Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum

Abstract

Background: 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. Genome projects of Colletotrichum species have already opened a new era for studying the evolution of pathogenesis in fungi.

Results: We 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.

Conclusions: This study illustrates the plasticity of Colletotrichum genomes, and shows that major changes in host range are associated with relatively recent changes in gene content.

Keywords: Anthracnose; CAZyme; Colletotrichum spp.; Fungal genomics; Plant pathogen.

Fig. 1

Evolutionary relationships among ten Colletotrichum species and seven additional species used for comparative analyses. The tree was constructed using Bayesian MCMC analysis constructed from the alignment based on the concatenated alignment of the five most phylogenetically informative single copy gene families

Fig. 2

Hierarchical clustering of IPR terms expanded in Colletotrichum acutatum and C. gloeosporioides species complexes compared to other Colletotrichum species and other model fungal genomes. Number of genes characterized by each IPR has been normalized using MeV 4.8.1. Hierarchical clustering of genes and species was performed and visualized using the package “pheatmap” 1.0.8 within R Overrepresented (orange to red) and underrepresented functional domains (blue) are depicted as fold changes relative to the IPR term mean

Fig. 3

a Distribution of secreted enzymes belonging to each CAZy (Carbohydrate Active enZymes) class identified in the genomes used in this study. The legend on the bottom reports the designation of enzyme classes: Glycoside Hydrolases (GH), Glycosyl Transferases (GT), Polysaccharide Lyases (PL), Carbohydrate Esterases (CE), Auxiliary Activities (AA). The legend on the bottom reports the designation of enzyme classes: Glycoside Hydrolases (GH), Glycosyl Transferases (GT), Polysaccharide Lyases (PL), Carbohydrate Esterases (CE), Auxiliary Activities (AA). b Extracellular secreted protease homologs classified according to the MEROPS database 10.0 [45] in Colletotrichum and other fungal genomes used in this study

Fig. 4

Phylogenetic reconstruction of secreted necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs). Blue branches highlight gene family expansions in Colletotrichum acutatum species complex and green branches expansions in other Colletotrichum species. The bar diagram shows the overall numbers of putative secreted NLPs identified in the genomes used in this study

Fig. 5

Lineage Specific Effector protein Candidates (LSECs) identified in Colletotrichum and other fungal genomes used in this study, based on no-BLAST sequence similarity with proteins predicted in other species (red) or other genera (green)

Fig. 6

a Secondary metabolite-related backbones genes including non-ribosomal peptide synthetases (NRPS), polyketide synthases (PKS), DMATS-family aromatic prenyltransferases (DMATS), and terpene synthases/cyclases (TS) identified in the fungal genomes used in this study. b Cytochrome P450 monooxygenases genes identified in Colletotrichum species and the other fungal genomes used in this study. c. Secondary metabolite clusters predicted by antiSMASH [48] in Colletotrichum and the other fungal genomes used in this study