Evolutionarily conserved plant genes responsive to root-knot nematodes identified by comparative genomics

Zotta Mota Ana, Fernandez Diana, Arraes Fabricio B.M., Petitot Anne-Sophie, Paes de Melo Bruno, Lisei de Sa Maria E., Grynberg Priscila, Passos Saraiva Mario A., Messenberg Guimaraes Patricia, Brasileiro Ana Christina Miranda, Albuquerque Erika Valeria Saliba, Danchin Etienne G. J., Grossi-de-Sa Maria Fatima. 2020. Evolutionarily conserved plant genes responsive to root-knot nematodes identified by comparative genomics. Molecular Genetics and Genomics, 295 (4) : 1063-1078.

Résumé : Root-knot nematodes (RKNs, genus Meloidogyne) affect a large number of crops causing severe yield losses worldwide, more specifically in tropical and sub-tropical regions. Several plant species display high resistance levels to Meloidogyne, but a general view of the plant immune molecular responses underlying resistance to RKNs is still lacking. Combining comparative genomics with differential gene expression analysis may allow the identification of widely conserved plant genes involved in RKN resistance. To identify genes that are evolutionary conserved across plant species, we used OrthoFinder to compared the predicted proteome of 22 plant species, including important crops, spanning 214 Myr of plant evolution. Overall, we identified 35,238 protein orthogroups, of which 6,132 were evolutionarily conserved and universal to all the 22 plant species (PLAnts Common Orthogroups—PLACO). To identify host genes responsive to RKN infection, we analyzed the RNA-seq transcriptome data from RKN-resistant genotypes of a peanut wild relative (Arachis stenosperma), coffee (Coffea arabica L.), soybean (Glycine max L.), and African rice (Oryza glaberrima Steud.) challenged by Meloidogyne spp. using EdgeR and DESeq tools, and we found 2,597 (O. glaberrima), 743 (C. arabica), 665 (A. stenosperma), and 653 (G. max) differentially expressed genes (DEGs) during the resistance response to the nematode. DEGs' classification into the previously characterized 35,238 protein orthogroups allowed identifying 17 orthogroups containing at least one DEG of each resistant Arachis, coffee, soybean, and rice genotype analyzed. Orthogroups contain 364 DEGs related to signaling, secondary metabolite production, cell wall-related functions, peptide transport, transcription regulation, and plant defense, thus revealing evolutionarily conserved RKN-responsive genes. Interestingly, the 17 DEGs-containing orthogroups (belonging to the PLACO) were also universal to the 22 plant species studied, suggesting that these core genes may be involved in ancestrally conserved immune responses triggered by RKN infection. The comparative genomic approach that we used here represents a promising predictive tool for the identification of other core plant defense-related genes of broad interest that are involved in different plant–pathogen interactions.

Mots-clés Agrovoc : Coffea arabica, expression des gènes, génome, gène, identification, rendement des cultures, conservation des ressources, Oryza glaberrima, réponse de la plante

Mots-clés libres : Transcriptome, Meloidogyne, Arachis, Soybean, Coffee, Rice

Agences de financement hors UE : Agropolis Fondation, Empresa Brasileira de Pesquisa Agropecuária, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Agence Nationale de la Recherche

Projets sur financement : (FRA) Agricultural Sciences for sustainable Development

Auteurs et affiliations

• Zotta Mota Ana, CIRAD-BIOS-UMR AGAP (FRA)
• Fernandez Diana, IRD (FRA)
• Arraes Fabricio B.M., EMBRAPA (BRA)
• Petitot Anne-Sophie, IRD (FRA)
• Paes de Melo Bruno, EMBRAPA (BRA)
• Lisei de Sa Maria E., EMBRAPA (BRA)
• Grynberg Priscila, EMBRAPA (BRA)
• Passos Saraiva Mario A., EMBRAPA (BRA)
• Messenberg Guimaraes Patricia, EMBRAPA (BRA)
• Brasileiro Ana Christina Miranda, EMBRAPA (BRA)
• Albuquerque Erika Valeria Saliba, EMBRAPA (BRA)
• Danchin Etienne G. J., INRA (FRA)
• Grossi-de-Sa Maria Fatima, EMBRAPA (BRA) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/605373/)

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