Identification and Multigene Phylogenetic Analysis Reveal Alternaria as the Primary Pathogen Causing European Plum (Prunus domestica) Brown Spot in Xinjiang, China

European plum (<i>Prunus domestica</i>) orchards in the Kashi region, Xinjiang, China, suffer from fruit brown spot disease. The disease typically appears as red spots on the fruit surface that expand into brown necrotic lesions; affected fruit flesh can shrink, and fruits can harden and drop. We isolate and identify pathogens associated with this disease in this plum from five Kashi counties. Of 210 fungal isolates obtained through standard tissue isolation, <i>Alternaria</i> accounted for 84.8%, with the remainder comprising species of <i>Aspergillus</i> (9.5%), <i>Diplodia</i> (3.3%), and <i>Neoscytalidium</i> (2.4%). Using PCR amplification and sequencing of five loci, pathogens were identified using multi-gene phylogenetic analyses, combined with observations of colony and spore morphology. Multi-locus sequences of <i>Alternaria</i> isolates were highly homologous to those of the <i>Alternaria alternata</i> type strain, and we refer them to an <i>A. alternata</i> species complex. Pathogenicity tests confirm that <i>Alternaria</i> isolates reproduce brown spot symptoms on European plum fruits. By demonstrating that <i>Alternaria</i> is the primary pathogen causing brown spot disease in European plum in Xinjiang, we clarify both the fungal species composition and taxonomic placement of the dominant pathogen associated with this disease.