Whole genome sequence of Wilsonomyces carpophilus, the causal agent of shot hole disease of stone fruits: insights into secreted proteins of a necrotrophic fungal repository
Authors: Nabi Asha , K Sehla , Padder Bilal A. , Sofi T.A. , Masoodi Khalid Z. , Shah Mehraj D. 
Published: November 2022

BackgroundShot hole is one of the common fungal diseases in stone fruitsviz., peach, plum, apricot and cherry, and almond in nuts, and is caused byWilsonomyces carpophilus. Our previous research found that both disease incidence and severity is significantly decreased after fungicide application. The pathogenicity studies proved the wide host range of the pathogen infecting all stone fruits and almond among nut crops, however, the mechanisms underlying the host-pathogen interaction was still limited. Additionally, the polymerase chain reaction (PCR) based molecular detection of the pathogen infecting different stone fruits using simple sequence repeat (SSR) markers was also unknown due to the unavailability of pathogen genome.Methods and ResultsWe examined theWilsonomyces carpophilusmorphology, pathology, and genomics. Whole genome sequencing of theW. carpophiluswas carried out by Illumina HiSeq and PacBio next generation sequencing (NGS) plate-forms by hybrid assembly. Molecular mechanisms employed by the pathogens to cause disease are altered as a result of constant selection pressure. The studies revealed that the necrotrophs are more lethal, with a complex pathogenicity mechanism and little-understood effector repositories. As a result, we underpin the information about necrotrophic plant pathogenic fungusW. carpophiluscausing shot hole disease in stone fruits such as peach, plum, apricot and cherry, and almonds among the nut crops. The isolates collected from five different hosts showed a significant difference in their morphology, however, the probability value (p=0.29) suggests in-significant difference in pathogenicity. Here, we report aW. carpophilusdraft genome assembly of 29.9 megabase (Accession number: PRJNA791904). A total of 10,901 protein-coding genes have been predicted, including heterokaryon incompatibility genes, cytochrome-p450 genes, kinases, sugar transporters, among others. In the genome assembly, we found 2851 simple sequence repeats (SSRs). The most prominent proteins showing the necrotrophic lifestyle of theW. carpophiluspathogen were hydrolases, polysaccharide-degrading enzymes, esterolytic, lipolytic, and proteolytic enzymes accounted for 225 released proteins. In the pathogen genome, we discovered tRNAs, rRNAs, and pseudogenes. Among 223 selected fungal species, the top-hit species distribution revealed the majority of hits against thePyrenochaetaspecies followed byAscochyta rabieiandAlternaria alternate.ConclusionsThese findings suggested that the draft genome of theWilsonomyces carpophilusis 29.9 MB based on Illumina HiSeq and PacBio hybrid sequencing assembly. The studies revealed that the necrotrophs are more lethal, with a complex pathogenicity mechanism and little-understood effector repositories. The isolates collected from five different hosts showed a significant difference in their morphology. Total 10901 protein-coding genes have been predicted in the genome including heterokaryon incompatibility and cytochrome-p450 genes, kinases, sugar transporters etc. We also found 2851 simple sequence repeats (SSRs). The prominent proteins showing necrotrophic lifestyle were hydrolases, polysaccharide-degrading enzymes, esterolytic, lipolytic and proteolytic enzymes accounted for 225 released proteins. In addition, we discovered tRNAs, rRNAs, and pseudogenes and the top-hit species distribution revealed the majority hits against thePyrenochaetaspecies followed byAscochyta rabiei.