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Colletotrichum higginsianum is an ascomycete fungus causing anthracnose disease on numerous cultivated plants in the familyBrassicaceae, as well as the model plant Arabidopsis thaliana. We report an assembly of the nuclear genome and gene annotation of this pathogen, which was obtained using a combination of PacBio long-read sequencing and optical mapping

Species of the genus Colletotrichum cause devastating anthracnose or blight diseases on numerous crop plants worldwide. C. higginsianum uses a hemibiotrophic strategy to infect Arabidopsis and other Brassicaceae. Compared to other hemibiotrophs, its genome contains an exceptionally large number of genes (78) encoding secondary metabolism (SM) key enzymes. As in other fungi, these key genes are organized into clusters that also contain genes encoding accessory enzymes of the same biosynthetic pathway and usually efflux transporters and pathway-specific transcription factors. A remarkable finding from RNA-Seq transcriptome profiling was that 27 SM clusters are specifically expressed only in planta by appressoria and/or biotrophic hyphae. Since each cluster potentially synthesizes one final metabolite, this suggests appressoria and biotrophic hyphae deliver a cocktail of different metabolites to the first infected host cell. At this early stage host cells remain alive, raising the possibility that these molecules function similar to protein effectors in host manipulation, rather than as simple phytotoxins. Work is ongoing to decipher how the expression of these SM gene clusters is so precisely regulated during the course of infection. We targeted C. higginsianum orthologs of the well-characterized global SM regulators LaeA, Hp1, Dim5, CclA and Kmt6 for genetic manipulation, with a view to inducing the fungus to synthesize appressorial metabolites in large quantities in culture. The aim is to obtain sufficient material for identification and structural determination (mass spectrometry, NMR) and for functional assays to evaluate their biological activities against plants, bacteria and fungi.