Isolation, identification, pathogenicity test and molecular characterization of Fusarium oxysporum f. sp. zingiberi causing Fusarium yellows disease from infected rhizomes of ginger (Zingiber officinale Rosc.)

Fusarium oxysporum f. sp. zingiberi, the cause of Fusarium yellows rhizome rot is a major threat to ginger. This fungus causes huge losses to the ginger plants in the field as well as rhizome rot during storage. The current investigation was carried out to identify and molecularly characterize F. oxysporum isolates associated with the rhizome rot of ginger in Solan, India. The fungal isolation and purification was done on potato dextrose agar (PDA) media. The pure culture was obtained by routine subcultures and maintained on PDA slants. The colonies were initially identified by morphological appearance which is pinkish white cottony and purple undersurface on PDA plates. Afterward, microscopic identification was performed which resulted in septate mycelium and sickle shaped macro and micro conidia. In vivo and in vitro pathogenicity assays were also performed which demonstrated the highly pathogenic nature of the fungus. Finally, the pathogen was confirmed by next generation sequencing using internal transcribed spacer (ITS) and Fusarium specific translation elongation factor 1 alpha (TEF1a) primers. Nucleotide sequence obtained after sequencing was analyzed with BLAST tool on NCBI and the pathogen was confirmed as F. oxysporum with maximum similarity with other isolates. Phylogenetic tree obtained clearly showed the similarity of our sequence with other strains of F. oxysporum and diversity with other Fusarium species along with outgroup fungi. The sequence was submitted to NCBI GenBank under accession number MT815912. This is the first report on sequence based characterization of F. oxysporum f. sp. zingiberi from infected ginger rhizomes in India.