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Genomics of Plant-Nematode Interactions
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Genomics of Plant-Nematode Interactions

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (31 May 2021) | Viewed by 18541

Special Issue Editors

Dr. Etienne G. J. Danchin

E-Mail Website
Guest Editor
Institut Sophia Agrobiotech, Universtié Côte d’Azur, INRAE, CNRS, Sophia Antipolis, France
Interests: adaptive evolution; genomics; agricultural pests
Dr. Sebastian Eves-van den Akker

E-Mail Website
Guest Editor
Department of Plant Sciences, University of Cambridge, Cambridge CB2 1TN, UK
Interests: plant-parasitic nematodes; genomics; effectors

Special Issue Information

Dear Colleagues,

Plant-parasitic nematodes cause substantial yield losses to the worldwide agricultural production and threaten food security in developed and developing countries. Recent advances in both data acquisition and sequencing technologies provide unprecedented opportunities for the study of plant–nematode interactions. Genomic resources of better quality, completeness, and therefore utility will underpin future academic and strategic innovation in plant-parasitic nematology. In this Special Issue, we aim to highlight both the novel application of technological/methodological advances to genome-wide studies of plant-parasitic nematodes, and analyses of such resources that address the fascinating biology of the study system(s).

Dr. Etienne G. J. Danchin
Dr. Sebastian Eves-van den Akker
Guest Editors

Manuscript Submission Information

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Keywords

  • Genomics
  • Next-generation sequencing
  • Transcriptomics
  • Regulation of gene expression
  • Plant-parasitic nematology
  • Phytopathology
  • Effectors

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Published Papers (4 papers)

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Research

25 pages, 3538 KiB  
Article
Genome Expression Dynamics Reveal the Parasitism Regulatory Landscape of the Root-Knot Nematode Meloidogyne incognita and a Promoter Motif Associated with Effector Genes
by Martine Da Rocha, Caroline Bournaud, Julie Dazenière, Peter Thorpe, Marc Bailly-Bechet, Clément Pellegrin, Arthur Péré, Priscila Grynberg, Laetitia Perfus-Barbeoch, Sebastian Eves-van den Akker and Etienne G. J. Danchin
Genes 2021, 12(5), 771; https://doi.org/10.3390/genes12050771 - 18 May 2021
Cited by 24 | Viewed by 5624
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, [...] Read more.
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. Full article
(This article belongs to the Special Issue Genomics of Plant-Nematode Interactions)
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14 pages, 1531 KiB  
Article
A Comprehensive Transcriptional Profiling of Pepper Responses to Root-Knot Nematode
by Weiming Hu, Krista Kingsbury, Shova Mishra and Peter DiGennaro
Genes 2020, 11(12), 1507; https://doi.org/10.3390/genes11121507 - 15 Dec 2020
Cited by 7 | Viewed by 2892
Abstract
Genetic resistance remains a key component in integrated pest management systems. The cosmopolitan root-knot nematode (RKN; Meloidogyne spp.) proves a significant management challenge as virulence and pathogenicity vary among and within species. RKN greatly reduces commercial bell pepper yield, and breeding programs continuously [...] Read more.
Genetic resistance remains a key component in integrated pest management systems. The cosmopolitan root-knot nematode (RKN; Meloidogyne spp.) proves a significant management challenge as virulence and pathogenicity vary among and within species. RKN greatly reduces commercial bell pepper yield, and breeding programs continuously develop cultivars to emerging nematode threats. However, there is a lack of knowledge concerning the nature and forms of nematode resistance. Defining how resistant and susceptible pepper cultivars mount defenses against RKN attacks can help inform breeding programs. Here, we characterized the transcriptional responses of the highly related resistant (Charleston Belle) and susceptible (Keystone Resistance Giant) pepper cultivars throughout early nematode infection stages. Comprehensive transcriptomic sequencing of resistant and susceptible cultivar roots with or without Meloidogyneincognita infection over three-time points; covering early penetration (1-day), through feeding site maintenance (7-days post-inoculation), produced > 300 million high quality reads. Close examination of chromosome P9, on which nematode resistance hotspots are located, showed more differentially expressed genes were upregulated in resistant cultivar at day 1 when compared to the susceptible cultivar. Our comprehensive approach to transcriptomic profiling of pepper resistance revealed novel insights into how RKN causes disease and the plant responses mounted to counter nematode attack. This work broadens the definition of resistance from a single loci concept to a more complex array of interrelated pathways. Focus on these pathways in breeding programs may provide more sustainable and enduring forms of resistance. Full article
(This article belongs to the Special Issue Genomics of Plant-Nematode Interactions)
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20 pages, 3634 KiB  
Article
The Genomic Impact of Selection for Virulence against Resistance in the Potato Cyst Nematode, Globodera pallida
by Kyriakos Varypatakis, Pierre-Yves Véronneau, Peter Thorpe, Peter J. A. Cock, Joanne Tze-Yin Lim, Miles R. Armstrong, Sławomir Janakowski, Mirosław Sobczak, Ingo Hein, Benjamin Mimee, John T. Jones and Vivian C. Blok
Genes 2020, 11(12), 1429; https://doi.org/10.3390/genes11121429 - 28 Nov 2020
Cited by 11 | Viewed by 3650
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) [...] Read more.
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. Full article
(This article belongs to the Special Issue Genomics of Plant-Nematode Interactions)
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25 pages, 1726 KiB  
Article
Comparative Genomics Reveals Novel Target Genes towards Specific Control of Plant-Parasitic Nematodes
by Priscila Grynberg, Roberto Coiti Togawa, Leticia Dias de Freitas, Jose Dijair Antonino, Corinne Rancurel, Marcos Mota do Carmo Costa, Maria Fatima Grossi-de-Sa, Robert N. G. Miller, Ana Cristina Miranda Brasileiro, Patricia Messenberg Guimaraes and Etienne G. J. Danchin
Genes 2020, 11(11), 1347; https://doi.org/10.3390/genes11111347 - 13 Nov 2020
Cited by 23 | Viewed by 5272
Abstract
Plant-parasitic nematodes cause extensive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. Chemical methods that have been deployed to control nematodes have [...] Read more.
Plant-parasitic nematodes cause extensive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. Chemical methods that have been deployed to control nematodes have largely been banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasite-specific proteins, ca. 1000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of these, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasite-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis constitutes a unique resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods. Full article
(This article belongs to the Special Issue Genomics of Plant-Nematode Interactions)
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