Stem-end and calyx-end rots are common in Red and Golden Delicious apples, while infections through fruit lenticels are common in Fuji. The decayed tissue is firm or spongy with light tan to brown, which is very similar to gray mold and Sphaeropsis rot. Brown to black specks with a white to light tan center may present on lenticels of red apple cultivars; however, gray mold apples also have similar specks. In the advanced stage, decayed area becomes black, full of pycnidia that are easily stuck to the surface of cardboard apple trays. Phacidiopycnis rot has a distinct odor, often not distinguishable from Sphaeropsis rot.
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