The phylogenetic position of 50 isolates of the genus Botryosphaeria isolated from 31 host plant species in the 19 families in Japan were analyzed using the combined sequences consisting of partial DNA sequences of rDNA ITS, rpb2, tef1-α, and tub2 regions. As a result, one isolate obtained from Gamblea innovans formed a clade with B. qingyuanensis from China. The other 49 isolates formed a large clade with B. dothidea epitype and its related species. Isolates from Brown blight of walnut and Guignardia canker of Japanese alder formed small subclades of B. dothidea, respectively. It was suggested that the host species and morphological characterstics may be effective in species distinction in this genus. However, the resolution for species distinction by the multi-region analyses adopted in the present study was seemed not to be enough to distinguish B. dothidea species complex. Therefore, we need alternative and additional phylogenetic approach that will divide species complex of B. dothidea. In addition, morphological, biological, and ecological characterization are necessary to reveal probable several species included in the species complex of B. dothidea.
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