Chili (Capsicum annuum L.) and brinjal (Solanum melongena L.) are the most widely grown solanaceous crops in the world. However, their production has reduced over several years due to the attack of various fungal and bacterial pathogens and various abiotic factors. Still, the major constrain in their production are pathogens with fungal etiology, especially the fungal wilt of solanaceous crops. Fusarium oxysporum and Fusarium solani have been previously identified as the pathogens causing wilt disease in chili and brinjal. Recently, a new fungal pathogen F. equiseti has been reported as the causal agent of wilt disease infecting chili. The current study focused on identifying fungal pathogens associated with the wilted plants of chili and brinjal, collected from different parts of the Himalayan region of Kashmir valley, through morpho-cultural and molecular characterization. DNA extraction, PCR amplification, and sequencing were performed on various isolates. DNA barcoding using the internal transcribed spacer region (ITS) was used to identify the pathogen followed by the pathogenicity test. Further confirmation of the pathogen was done by sequencing of transcription elongation factor (TEF) and Calmodulin (CAL2). In current study Fusarium chlamydosporum has been reported as the wilt causing pathogen of chili and brinjal for the first time in Kashmir Himalayas.

BackgroundShot hole is one of the common fungal diseases in stone fruits viz., peach, plum, apricot and cherry, and almond in nuts, and is caused by Wilsonomyces carpophilus. Our previous research found that both disease incidence and severity is signi cantly 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 the Wilsonomyces carpophilus morphology, pathology, and genomics. Whole genome sequencing of the W. carpophilus was 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 fungus W. carpophiluscausing shot hole disease in stone fruits such as peach, plum, apricot and cherry, and almonds among the nut crops. The isolates collected from ve different hosts showed a signi cant difference in their morphology, however, the probability value (p=0.29) suggests in-signi cant difference in pathogenicity. Here, we report a W. carpophilus draft 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 the W. carpophilus pathogen were hydrolases, polysaccharidedegrading 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 the Pyrenochaeta species followed by Ascochyta rabiei andAlternaria alternate. ConclusionsThese ndings suggested that the draft genome of the Wilsonomyces carpophilus is 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 ve different hosts showed a signi cant 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 fo...

BackgroundThe conidial Ascomycota fungus Wilsonomyces carpophilus causing shot hole of stone fruits is a major constrain in the production of stone fruits worldwide. Shot hole disease symptoms appear on leaves, fruits, and twigs. Successful isolation of the pathogen from different hosts on synthetic culture medium is a time consuming and tedious procedure for identi cation of the pathogen based on morpho-cultural characterization. Methods and ResultsThe current research was carried out to develop a successful detection protocol for shot hole disease of stone fruits viz., peach, plum, apricot, cherry and almond using PCR based SSR markers that were designed from the Wilsonomyces carpophilus genome using Genome-wide Microsatellite Analysing Tool package (GMATA) software to detect the pathogen at early stages. Diseased leaf samples of stone fruits were collected and the pathogen isolated on potato dextrose agar (PDA) medium and maintained on Asthana and Hawkers' medium. For detection protocol, healthy and infected leaf samples of stone fruits were collected and DNA was extracted from the isolated pathogen cultures as well as from leaves infected shot hole disease along with the healthy control (DNA from healthy leaves of stone fruits). The successful ampli cation was observed in DNA extracted from all the pathogen isolates and from leaf samples with shot hole symptoms but was not observed in control (DNA from healthy leaves) thus con rming the detection of this disease from all the infected samples. ConclusionPCR based SSR makers were successfully designed for the for Wilsonomyces carpophilus causing shot hole disease in stone fruits and almond in nuts rst time. PCR based detection protocol was successfully developed for the detection of pathogen directly from infected leaves of stone fruits such as peach, plum, apricot, cherry and almond among the nuts.

Background The conidial Ascomycota fungus Wilsonomyces carpophilus causing shot hole of stone fruits is a major constrain in the production of stone fruits worldwide. Shot hole disease symptoms appear on leaves, fruits, and twigs. Successful isolation of the pathogen from different hosts on synthetic culture medium is a time consuming and tedious procedure for identification of the pathogen based on morpho-cultural characterization. Methods and Results The current research was carried out to develop a successful detection protocol for shot hole disease of stone fruits viz., peach, plum, apricot, cherry and almond using PCR based SSR markers that were designed from the Wilsonomyces carpophilus genome using Genome-wide Microsatellite Analysing Tool package (GMATA) software to detect the pathogen at early stages. Diseased leaf samples of stone fruits were collected and the pathogen isolated on potato dextrose agar (PDA) medium and maintained on Asthana and Hawkers’ medium. For detection protocol, healthy and infected leaf samples of stone fruits were collected and DNA was extracted from the isolated pathogen cultures as well as from leaves infected shot hole disease along with the healthy control (DNA from healthy leaves of stone fruits). The successful amplification was observed in DNA extracted from all the pathogen isolates and from leaf samples with shot hole symptoms but was not observed in control (DNA from healthy leaves) thus confirming the detection of this disease from all the infected samples. Conclusion PCR based SSR makers were successfully designed for the for Wilsonomyces carpophilus causing shot hole disease in stone fruits and almond in nuts first time. PCR based detection protocol was successfully developed for the detection of pathogen directly from infected leaves of stone fruits such as peach, plum, apricot, cherry and almond among the nuts.