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6. The neighbouring genes AvrLm10A and AvrLm10B are part of a large multigene family of cooperating effector genes conserved in Dothideomycetes and Sordariomycetes

Author

Talbi, Nacera, primary, Fokkens, Like, additional, Audran, Corinne, additional, Petit‐Houdenot, Yohann, additional, Pouzet, Cécile, additional, Blaise, Françoise, additional, Gay, Elise J., additional, Rouxel, Thierry, additional, Balesdent, Marie‐Hélène, additional, Rep, Martijn, additional, and Fudal, Isabelle, additional

Published
2023
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7. The neighbouring genes AvrLm10A and AvrLm10B are part of a large multigene family of cooperating effector genes conserved in Dothideomycetes and Sordariomycetes

Author

Talbi, Nacera, Fokkens, Like, Audran, Corinne, Petit‐Houdenot, Yohann, Pouzet, Cécile, Blaise, Françoise, Gay, Elise J., Rouxel, Thierry, Balesdent, Marie Hélène, Rep, Martijn, Fudal, Isabelle, Talbi, Nacera, Fokkens, Like, Audran, Corinne, Petit‐Houdenot, Yohann, Pouzet, Cécile, Blaise, Françoise, Gay, Elise J., Rouxel, Thierry, Balesdent, Marie Hélène, Rep, Martijn, and Fudal, Isabelle

Abstract

Fungal effectors (small-secreted proteins) have long been considered as species or even subpopulation-specific. The increasing availability of high-quality fungal genomes and annotations has allowed the identification of trans-species or trans-genera families of effectors. Two avirulence effectors, AvrLm10A and AvrLm10B, of Leptosphaeria maculans, the fungus causing stem canker of oilseed rape, are members of such a large family of effectors. AvrLm10A and AvrLm10B are neighbouring genes, organized in divergent transcriptional orientation. Sequence searches within the L. maculans genome showed that AvrLm10A/AvrLm10B belong to a multigene family comprising five pairs of genes with a similar tail-to-tail organization. The two genes, in a pair, always had the same expression pattern and two expression profiles were distinguished, associated with the biotrophic colonization of cotyledons and/or petioles and stems. Of the two protein pairs further investigated, AvrLm10A_like1/AvrLm10B_like1 and AvrLm10A_like2/AvrLm10B_like2, the second one had the ability to physically interact, similarly to what was previously described for the AvrLm10A/AvrLm10B pair, and cross-interactions were also detected for two pairs. AvrLm10A homologues were identified in more than 30 Dothideomycete and Sordariomycete plant-pathogenic fungi. One of them, SIX5, is an effector from Fusarium oxysporum f. sp. lycopersici physically interacting with the avirulence effector Avr2. We found that AvrLm10A/SIX5 homologues were associated with at least eight distinct putative effector families, suggesting that AvrLm10A/SIX5 is able to cooperate with different effectors. These results point to a general role of the AvrLm10A/SIX5 proteins as “cooperating proteins”, able to interact with diverse families of effectors whose encoding gene is co-regulated with the neighbouring AvrLm10A homologue.

Published
2023

9. A new avirulence gene of Leptosphaeria maculans , AvrLm14 , identifies a resistance source in American broccoli ( Brassica oleracea ) genotypes

Author

Degrave, Alexandre, primary, Wagner, Marine, additional, George, Pierre, additional, Coudard, Laurent, additional, Pinochet, Xavier, additional, Ermel, Magali, additional, Gay, Elise J., additional, Fudal, Isabelle, additional, Moreno‐Rico, Onesimo, additional, Rouxel, Thierry, additional, and Balesdent, Marie‐Hélène, additional

Published
2021
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10. Additional file 22 of Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant

Author

Gay, Elise J., Soyer, Jessica L., Lapalu, Nicolas, Linglin, Juliette, Fudal, Isabelle, Silva, Corinne Da, Wincker, Patrick, Jean-Marc Aury, Cruaud, Corinne, Levrel, Anne, Lemoine, Jocelyne, Delourme, Regine, Rouxel, Thierry, and Balesdent, Marie-Hélène

Abstract

Additional file 22: Table S7. Genes with more than 10 reads in (A) at least one of the four replicates of samples at 24 h or 48 h after ascospore ejection on cotyledons (B) at least one of the nine replicates from the three samples of stem base tissues at 2, 3 or 5 months post sowing.

Published
2021
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11. Additional file 16 of Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant

Author

Gay, Elise J., Soyer, Jessica L., Lapalu, Nicolas, Linglin, Juliette, Fudal, Isabelle, Silva, Corinne Da, Wincker, Patrick, Jean-Marc Aury, Cruaud, Corinne, Levrel, Anne, Lemoine, Jocelyne, Delourme, Regine, Rouxel, Thierry, and Balesdent, Marie-Hélène

Abstract

Additional file 16: S4 Text. Comparison between the v1 and v2 versions of gene model annotations.

Published
2021
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12. Additional file 6 of Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant

Author

Gay, Elise J., Soyer, Jessica L., Lapalu, Nicolas, Linglin, Juliette, Fudal, Isabelle, Silva, Corinne Da, Wincker, Patrick, Jean-Marc Aury, Cruaud, Corinne, Levrel, Anne, Lemoine, Jocelyne, Delourme, Regine, Rouxel, Thierry, and Balesdent, Marie-Hélène

Abstract

Additional file 6: S3 Text. Generation of a new repertoire of small secreted proteins considered as candidate effectors.

Published
2021
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13. Additional file 4 of Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant

Author

Gay, Elise J., Soyer, Jessica L., Lapalu, Nicolas, Linglin, Juliette, Fudal, Isabelle, Silva, Corinne Da, Wincker, Patrick, Jean-Marc Aury, Cruaud, Corinne, Levrel, Anne, Lemoine, Jocelyne, Delourme, Regine, Rouxel, Thierry, and Balesdent, Marie-Hélène

Abstract

Additional file 4: S2 Text. Reproducibility between replicates.

Published
2021
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14. A gene‐for‐gene interaction involving a ‘late’ effector contributes to quantitative resistance to the stem canker disease in Brassica napus

Author

Jiquel, Audren, primary, Gervais, Julie, additional, Geistodt‐Kiener, Aude, additional, Delourme, Régine, additional, Gay, Elise J., additional, Ollivier, Bénédicte, additional, Fudal, Isabelle, additional, Faure, Sébastien, additional, Balesdent, Marie‐Hélène, additional, and Rouxel, Thierry, additional

Published
2021
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15. Large-scale transcriptomics to dissect two years of the life of a fungal phytopathogen interacting with its host plant

Author

Gay, Elise J., primary, Soyer, Jessica L., additional, Lapalu, Nicolas, additional, Linglin, Juliette, additional, Fudal, Isabelle, additional, Da Silva, Corinne, additional, Wincker, Patrick, additional, Aury, Jean-Marc, additional, Cruaud, Corinne, additional, Levrel, Anne, additional, Lemoine, Jocelyne, additional, Delourme, Regine, additional, Rouxel, Thierry, additional, and Balesdent, Marie-Hélène, additional

Published
2020
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17. De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing

Author

Dutreux, Fabien, Da Silva, Corinne, d’Agata, Léo, Couloux, Arnaud, Gay, Elise J., Istace, Benjamin, Lapalu, Nicolas, Lemainque, Arnaud, Linglin, Juliette, Noel, Benjamin, Wincker, Patrick, Cruaud, Corinne, Rouxel, Thierry, Balesdent, Marie-Hélène, Aury, Jean-Marc, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Genoscope, Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), France Genomique [ANR-10-INBS-09-08], PROMOSOL (Association pour la promotion de la selection des plantes oleagineuses), French National research agency (ANR) [ANR-12-ADAP-0009], Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
Statistics and Probability, Data Descriptor, oilseed rape, Leptosphaeria maculans, Leptosphaeria biglobosa, Brassica napus, Leptosphaeria genomes, oilseed rape, canola, [SDV]Life Sciences [q-bio], Library and Information Sciences, canola, Education, Ascomycota, Genome assembly algorithms, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, DNA sequencing, Sequence Analysis, RNA, Comparative genomics, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Genomics, Computer Science Applications, [SDE]Environmental Sciences, Genome, Fungal, Statistics, Probability and Uncertainty, Information Systems
Abstract

open; International audience; Leptosphaeria maculans and Leptosphaeria biglobosa are ascomycete phytopathogens of Brassica napus (oilseed rape, canola). Here we report the complete sequence of three Leptosphaeria genomes (L. maculans JN3, L. maculans Nz-T4 and L. biglobosa G12-14). Nz-T4 and G12-14 genome assemblies were generated de novo and the reference JN3 genome assembly was improved using Oxford Nanopore MinION reads. The new assembly of L. biglobosa showed the existence of AT rich regions and pointed to a genome compartmentalization previously unsuspected following Illumina sequencing. Moreover nanopore sequencing allowed us to generate a chromosome-level assembly for the L. maculans reference isolate, JN3. The genome annotation was supported by integrating conserved proteins and RNA sequencing from Leptosphaeria-infected samples. The newly produced high-quality assemblies and annotations of those three Leptosphaeria genomes will allow further studies, notably focused on the tripartite interaction between L. maculans, L. biglobosa and oilseed rape. The discovery of as yet unknown effectors will notably allow progress in B. napus breeding towards L. maculans resistance.

Published
2018
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