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Fanelli E, Gaffuri F, Troccoli A, Sacchi S, De Luca F. New occurrence of
Meloidogyne graminicola
(Nematoda: Meloidogyninae) from rice fields in Italy: Variability and phylogenetic relationships. Ecol Evol 2022; 12:e9326. [PMID: 36188499 PMCID: PMC9486484 DOI: 10.1002/ece3.9326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/22/2022] [Accepted: 09/01/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Elena Fanelli
- Istituto per la Protezione Sostenibile delle Piante, Bari Consiglio Nazionale delle Ricerche Bari Italy
| | - Francesca Gaffuri
- Laboratorio Fitosanitario Regione Lombardia presso Fondazione Minoprio Vertemate con Minoprio Italy
| | - Alberto Troccoli
- Istituto per la Protezione Sostenibile delle Piante, Bari Consiglio Nazionale delle Ricerche Bari Italy
| | - Stefano Sacchi
- Laboratorio Fitosanitario Regione Lombardia presso Fondazione Minoprio Vertemate con Minoprio Italy
| | - Francesca De Luca
- Istituto per la Protezione Sostenibile delle Piante, Bari Consiglio Nazionale delle Ricerche Bari Italy
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Soares MR, Carneiro RM, Dias-Arieira CR. Response of different crops and weeds to three biotypes of Meloidogyne graminicola: crop rotation and succession strategies for irrigated rice fields. NEMATOLOGY 2022. [DOI: 10.1163/15685411-bja10155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
Rice, one of the most consumed cereal crops worldwide, is commonly grown under flooded conditions, which directly influences the nematode community. Meloidogyne graminicola is the predominant species in rice fields, causing significant damage and requiring integrated management practices. This study aimed to investigate the response of different Poaceae crops, soybean, and common weeds of rice to three biotypes of M. graminicola (G1, G2 and G3) recently detected in Brazil. The highest reproduction factor (RF) for the three nematode populations was detected in the weeds Echinochloa colonum and E. crus-galli, followed by rice and Italian ryegrass. Wheat ‘TBio Sonic’ and millet ‘ADR 500’ served as poor hosts to the nematodes, whereas black oat, white oat, signalgrass, millet ‘ADR 905’, maize, wheat ‘TBio Toruk’, and soybean acted as non-hosts (RF < 1) in both experiments. Of the three M. graminicola biotypes, G1 was the most aggressive, followed by G3 and G2 (lowest RF values). The findings of the current study can support the selection of crop rotation or succession approaches for the management of different biotypes of M. graminicola in irrigated rice fields.
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Affiliation(s)
- Mayra R.C. Soares
- Department of Agronomy, Universidade Estadual de Maringá (UEM), bloco J35, Avenida Columbus, 5790, Jardim Universitário, Maringá, Paraná, 87020-900, Brazil
| | | | - Claudia R. Dias-Arieira
- Department of Agronomy/Nematology, Universidade Estadual de Maringá, Umuarama, campus (CAU), Estrada Paca, São Cristóvão, Umuarama, Paraná, 87507-190, Brazil
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Somvanshi VS, Dash M, Bhat CG, Budhwar R, Godwin J, Shukla RN, Patrignani A, Schlapbach R, Rao U. An improved draft genome assembly of Meloidogyne graminicola IARI strain using long-read sequencing. Gene 2021; 793:145748. [PMID: 34077775 DOI: 10.1016/j.gene.2021.145748] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 01/10/2023]
Abstract
The rice root-knot nematode Meloidogyne graminicola is a major biotic stress for the rice crop under upland, rain-fed lowland and irrigated cultivation conditions. Here, we present an improved draft genome assembly of M. graminicola IARI strain using the long-read sequencing approach (PacBio Sequel platform). The assembled genome size was 36.86 Mb with 514 contigs and N50 value of 105 kb. BUSCO estimated the genome to be 88.6% complete. Meloidogyne graminicola genome contained 17.83% repeat elements and showed 14,062 protein-coding gene models, 4,974 conserved orthologous genes, 561 putative secreted proteins, 49 RNAi pathway genes, 1,853 proteins involved in pathogen-host interactions, 1,575 carbohydrate-active enzymes, and 32,138 microsatellites. Five of the carbohydrate-active enzymes were found only in M. graminicola genome and were not present in any other analysed root-knot nematode genome. Together with the previous two genome assemblies, this improved genome assembly would facilitate comparative and functional genomics for M. graminicola.
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Affiliation(s)
- Vishal Singh Somvanshi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi 110012, India
| | - Manoranjan Dash
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi 110012, India
| | - Chaitra G Bhat
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi 110012, India
| | - Roli Budhwar
- Bionivid Technology Private Limited, 209, 4th Cross Rd, B Channasandra, Kasturi Nagar, Bengaluru, Karnataka 560043, India
| | - Jeffrey Godwin
- Bionivid Technology Private Limited, 209, 4th Cross Rd, B Channasandra, Kasturi Nagar, Bengaluru, Karnataka 560043, India
| | - Rohit N Shukla
- Bionivid Technology Private Limited, 209, 4th Cross Rd, B Channasandra, Kasturi Nagar, Bengaluru, Karnataka 560043, India
| | - Andrea Patrignani
- Functional Genomics Center Zurich, Winterthurerstr. 190, Y32H52, 8057 Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, Winterthurerstr. 190, Y32H52, 8057 Zurich, Switzerland
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi 110012, India.
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Montarry J, Mimee B, Danchin EGJ, Koutsovoulos GD, Ste-Croix DT, Grenier E. Recent Advances in Population Genomics of Plant-Parasitic Nematodes. Phytopathology 2021; 111:40-48. [PMID: 33151824 DOI: 10.1094/phyto-09-20-0418-rvw] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Plant-parasitic nematodes are a costly burden of crop production. Ubiquitous in nature, phytoparasitic nematodes are associated with nearly every important agricultural crop and represent a significant constraint on global food security. Population genetics is a key discipline in plant nematology to understand aspects of the life strategies of these parasites, in particular their modes of reproduction, geographic origins, evolutionary histories, and dispersion abilities. Advances in high-throughput sequencing technologies have enabled a recent but active effort in genomic analyses of plant-parasitic nematodes. Such genomic approaches applied to multiple populations are providing new insights into the molecular and evolutionary processes that underpin the establishment of these nematodes and into a better understanding of the genetic and mechanistic basis of their pathogenicity and adaptation to their host plants. In this review, we attempt to update information about genome resources and genotyping techniques useful for nematologists who are thinking about initiating population genomics or genome sequencing projects. This review is intended also to foster the development of population genomics in plant-parasitic nematodes through highlighting recent publications that illustrate the potential for this approach to identify novel molecular markers or genes of interest and improve our knowledge of the genome variability, pathogenicity, and evolutionary potential of plant-parasitic nematodes.
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Affiliation(s)
| | - Benjamin Mimee
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Québec, Canada
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, Université Côte d'Azur, INRAE, CNRS, Sophia Antipolis, France
| | | | - Dave T Ste-Croix
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Québec, Canada
| | - Eric Grenier
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35650, Le Rheu, France
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Phan NT, Orjuela J, Danchin EGJ, Klopp C, Perfus‐Barbeoch L, Kozlowski DK, Koutsovoulos GD, Lopez‐Roques C, Bouchez O, Zahm M, Besnard G, Bellafiore S. Genome structure and content of the rice root-knot nematode ( Meloidogyne graminicola). Ecol Evol 2020; 10:11006-11021. [PMID: 33144944 PMCID: PMC7593179 DOI: 10.1002/ece3.6680] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/04/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022] Open
Abstract
Discovered in the 1960s, Meloidogyne graminicola is a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this study, using a combination of Oxford Nanopore Technologies and Illumina sequencing data, we generated a highly contiguous reference genome (283 scaffolds with an N50 length of 294 kb, totaling 41.5 Mb). The completeness scores of our assembly are among the highest currently published for Meloidogyne genomes. We predicted 10,284 protein-coding genes spanning 75.5% of the genome. Among them, 67 are identified as possibly originating from horizontal gene transfers (mostly from bacteria), which supposedly contribute to nematode infection, nutrient processing, and plant defense manipulation. Besides, we detected 575 canonical transposable elements (TEs) belonging to seven orders and spanning 2.61% of the genome. These TEs might promote genomic plasticity putatively related to the evolution of M. graminicola parasitism. This high-quality genome assembly constitutes a major improvement regarding previously available versions and represents a valuable molecular resource for future phylogenomic studies of Meloidogyne species. In particular, this will foster comparative genomic studies to trace back the evolutionary history of M. graminicola and its closest relatives.
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Affiliation(s)
- Ngan Thi Phan
- IRD‐CIRAD‐University of MontpellierUMR Interactions Plantes Microorganismes Environnement (IPME)MontpellierFrance
| | - Julie Orjuela
- IRD‐CIRAD‐University of MontpellierUMR Interactions Plantes Microorganismes Environnement (IPME)MontpellierFrance
| | | | - Christophe Klopp
- Plateforme BioInfo GenotoulUR875INRAECastanet‐Tolosan cedexFrance
| | | | - Djampa K. Kozlowski
- Institut Sophia AgrobiotechINRAECNRSUniversité Côte d’AzurSophia AntipolisFrance
| | | | | | | | - Margot Zahm
- Plateforme BioInfo GenotoulUR875INRAECastanet‐Tolosan cedexFrance
| | | | - Stéphane Bellafiore
- IRD‐CIRAD‐University of MontpellierUMR Interactions Plantes Microorganismes Environnement (IPME)MontpellierFrance
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Chapuis E, Ali N, Noûs C, Besnard G. Adaptive response to olive cultivation in a generalist parasitic nematode (Meloidogyne javanica). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractCultivated plants usually differ from their wild progenitors in several morphological and/or physiological traits. Their microbe communities might also differ because of adaptation to new conditions related to cultivation. To test this hypothesis, we investigated morphological traits in a parthenogenetic root-knot nematode (Meloidogyne javanica) from natural and agricultural environments. Seventeen populations of M. javanica were sampled on cultivated and wild olives in Morocco, then maintained in controlled conditions for a ‘common garden’ experiment. We estimated the genetic variation based on three traits (stylet size, neck width and body width) by a quantitative genetic design (ten families per population and nine individuals per family were measured), and molecular variation was investigated with a mitochondrial marker to identify the genetic lineages of nematode isolates sampled from wild and cultivated olives. Significant morphological differences were detected between individuals from wild vs. cultivated hosts for the three traits, whereas no phylogenetic clustering was observed among isolates collected on those two hosts. Our results thus suggest an adaptive response of the asexual parasite, possibly related to the deep modification of soil nematode communities between natural olive stands and orchards.
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Affiliation(s)
- Elodie Chapuis
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Nadeen Ali
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | - Guillaume Besnard
- CNRS, UPS, IRD, UMR5174, EDB, Université Toulouse III Paul Sabatier, Toulouse Cedex, France
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