Intraspecific Comparative Analysis Reveals Genomic Variation of Didymella arachidicola and Pathogenicity Factors Potentially Related to Lesion Phenotype

Simple Summary Didymella arachidicola, the causal agent of peanut web blotch, leads to severe defoliation at the late growth stage of peanuts, and eventually to significant yield losses of up to 30%. The biology, ecology, and taxonomy of this phytopathogenic fungi have been well-studied; however, no study has focused on its genomic variation and pathogenic phenotype. Herein, we reported the first chromosome-scale genome assembly of D. arachidicola, which provides a reliable baseline for further comparative studies of plant pathogenic fungi. Combined with genome re-sequencing, we revealed the genomic variation within the D. arachidicola population, as well as comprehensively analyzed the pathogenicity-related genes to preliminarily explain their roles in forming different lesion phenotypes of peanut web blotch. This work set a genomic foundation and an adaptive landscape of D. arachidicola for understanding its genomic diversity and adaptive evolution, in parallel to the correlation of genotype and phenotype underlying the evolutionary force. Didymella arachidicola is one of the most important fungal pathogens, causing foliar disease and leading to severe yield losses of peanuts (Arachis hypogaea L.) in China. Two main lesion phenotypes of peanut web blotch have been identified as reticulation type (R type) and blotch type (B type). As no satisfactory reference genome is available, the genomic variations and pathogenicity factors of D. arachidicola remain to be revealed. In the present study, we collected 41 D. arachidicola isolates from 26 geographic locations across China (33 for R type and 8 for B type). The chromosome-scale genome of the most virulent isolate (YY187) was assembled as a reference using PacBio and Hi-C technologies. In addition, we re-sequenced 40 isolates from different sampling sites. Genome-wide alignments showed high similarity among the genomic sequences from the 40 isolates, with an average mapping rate of 97.38%. An average of 3242 SNPs and 315 InDels were identified in the genomic variation analysis, which revealed an intraspecific polymorphism in D. arachidicola. The comparative analysis of the most and least virulent isolates generated an integrated gene set containing 512 differential genes. Moreover, 225 genes individually or simultaneously harbored hits in CAZy-base, PHI-base, DFVF, etc. Compared with the R type reference, the differential gene sets from all B type isolates identified 13 shared genes potentially related to lesion phenotype. Our results reveal the intraspecific genomic variation of D. arachidicola isolates and pathogenicity factors potentially related to different lesion phenotypes. This work sets a genomic foundation for understanding the mechanisms behind genomic diversity driving different pathogenic phenotypes of D. arachidicola.