title: Dual RNA-seq reveals Meloidogyne graminicola transcriptome and candidate effectors during the interaction with rice plants.
abstract: Root-knot nematodes secrete proteinaceous effectors into plant tissues to facilitate infection by suppressing host defences and reprogramming the host metabolism to their benefit. Meloidogyne graminicola is a major pest of rice (Oryza sativa) in Asia and Latin America, causing important crop losses. The goal of this study was to identify M. graminicola pathogenicity genes expressed during the plant-nematode interaction. Using the dual RNA-sequencing (RNA-seq) strategy, we generated transcriptomic data of M. graminicola samples covering the pre-parasitic J2 stage and five parasitic stages in rice plants, from the parasitic J2 to the adult female. In the absence of a reference genome, a de novo M. graminicola transcriptome of 66 396 contigs was obtained from those reads that were not mapped on the rice genome. Gene expression profiling across the M. graminicola life cycle revealed key genes involved in nematode development and provided insights into the genes putatively associated with parasitism. The development of a 'secreted protein prediction' pipeline revealed a typical set of proteins secreted by nematodes, as well as a large number of cysteine-rich proteins and putative nuclear proteins. Combined with expression data, this pipeline enabled the identification of 15 putative effector genes, including two homologues of well-characterized effectors from cyst nematodes (CLE-like and VAP1) and a metallothionein. The localization of gene expression was assessed by in situ hybridization for a subset of candidates. All of these data represent important molecular resources for the elucidation of M. graminicola biology and for the selection of potential targets for the development of novel control strategies for this nematode species.
authors.affiliation: IRD, UMR IRD-Cirad-UM2 Interactions Plantes-Microbes-Environnement, 34394, Montpellier Cedex 5, France.
authors.forename: Anne-Sophie
authors.initials: AS
authors.lastname: Petitot
authors.affiliation: IRD, UMR IRD-Cirad-UM2 Interactions Plantes-Microbes-Environnement, 34394, Montpellier Cedex 5, France.
authors.forename: Alexis
authors.initials: A
authors.lastname: Dereeper
authors.affiliation: IRD, UMR IRD-Cirad-UM2 Interactions Plantes-Microbes-Environnement, 34394, Montpellier Cedex 5, France.
authors.forename: Mawusse
authors.initials: M
authors.lastname: Agbessi
authors.affiliation: CEA, Institut de Génomique, GENOSCOPE - Centre National de Séquençage, 91057, Evry Cedex, France.
authors.forename: Corinne
authors.initials: C
authors.lastname: Da Silva
authors.affiliation: CEA, Institut de Génomique, GENOSCOPE - Centre National de Séquençage, 91057, Evry Cedex, France.
authors.forename: Julie
authors.initials: J
authors.lastname: Guy
authors.affiliation: INRA, UMR Amélioration Génétique et Adaptation des Plantes, 34060, Montpellier Cedex 1, France.
authors.forename: Morgane
authors.initials: M
authors.lastname: Ardisson
authors.affiliation: IRD, UMR IRD-Cirad-UM2 Interactions Plantes-Microbes-Environnement, 34394, Montpellier Cedex 5, France.
authors.forename: Diana
authors.initials: D
authors.lastname: Fernandez
mesh_terms: D000818:Animals; D019295:Computational Biology; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D054884:Host-Pathogen Interactions / Q000235:genetics*; D008018:Life Cycle Stages / Q000235:genetics; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000235:genetics* / Q000469:parasitology*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*; D014431:Tylenchoidea / Q000235:genetics* / Q000254:growth & development
keywords: Meloidogyne graminicola; Oryza sativa; dual RNA-seq; effector genes; expression profiling; plant-parasitic nematode