Tree begins autumn pruning, putting leaves everywhere (5)
I believe the answer is:
Here is my best explanation:
'tree' is the definition.
(apple is a kind of tree)
'begins autumn pruning putting leaves everywhere' is the subsidiary indication.
'begins' indicates taking the first letters.
The initial letters of 'autumn pruning putting leaves everywhere' is 'apple'.
(Other definitions for apple that I've seen before include "Wood", "Pomaceous fruit", "US computer company", "sometimes green", "big in New York", "Fruit that keeps doctor away?", "Tree of the rose family", "Granny Smith, for one", "pie?" and "Jonathan, for example".)