Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi

Abstract

Summary 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.

The CD1/CD2 marker for specific detection of Colletotrichum lindemuthianum is an iron transporter pseudogene

“…The similarity between the Ftr1 pseudogene in C. lindemuthianum and C. orbiculare strongly suggests an evolutionary event that occurred previous to the separation of these closely related species (Liu et al, 2007;Cannon et al, 2012). The availability of the genomes of C. lindemuthianum, currently under study by our group, and C. orbiculare (Gan et al, 2013) will facilitate such evolutionary studies as well as a deeper understanding of key aspects of the host-pathogen interaction of this species complex. All these information may help to test the hypothesis of separation of these taxa from Colletotrichum at generic level due to its basal position in the phylogenectic studies developed for this genus (Cannon et al, 2012).…”

“…According to this analysis, the exact size for the CD1/CD2 amplicon must be 636 bp in the Colombian C. lindemuthianum isolates. A BLASTN search in the NCBI database resulted in a single hit to a 1,134,473 bp unplaced genomic scaffold of C. orbiculare MAFF 240422 (gb: KB726112) (Gan et al, 2013).…”

“…DNA sequencing has also been used to differentiate closely related species within the main Colletotrichum clades Cannon et al, 2012;Damm et al, 2013). The partial annotated genomes of C. higginsianum and C. graminicola, pathogens of maize (O'Connell et al, 2012) and of C. orbiculare and C. gloeosporioides isolated from strawberry (Gan et al, 2013) have identified pathogenicity-related genes.…”

Recognition of Verticillium effector Ave1 by tomato immune receptor Ve1 mediates Verticillium resistance in diverse plant species

“…citri (XacPNP), the fungal tomato wilt pathogen Fusarium oxysporum f. sp. lycopersici (FoAve1), the fungal sugar beet leaf spot pathogen Cercospora beticola (CbAve1), the crucifer anthracnose pathogen Colletotrichum higginsianum (ChAve1) and the cucurbit anthracnose pathogen Colletotrichum orbiculare (CoAve1) Gan et al, 2013), and a few of these homologs are differentially recognized by tomato Ve1 . Consequently, Ve1 1 was found to mediate resistance towards F. oxysporum in tomato, demonstrating involvement of this tomato immune receptor in resistance against multiple fungal pathogens ( .…”

“…Constructs for constitutive expression of Ave1, FoAve1, CbAve1, ChAve1 were described previously . CoAve1 (Gan et al, 2013) and XacPNP (Gottig et al, 2008) were obtained by gene synthesis (Eurofins MWG Operon, Ebersberg, Germany), and subsequently recombined into the destination vector pSol2092 (Zhang et al, 2013a) to generate expression constructs pSol2092_CoAve1 and pSol2092_XacPNP. All constructs were transformed to Agrobacterium tumefaciens strain GV3101 (pMP90) by electroporation.…”