Genetic variation of Colletotrichum spp. causing leaf anthracnose disease in citrus (Citrus spp.) on Java, Indonesia

Abstract

Citrus is an important horticultural commodity in Indonesia, particularly for fresh consumption and as a raw material for processed products. Anthracnose caused by Colletotrichum spp. is an important disease of citrus that can substantially affect plant health and productivity. However, information on the diversity and identity of Colletotrichum species associated with citrus anthracnose in Java, Indonesia, remains limited. In this study, twelve Colletotrichum isolates were obtained from citrus leaves showing anthracnose symptoms collected from several citrus-growing regions in Java. The isolates were characterized based on morphological characteristics and genetic fingerprinting using repetitive element sequence-based PCR (rep-PCR) with BOX and ERIC primers. Seven representative isolates were subsequently selected for multilocus molecular identification and phylogenetic analysis based on partial sequences of five loci: internal transcribed spacer (ITS), actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-tubulin (TUB2), and Apn2-Mat1-2 intergenic spacer (ApMat). The multilocus phylogenetic analysis placed the representative isolates into two major lineages corresponding to Colletotrichum siamense and the C. gloeosporioides species complex. Morphological characteristics were generally consistent with their molecular placement, although considerable overlap was observed among isolates. Pathogenicity assays on detached citrus leaves showed that all representative isolates produced anthracnose-like lesions, with differences in lesion development among isolates. These findings demonstrate the occurrence of genetically and phenotypically variable Colletotrichum isolates associated with citrus leaf anthracnose in Java and provide baseline information for further studies on pathogen diversity and disease management.