Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors

David Lopez, Sébastien Ribeiro, Philippe Label, Boris Fumanal, Jean-Stéphane Venisse, Annegret Kohler, Ricardo R. de Oliveira, Kurt Labutti, Anna Lipzen, Kathleen Lail, Diane Bauer, Robin A. Ohm, Kerrie W. Barry, Joseph Spatafora, Igor V. Grigoriev, Francis M. Martin, Valérie Pujade-Renaud

Corynespora cassiicola is an Ascomycetes fungus with a broad host range and diverse life styles. Mostly known as a necrotrophic plant pathogen, it has also been associated with rare cases of human infection. In the rubber tree, this fungus causes theCorynesporaleaf fall (CLF) disease, which increasingly affects natural rubber production in Asia and Africa. It has also been found as an endophyte in South American rubber plantations where no CLF outbreak has yet occurred. TheC. cassiicolaspecies is genetically highly diverse, but no clear relationship has been evidenced between phylogenetic lineage and pathogenicity. Cassiicolin, a small glycosylated secreted protein effector, is thought to be involved in the necrotrophic interaction with the rubber tree but some virulentC. cassiicolaisolates do not have a cassiicolin gene. This study set out to identify other putative effectors involved in CLF. The genome of a highly virulentC. cassiicolaisolate from the rubber tree (CCP) was sequenced and assembled.In silicoprediction revealed 2870 putative effectors, comprising CAZymes, lipases, peptidases, secreted proteins and enzymes associated with secondary metabolism. Comparison with the genomes of 44 other fungal species, focusing on effector content, revealed a striking proximity with phylogenetically unrelated species (Colletotrichum acutatum, Colletotrichum gloesporioides, Fusarium oxysporum, nectria hematococca, andBotrosphaeria dothidea) sharing life style plasticity and broad host range. Candidate effectors involved in the compatible interaction with the rubber tree were identified by transcriptomic analysis. Differentially expressed genes included 92 putative effectors, among which cassiicolin and two other secreted singleton proteins. Finally, the genomes of 35C. cassiicolaisolates representing the genetic diversity of the species were sequenced and assembled, and putative effectors identified. At the intraspecific level, effector-based classification was found to be highly consistent with the phylogenomic trees. Identification of lineage-specific effectors is a key step toward understandingC. cassiicolavirulence and host specialization mechanisms.