The genomics of colletotrichum

Members of the genus Colletotrichum cause anthracnose diseases on nearly every crop grown for food, fiber, and forage worldwide. Colletotrichum fungi display a broad range of lifestyles, including plant associations occupying a continuum from necrotrophy to intracellular hemibiotrophy (IH) to endophytism. There are at least three major variants of IH, differing in the duration of biotrophy and synchronization of the switch to necrotrophy. Comparative genomic analyses may uncover how these lifestyles evolved and their functional relationships, identify commonalities as potential conserved targets for control and management, and transform our current understanding of Colletotrichum taxonomy. The genome sequences of four species were recently published: C. graminicola; C. higginsianum; C. obiculare; and C. fructicola (reported as C. gloeosporioides). These species occupy distinct monophyletic lineages in the genus and represent three different lifestyles (two variants of IH, and necrotrophy). The Colletotrichum genomes are relatively large (58-88 Mb), and encode between 11,000 and 16,000 genes. They share little synteny, suggesting that large-scale genome rearrangements were common during the evolutionary history of the genus. Several gene families are expanded in Colletotrichum relative to other sequenced ascomycetes, including those encoding carbohydrate-active enzymes, secondary metabolism enzymes, secreted proteases, and putative secreted effectors. Analysis of the in planta transcriptomes of C. higginsianum, C. graminicola, and C. orbiculare suggested that appressoria and biotrophic intracellular hyphae function as platforms for the secretion of effectors and secondary metabolites to establish host compatibility, while hyphae developing after the switch to necrotrophy are primarily involved in secreting cell wall degrading enzymes and nutrient uptake.