Whole-Genome Sequencing and Genome Annotation of Pathogenic Elsinoë batatas Causing Stem and Foliage Scab Disease in Sweet Potato

A pathogen strain responsible for sweet potato stem and foliage scab disease was isolated from sweet potato stems. Through a phylogenetic analysis based on the rDNA internal transcribed spacer (ITS) region, combined with morphological methods, the isolated strain was identified as <i>Elsinoë batatas.</i> To comprehensively analyze the pathogenicity of the isolated strain from a genetic perspective, the whole-genome sequencing of <i>E. batatas</i> HD-1 was performed using both the PacBio and Illumina platforms. The genome of <i>E. batatas</i> HD-1 is about 26.31 Mb long in 167 scaffolds, with a GC content of 50.81%, and 7898 protein-coding genes, 131 non-coding RNAs, and 1954 interspersed repetitive sequences were predicted. Functional annotation revealed that 408 genes encode virulence factors involved in plant disease (DFVF-Plant). Notably, twenty-eight of these virulence genes encode secretory carbohydrate-active enzymes (CAZymes), including two endo-1,4-β-xylanase genes and seven cutinase genes, which suggested that endo-1,4-β-xylanase and cutinase play a vital role in the pathogenicity of <i>E. batatas</i> HD-1 within sweet potato. In total, twelve effectors were identified, including five LysM effectors and two CDIP effectors, suggesting that LysM and CDIP effectors play significant roles in the interaction between <i>E. batatas</i> HD-1 and sweet potato. Additionally, our analysis of biosynthetic gene clusters (BGCs) showed that two gene clusters are involved in melanin and choline metabolism. This study enriches the genomic resources of <i>E. batatas</i> and provides a theoretical foundation for future investigations into the pathogenic mechanisms of its infection in sweet potatoes, as well as potential targets for disease control.