Whole-genome sequencing and comparative genomic analysis of Plenodomus biglobosus

Blackleg disease, caused by Plenodomus biglobosus , presents a significant global threat to production. This pathogen reduces both yield and crop quality in Brassica species and is capable of cross-infecting other cruciferous vegetables. To better understand its infection mechanisms and virulence strategies, we performed whole-genome sequencing and assembly of the P. biglobosus nm-1 strain, isolated from the canola-producing region in Hailar, Inner Mongolia, using PacBio long-read sequencing technology. We also conducted comparative genomic analyses with three related Plennodomus species: P. lingam (the causal agent of canola stem base ulcer), P. lindquistii (sunflower blackleg), and P. tracheiphilus (citrus wilt). We assembled the genome of P. biglobosus nm-1, yielding a total size of 33.18 Mb, comprising 35 scaffolds and 9002 predicted genes, with a GC content of 49.56%. Functional genome annotation revealed 1,387 carbohydrate-active enzymes (CAZymes), including 526 glycoside hydrolases (GHs), which plays key roles in cellulose degradation. Pathogen-Host Interaction Database (PHI) analysis identified several pathogenicity-related genes. Comparative genomic analysis among four related plant pathogens identified 18,933 gene families, with 7,417 shared among all species. Phylogenetic and genome collinearity analysis confirmed that P. biglobosus is most closely related to P. lingam . In terms of carbohydrate-active enzymes, four pathogens breach plant mechanical barriers through synergistic action of pectin degradation and lignocellulose decomposition. Regarding transport proteins, P. tracheiphilus exhibited the highest number of DHA1 transporters, while P. lindquistii had a great number of DHA2 transporters. In P. biglobosus , core secondary metabolism genes encode products such as clavulanic acid and choline, etc., which may facilitate host infection. Conversely, in P. lingam and P. lindquistii , genes encode acrylamide toxins. These virulence-associated metabolites likely contribute to host specificity among Plenodomus species. Using whole genome shotgun sequencing, we conducted a comprehensive analysis of the P. biglobosus genome and identified several candidate genes potentially involved in pathogenicity. Through comparative genomics, we further investigated the key virulence factors and effectors across the four pathogens. These components play an essential role in pathogen-host plant interactions. Our findings provide valuable insights into the infection strategies and pathogenic mechanisms of blackleg pathogens.