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. 2024 Sep 13;10(9):651.
doi: 10.3390/jof10090651.

Comparative Genomic Analyses of Colletotrichum lindemuthianum Pathotypes with Different Virulence Levels and Lifestyles

Ma Irene Morelos-Martínez  1 , Horacio Cano-Camacho  1 , Karla Morelia Díaz-Tapia  1 , June Simpson  2 , Everardo López-Romero  3 , María Guadalupe Zavala-Páramo  1
Affiliations

Comparative Genomic Analyses of Colletotrichum lindemuthianum Pathotypes with Different Virulence Levels and Lifestyles

Ma Irene Morelos-Martínez et al. J Fungi (Basel). .

Abstract

Colletotrichum lindemuthianum is the most frequent pathogenic fungus of the common bean Phaseolus vulgaris. This filamentous fungus employs a hemibiotrophic nutrition/infection strategy, which is characteristic of many Colletotrichum species. Due to host-pathogen coevolution, C. lindemuthianum includes pathotypes with a diversity of virulence against differential common bean varieties. In this study, we performed comparative genomic analyses on three pathotypes with different virulence levels and a non-pathogenic pathotype, isolated from different geographical areas in Mexico. Our results revealed large genomes with high transposable element contents that have undergone expansions, generating intraspecific diversity. All the pathotypes exhibited a similar number of clusters of orthologous genes (COGs) and Gene Ontology (GO) terms. TFomes contain families that are typical in fungal genomes; however, they show different contents between pathotypes, mainly in transcription factors with the fungal-specific TF and Zn2Cys6 domains. Peptidase families mainly contain abundant serine peptidases, metallopeptidases, and cysteine peptidases. In the secretomes, the number of genes differed between the pathotypes, with a high percentage of candidate effectors. Both the virulence gene and CAZyme gene content for each pathotype was abundant and diverse, and the latter was enriched in hemicellulolytic enzymes. We provide new insights into the nature of intraspecific diversity among C. lindemuthianum pathotypes and the origin of their ability to rapidly adapt to genetic changes in its host and environmental conditions.

Keywords: CAZymes; TFomes; effectors; genomic; intraspecific diversity; pathotypes; proteases; transposable elements; virulence genes.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Percentage of repetitive and transposable element families in the genomes of the Mexican pathotypes P0, P1088, P1472, P2395, and the Brazilian strain S89 of C. lindemuthianum.
Figure 2
Figure 2
Plots of the copy-number divergence analysis of TE classes, based on Kimura distances for the genomes of Mexican C. lindemuthianum pathotypes and strain S89 from Brazil. The percentage of TEs in the genomes is represented on the Y axis and Kimura distance values are plotted on the X axis in which TE copies with recent divergence are close to 0 and copies with previous divergence are close to 60).
Figure 3
Figure 3
Venn diagram summarizing the annotations shared among C. lindemuthianum pathotypes and the unique annotations for each pathotype.
Figure 4
Figure 4
Phylogenomic relationships among the C. lindemuthianum pathotypes.
Figure 5
Figure 5
Functional classification of clusters of orthologous genes (COGs) of C. lindemuthianum pathotypes.
Figure 6
Figure 6
Heatmap representation of numbers of TF genes found in the C. lindemuthianum pathotypes.
Figure 7
Figure 7
Peptidase families found in C. lindemuthianum pathotypes.
Figure 8
Figure 8
Venn diagrams summarizing the comparison of numbers of virulence factors involved in pathogenicity identified using the plant–pathogen interactions (PHI) database. (A) Comparison of the predicted virulence factors of C. lindemuthianum pathotypes with the PHI database. (B) Comparison of the predicted virulence factors between C. lindemuthianum pathotypes and those of the genus Colletotrichum.
Figure 9
Figure 9
Number of CAZyme families in the C. lindemuthianum pathotypes.
Figure 10
Figure 10
Heatmap representation of the CAZyme families in the C. lindemuthianum pathotypes.
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