Whole genome sequencing of Wilsonomyces carpophilus , an incitant of shot hole disease in stone fruits: insights into secreted proteins of a necrotrophic fungal repository

Background Shot hole is one of the important fungal diseases in stone fruits viz., peach, plum, apricot and cherry caused by Wilsonomyces carpophilus and almond among nut crops. Fungicides significantly decrease the disease. Pathogenicity studies proved a wide host range of the pathogen infecting all stone fruits and almond among the nut crops, however, the mechanism underlying host-pathogen interaction is still unknown. Molecular detection of the pathogen using polymerase chain reaction (PCR) based simple sequence repeat (SSR) markers is also unknown due to the unavailability of the pathogen genome. Methods and results We examined the morphology, pathology and genomics of the Wilsonomyces carpophilus . Whole genome sequencing of the W. carpophilus was carried out by Illumina HiSeq and PacBio high throughput sequencing plate-forms through hybrid assembly. Constant selection pressure alters the molecular mechanism of the pathogen causing disease. The studies revealed that the necrotrophs are more lethal with a complex pathogenicity mechanism and little-understood effector repositories. The different isolates of necrotrophic fungus W. carpophilus causing shot hole in stone fruits namely peach, plum, apricot and cherry, and almonds among the nut crops showed a significant variation in their morphology, however, the probability value (p = 0.29) suggests in-significant difference in the pathogenicity. Here, we reported draft genome of W. carpophilus of size 29.9 Mb (Accession number: PRJNA791904). A total of 10,901 protein-coding genes were predicted, including heterokaryon incompatibility genes, cytochrome-p450 genes, kinases, sugar transporters among others. We found 2851 simple sequence repeats (SSRs), tRNAs, rRNAs and pseudogenes in the genome. The most prominent proteins showing necrotrophic lifestyle of the pathogen were hydrolases, polysaccharide-degrading enzymes, esterolytic, lipolytic, and proteolytic enzymes accounted for 225 released proteins. Among the 223 fungal species, top-hit species distribution revealed the majority of hits against the Pyrenochaeta species followed by Ascochyta rabiei and Alternaria alternata. Conclusion Draft genome of W. carpophilus is 29.9 Mb based on Illumina HiSeq and PacBio hybrid assembly. The necrotrophs are more lethal with a complex pathogenicity mechanism. A significant variation in morphology was observed in different pathogen isolates. A total of 10,901 protein-coding genes were predicted in the pathogen genome including heterokaryon incompatibility, cytochrome-p450 genes, kinases and sugar transporters. We found 2851 SSRs, tRNAs, rRNAs and pseudogenes, and prominent proteins showing necrotrophic lifestyle such as hydrolases, polysaccharide-degrading enzymes, esterolytic, lipolytic and proteolytic enzymes. The top-hit species distribution were against the Pyrenochaeta spp. followed by Ascochyta rabiei.