Table 1.
The list of fungal genomes used for comparative analysis with C. truncatum sequenced in the present study (in bold).
Table 2.
Assembly statistics of the C. truncatum genome assembly.
Fig 1.
The synteny plot between C. higginsianum and C. truncatum genomes obtained using SyMAP.
The circular plot shows some of the syntenic blocks between the scaffolds of C. truncatum in lower half of the circle mapping to the reference chromosomes of C. higginsianum in upper half joined with the lines of same colour as the reference.
Fig 2.
A maximum likelihood tree of Colletotrichum species and other fungi with diverse lifestyles.
Bootstrap support values (1000 replicates) of 100% were obtained at the nodes. A. nidulans was taken as an outgroup for the analysis. The Colletotrichum species complexes and the families are shown in parallel. C. truncatum, C. gloeosporioides and C. orbiculare form a separate clade in the Colletotrichum genus suggesting their origin from a common ancestor.
Fig 3.
Work flow for functional annotation of some of the gene categories relevant to pathogenicity.
A stringent pipeline of tools was used to predict 1257 proteins that are highly likely to be secreted and other important categories like carbohydrate active enzymes (CAZymes), proteases and secondary metabolism (SM) gene clusters. 310 of the secreted proteins were predicted to be putative effectors, 477 were secreted CAZymes and 71 were secreted proteases. Secondary metabolite backbone genes were not detected in the secretome.
Fig 4.
Analysis of different CAZyme families in C. truncatum.
(A) The total number and category of CAZymes in predicted proteome (outer circle), secretome (middle circle) and putative effectors (inner circle) are shown. (B) The fraction of genes of major families of all the CAZyme classes, viz., glycoside hydrolases (GHs), glycosyltransferase (GTs), auxillary activities (AAs), carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs) and polysaccharide lyases (PLs) are shown.
Fig 5.
The heatmap showing important fungal and plant cell wall degrading CAZyme families in the proteomes of different fungi.
The members of graminicola species complex that specifically infect monocot hosts clustered away from the rest of the Colletotrichum species while C. fructicola and C. truncatum with broad host range showed the maximum expansion of pectin degrading CAZyme families within the genus.
Fig 6.
The comparative analysis of protease families in different fungal genomes.
Phylogenetic tree of fungi with diverse lifestyles is shown with corresponding protease families in each fungal genome. C. truncatum had the largest protease component among Colletotrichum species due to expansion of metallo- and serine proteases.
Fig 7.
The comparative analysis of secondary metabolite (SM) gene clusters (line graph) and SM backbone genes (bar graph) predicted in different fungi using SMURF.
Colletotrichum species had maximum expansion of SM backbone genes among all the fungi analysed, while Verticillium species showed contraction of these genes.
Fig 8.
Venn diagram showing the overlap of different gene categories relevant to fungal pathogenicity.
Overlap of secretory proteins and PHI-homologues with CAZymes and proteases (A), and cytochrome P450 and transporters with homologues in TCDB (B) representing the putative pathogenicity related genes with diverse functions.
Fig 9.
Differentially expressed genes under different conditions and infection stages in vitro and in planta.
(A) Number of differentially regulated genes of C. truncatum in APR and PDA compared to CZ and APR compared to PDA. (B) Number of differentially regulated genes of C. truncatum in planta at 24 and 72 hpi compared to 0 hpi (control, uninfected chilli) and at 72 hpi in comparison to 24 hpi. (C) Number of differentially regulated genes of chilli for 24 and 72 hpi in comparison to 0 hpi.
Fig 10.
The number of secreted proteins and putative effectors, predicted using EffectorP, in all the fungal species analysed.
C. fructicola and C. truncatum had the largest number of secreted proteins while Magnaporthe species had the largest effector component.