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Cinchona calisaya (quina) is a medicinal plant native to southern Andes forest of South America. This plant and a some of its fungal endophytes have been known for their alkaloid activity against malarial diseases. However, information regarding fungal endophyte diversity within this plant is scarce. Therefore, it is necessary to carry out an endophyte diversity study on C. calisaya in order to reveal the entire fungal endophyte assemblage within this plant. The endophytes were analyzed using a culture‒dependent method, followed by molecular phylogenetic analysis based on complete nucleotide sequence data generated from the internal transcribed spacer (ITS) of ribosomal DNA region. Several common fungal endophytes genera were determined as follows: Diaporthe/Phomopsis, Glomerella/Colletotrichum, Guignardia/Phyllosticta, Fusarium, Pestalotiopsis, Cladosporium, Aspergillus, Penicillium and Trichoderma. Several members of plant pathogenic and saprobic fungi such as Cercospora, Ilyonectria, Pyrigemmula, Neofusicoccum, Leptosphaerulina and Peyronellaea were also reported here as endophytes. Among the endophytes, species of Diaporthe (Diaporthaceae) were the most common fungal endophytes in the quina plant, followed by species of Colletotrichum (Glomerellaceae) and Fusarium (Nectriaceae). Molecular phylogenetic analysis of ITS sequence data revealed many distinct undetermined clades in the fungal endophyte assemblages, which indicates that many cryptic species are probably present within tissues of C. calisaya.

Endophytic fungal diversity from Cinchona calisaya based on phylogenetic analysis of the ITS ribosomal DNA sequence data