic level, 11 genes were found that represent candidate Avr genes. Most of the variant calls determining selection were associated with H3-selected populations, while many of them seem to be organised in genomic islands facilitating selection evolution. These phenotypic and genomic findings combined with histological studies performed revealed potential mechanisms underlying selection in G. pallida.
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15
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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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16
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Wixom AQ, Casavant NC, Sonnen TJ, Kuhl JC, Xiao F, Dandurand LM, Caplan AB. Initial responses of the trap-crop, Solanum sisymbriifolium, to Globodera pallida invasions. THE PLANT GENOME 2020; 13:e20016. [PMID: 33016605 DOI: 10.1002/tpg2.20016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/02/2020] [Accepted: 02/22/2020] [Indexed: 06/11/2023]
Abstract
Many researchers today are looking for mechanisms underlying plant defenses against nematodes by identifying differentially expressed genes in domesticated hosts. In order to provide a different perspective, we analyzed the root transcriptome of an undomesticated non-host species, Solanum sisymbriifolium Lamark (SSI) before and after Globodera pallida infection. Utilizing RNAseq analyses, we identified changes in the expression of 277 transcripts. Many of these genes were not annotated; however, the annotated set included peroxidases, reactive oxygen species-producing proteins, and regulators of cell death. Importantly, 60% of the nematode-responsive genes did not respond to physical damage to root tissues, or to exogenous treatments with either salicylic acid or methyl jasmonate. Based on this, we speculate that the majority of changes in SSI gene expression were promoted by either nematode effectors, pathogen-associated molecular patterns (PAMPs), or by exposure to untested endogenous signaling molecules such as ethylene, or by exposure to multiple stimuli. This study incorporates our findings into a model that accounts for part of this plant's unusual resistance to nematodes.
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Affiliation(s)
- Alexander Q Wixom
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844-2333, USA
| | - N Carol Casavant
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844-2333, USA
| | | | - Joseph C Kuhl
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844-2333, USA
| | - Fangming Xiao
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844-2333, USA
| | - Louise-Marie Dandurand
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID, 83844-2329, USA
| | - Allan B Caplan
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844-2333, USA
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17
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Diaz‐Granados A, Sterken MG, Overmars H, Ariaans R, Holterman M, Pokhare SS, Yuan Y, Pomp R, Finkers‐Tomczak A, Roosien J, Slootweg E, Elashry A, Grundler FM, Xiao F, Goverse A, Smant G. The effector GpRbp-1 of Globodera pallida targets a nuclear HECT E3 ubiquitin ligase to modulate gene expression in the host. MOLECULAR PLANT PATHOLOGY 2020; 21:66-82. [PMID: 31756029 PMCID: PMC6913204 DOI: 10.1111/mpp.12880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plant-parasitic nematodes secrete effectors that manipulate plant cell morphology and physiology to achieve host invasion and establish permanent feeding sites. Effectors from the highly expanded SPRYSEC (SPRY domain with a signal peptide for secretion) family in potato cyst nematodes have been implicated in activation and suppression of plant immunity, but the mechanisms underlying these activities remain largely unexplored. To study the host mechanisms used by SPRYSEC effectors, we identified plant targets of GpRbp-1 from the potato cyst nematode Globodera pallida. Here, we show that GpRbp-1 interacts in yeast and in planta with a functional potato homologue of the Homology to E6-AP C-Terminus (HECT)-type ubiquitin E3 ligase UPL3, which is located in the nucleus. Potato lines lacking StUPL3 are not available, but the Arabidopsis mutant upl3-5 displaying a reduced UPL3 expression showed a consistently small but not significant decrease in susceptibility to cyst nematodes. We observed a major impact on the root transcriptome by the lower levels of AtUPL3 in the upl3-5 mutant, but surprisingly only in association with infections by cyst nematodes. To our knowledge, this is the first example that a HECT-type ubiquitin E3 ligase is targeted by a pathogen effector and that a member of this class of proteins specifically regulates gene expression under biotic stress conditions. Together, our data suggest that GpRbp-1 targets a specific component of the plant ubiquitination machinery to manipulate the stress response in host cells.
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Affiliation(s)
| | - Mark G. Sterken
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Hein Overmars
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Roel Ariaans
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Martijn Holterman
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Somnath S. Pokhare
- Department of Molecular PhytomedicineUniversity of BonnBonnGermany
- ICAR National Rice Research InstituteCuttack753006India
| | - Yulin Yuan
- Department of Plant SciencesUniversity of IdahoMoscowUSA
| | - Rikus Pomp
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Anna Finkers‐Tomczak
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
- KeyGene N.V.WageningenNetherlands
| | - Jan Roosien
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Erik Slootweg
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Abdenaser Elashry
- Department of Molecular PhytomedicineUniversity of BonnBonnGermany
- Strube Research GmbHHauptstrasse 138387SöllingenGermany
| | | | - Fangming Xiao
- Department of Plant SciencesUniversity of IdahoMoscowUSA
| | - Aska Goverse
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Geert Smant
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
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18
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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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19
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Mourad AMI, Sallam A, Belamkar V, Mahdy E, Bakheit B, Abo El-Wafaa A, Stephen Baenziger P. Genetic architecture of common bunt resistance in winter wheat using genome-wide association study. BMC PLANT BIOLOGY 2018; 18:280. [PMID: 30424724 PMCID: PMC6234641 DOI: 10.1186/s12870-018-1435-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 09/23/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Common bunt (caused by Tilletia caries and T. foetida) has been considered as a major disease in wheat (Triticum aestivum) following rust (Puccinia spp.) in the Near East and is economically important in the Great Plains, USA. Despite the fact that it can be easily controlled using seed treatment with fungicides, fungicides often cannot or may not be used in organic and low-input fields. Planting common bunt resistant genotypes is an alternative. RESULTS To identify resistance genes for Nebraska common bunt race, the global set of differential lines were inoculated. Nine differential lines carrying nine different genes had 0% infected heads and seemed to be resistant to Nebraska race. To understand the genetic basis of the resistance in Nebraska winter wheat, a set of 330 genotypes were inoculated and evaluated under field conditions in two locations. Out of the 330 genotypes, 62 genotypes had different degrees of resistance. Moreover, plant height, chlorophyll content and days to heading were scored in both locations. Using genome-wide association study, 123 SNPs located on fourteen chromosomes were identified to be associated with the resistance. Different degrees of linkage disequilibrium was found among the significant SNPs and they explained 1.00 to 9.00% of the phenotypic variance, indicating the presence of many minor QTLs controlling the resistance. CONCLUSION Based on the chromosomal location of some of the known genes, some SNPs may be associated with Bt1, Bt6, Bt11 and Bt12 resistance loci. The remaining significant SNPs may be novel alleles that were not reported previously. Common bunt resistance seems to be an independent trait as no correlation was found between a number of infected heads and chlorophyll content, days to heading or plant height.
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Affiliation(s)
- Amira M. I. Mourad
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE USA
- Department of Agronomy, Faculty of Agriculture, Assiut University, Asyut, Egypt
| | - Ahmed Sallam
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE USA
- Department of Genetics, Faculty of Agriculture, Assiut University, Asyut, Egypt
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE USA
| | - Ezzat Mahdy
- Department of Agronomy, Faculty of Agriculture, Assiut University, Asyut, Egypt
| | - Bahy Bakheit
- Department of Agronomy, Faculty of Agriculture, Assiut University, Asyut, Egypt
| | - Atif Abo El-Wafaa
- Department of Agronomy, Faculty of Agriculture, Assiut University, Asyut, Egypt
| | - P. Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE USA
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20
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Gardner M, Dhroso A, Johnson N, Davis EL, Baum TJ, Korkin D, Mitchum MG. Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines. Sci Rep 2018; 8:2505. [PMID: 29410430 PMCID: PMC5802810 DOI: 10.1038/s41598-018-20536-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 01/12/2018] [Indexed: 11/08/2022] Open
Abstract
Soybean cyst nematode (SCN) Heterodera glycines is an obligate parasite that relies on the secretion of effector proteins to manipulate host cellular processes that favor the formation of a feeding site within host roots to ensure its survival. The sequence complexity and co-evolutionary forces acting upon these effectors remain unknown. Here we generated a de novo transcriptome assembly representing the early life stages of SCN in both a compatible and an incompatible host interaction to facilitate global effector mining efforts in the absence of an available annotated SCN genome. We then employed a dual effector prediction strategy coupling a newly developed nematode effector prediction tool, N-Preffector, with a traditional secreted protein prediction pipeline to uncover a suite of novel effector candidates. Our analysis distinguished between effectors that co-evolve with the host genotype and those conserved by the pathogen to maintain a core function in parasitism and demonstrated that alternative splicing is one mechanism used to diversify the effector pool. In addition, we confirmed the presence of viral and microbial inhabitants with molecular sequence information. This transcriptome represents the most comprehensive whole-nematode sequence currently available for SCN and can be used as a tool for annotation of expected genome assemblies.
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Affiliation(s)
- Michael Gardner
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Andi Dhroso
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, USA
| | - Nathan Johnson
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, USA
| | - Eric L Davis
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, USA
| | - Dmitry Korkin
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, USA.
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, USA.
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21
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Mei Y, Wright KM, Haegeman A, Bauters L, Diaz-Granados A, Goverse A, Gheysen G, Jones JT, Mantelin S. The Globodera pallida SPRYSEC Effector GpSPRY-414-2 That Suppresses Plant Defenses Targets a Regulatory Component of the Dynamic Microtubule Network. FRONTIERS IN PLANT SCIENCE 2018; 9:1019. [PMID: 30050557 PMCID: PMC6052128 DOI: 10.3389/fpls.2018.01019] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/22/2018] [Indexed: 05/09/2023]
Abstract
The white potato cyst nematode, Globodera pallida, is an obligate biotrophic pathogen of a limited number of Solanaceous plants. Like other plant pathogens, G. pallida deploys effectors into its host that manipulate the plant to the benefit of the nematode. Genome analysis has led to the identification of large numbers of candidate effectors from this nematode, including the cyst nematode-specific SPRYSEC proteins. These are a secreted subset of a hugely expanded gene family encoding SPRY domain-containing proteins, many of which remain to be characterized. We investigated the function of one of these SPRYSEC effector candidates, GpSPRY-414-2. Expression of the gene encoding GpSPRY-414-2 is restricted to the dorsal pharyngeal gland cell and reducing its expression in G. pallida infective second stage juveniles using RNA interference causes a reduction in parasitic success on potato. Transient expression assays in Nicotiana benthamiana indicated that GpSPRY-414-2 disrupts plant defenses. It specifically suppresses effector-triggered immunity (ETI) induced by co-expression of the Gpa2 resistance gene and its cognate avirulence factor RBP-1. It also causes a reduction in the production of reactive oxygen species triggered by exposure of plants to the bacterial flagellin epitope flg22. Yeast two-hybrid screening identified a potato cytoplasmic linker protein (CLIP)-associated protein (StCLASP) as a host target of GpSPRY-414-2. The two proteins co-localize in planta at the microtubules. CLASPs are members of a conserved class of microtubule-associated proteins that contribute to microtubule stability and growth. However, disruption of the microtubule network does not prevent suppression of ETI by GpSPRY-414-2 nor the interaction of the effector with its host target. Besides, GpSPRY-414-2 stabilizes its target while effector dimerization and the formation of high molecular weight protein complexes including GpSPRY-414-2 are prompted in the presence of the StCLASP. These data indicate that the nematode effector GpSPRY-414-2 targets the microtubules to facilitate infection.
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Affiliation(s)
- Yuanyuan Mei
- Dundee Effector Consortium, Cell and Molecular Sciences Group, The James Hutton Institute, Dundee, United Kingdom
- Faculty of Bioscience Engineering, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Kathryn M. Wright
- Dundee Effector Consortium, Cell and Molecular Sciences Group, The James Hutton Institute, Dundee, United Kingdom
| | - Annelies Haegeman
- Faculty of Bioscience Engineering, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Lander Bauters
- Faculty of Bioscience Engineering, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Amalia Diaz-Granados
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Godelieve Gheysen
- Faculty of Bioscience Engineering, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - John T. Jones
- Dundee Effector Consortium, Cell and Molecular Sciences Group, The James Hutton Institute, Dundee, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Sophie Mantelin
- Dundee Effector Consortium, Cell and Molecular Sciences Group, The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Sophie Mantelin
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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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