title: Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi.
abstract: Hemibiotrophic fungal plant pathogens represent a group of agronomically significant disease-causing agents that grow first on living tissue and then cause host death in later, necrotrophic growth. Among these, Colletotrichum spp. are devastating pathogens of many crops. Identifying expanded classes of genes in the genomes of phytopathogenic Colletotrichum, especially those associated with specific stages of hemibiotrophy, can provide insights on how these pathogens infect a large number of hosts. The genomes of Colletotrichum orbiculare, which infects cucurbits and Nicotiana benthamiana, and C. gloeosporioides, which infects a wide range of crops, were sequenced and analyzed, focusing on features with potential roles in pathogenicity. Regulation of C. orbiculare gene expression was investigated during infection of N. benthamiana using a custom microarray. Genes expanded in both genomes compared to other fungi included sequences encoding small, secreted proteins (SSPs), secondary metabolite synthesis genes, proteases and carbohydrate-degrading enzymes. Many SSP and secondary metabolite synthesis genes were upregulated during initial stages of host colonization, whereas the necrotrophic stage of growth is characterized by upregulation of sequences encoding degradative enzymes. Hemibiotrophy in C. orbiculare is characterized by distinct stage-specific gene expression profiles of expanded classes of potential pathogenicity genes.
authors.affiliation: Plant Science Center, RIKEN, Yokohama, Japan.
authors.forename: Pamela
authors.initials: P
authors.lastname: Gan
authors.affiliation: Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
authors.forename: Kyoko
authors.initials: K
authors.lastname: Ikeda
authors.affiliation: Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Irieda
authors.affiliation: Research Institute for Biological Sciences, Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Okayama, Japan.
authors.forename: Mari
authors.initials: M
authors.lastname: Narusaka
authors.affiliation: Max Planck Institute for Plant Breeding Research, Cologne, Germany.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: O'Connell
authors.affiliation: Research Institute for Biological Sciences, Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Okayama, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Narusaka
authors.affiliation: Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Takano
authors.affiliation: Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan.
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Kubo
authors.affiliation: Plant Science Center, RIKEN, Yokohama, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Shirasu
mesh_terms: D001482:Base Composition; D020231:Colletotrichum / Q000235:genetics / Q000502:physiology*; D019662:Cucurbitaceae / Q000382:microbiology; D004271:DNA, Fungal; D020869:Gene Expression Profiling; D005800:Genes, Fungal; D016681:Genome, Fungal; D023281:Genomics; D010935:Plant Diseases / Q000382:microbiology; D017422:Sequence Analysis, DNA; D014026:Nicotiana / Q000382:microbiology; D059467:Transcriptome
chemical_list: D004271:DNA, Fungal