Abstract
BackgroundMany species belonging to the genus Colletotrichum cause anthracnose disease on a wide range of plant species. In addition to their economic impact, the genus Colletotrichum is a useful model for the study of the evolution of host specificity, speciation and reproductive behaviors. Genome projects of Colletotrichum species have already opened a new era for studying the evolution of pathogenesis in fungi.ResultsWe sequenced and annotated the genomes of four strains in the Colletotrichum acutatum species complex (CAsc), a clade of broad host range pathogens within the genus. The four CAsc proteomes and secretomes along with those representing an additional 13 species (six Colletotrichum spp. and seven other Sordariomycetes) were classified into protein families using a variety of tools. Hierarchical clustering of gene family and functional domain assignments, and phylogenetic analyses revealed lineage specific losses of carbohydrate-active enzymes (CAZymes) and proteases encoding genes in Colletotrichum species that have narrow host range as well as duplications of these families in the CAsc. We also found a lineage specific expansion of necrosis and ethylene-inducing peptide 1 (Nep1)-like protein (NLPs) families within the CAsc.ConclusionsThis study illustrates the plasticity of Colletotrichum genomes, and shows that major changes in host range are associated with relatively recent changes in gene content.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2917-6) contains supplementary material, which is available to authorized users.
Highlights
Many species belonging to the genus Colletotrichum cause anthracnose disease on a wide range of plant species
The truncatum clade includes one major species (C. truncatum) and two poorly-known species (C. curcumae and C. jasminigenum); the second species has been removed from the analyses because the only existing isolate seems to be originated by hybridization event between one isolate of C. truncatum and one belonging to the CGsc
We compared the gene content of several members of the genus Colletotrichum and found that changes in several gene families, carbohydrate-active enzymes (CAZymes) and proteases are associated with two distantly related lineages of Colletotrichum spp. that have broad host range. In this manuscript, we provide an analysis of adaptations in gene content that are associated with broad host range in Colletotrichum spp
Summary
Many species belonging to the genus Colletotrichum cause anthracnose disease on a wide range of plant species. In addition to their economic impact, the genus Colletotrichum is a useful model for the study of the evolution of host specificity, speciation and reproductive behaviors. Plant pathogenic fungi exhibit remarkable differences in the number and diversity of hosts they are able to colonize and/or infect Based on their host range, phytopathogenic fungi can be categorised as specialists infecting a single plant or a small group of closely related plants (narrow host range), generalists associated with a wide variety of plants in diverse environments (broad host range), and transitional species capable of infecting. The trajectory of evolution of specialists and generalists in Colletotrichum pathogens, and how this change is mirrored in the genomic architecture of various species remain to be addressed
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