Phylogenomic appraisal of morpho-pathogenicity try-out based identified pathogen causing stem and crown rot in Trifolium alexandrinum L.

Egyptian clover (Trifolium alexandrinum L.) is a leguminous crop cultivated in subtropical regions of the world as winter fodder. Stem and Crown rot of E. clover caused significant crop losses in Pakistan for the last few years. White mycelia and sclerotia of the fungus appeared on plants. The two-year survey data (2017-2018) of E. clover growing Provinces Punjab and Khyber Pakhtunkhwa revealed that the average disease severity index of Stem and Crown rot was 65.4% (2017) and 67.7% (2018) in Punjab and 60.9% (2017) and 64.8% (2018) in KPK. Putative fungal pathogen from infected plant tissues was isolated and identified using an integrated taxonomic study. Hyphae septate, almost transparent, developed into sclerotia (hard black) on PDA culture media. Internal transcribed spacer (ITS), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), 28S rRNA region (LSU), Calmodulin (CAL), and heat shock protein (HSP60) genetic regions were explored and deposited to NCBI with MT995056, MT937071, MT995060, MT954957, and MT978151 GenBank accession numbers respectively. Mophogenomics identified the fungus as Sclerotinia trifoliorum Erikss and proved to be a pathogen of Egyptian clover by fulfilling Koch's postulates. The average disease severity index was 44.6% on the cultivar Early (Agaiti), 20.8% on Late (Pachati) in Punjab province and 41.7% on Early (Agaiti) and 19.21% on Late (Pachati) in KPK province.