Coffee substitute that comes in a cup (5)
I believe the answer is:
acorn
'coffee substitute that' is the definition.
The definition and answer can be both plants as well as being singular nouns.
Maybe you can see a link between them that I can't see?
'in a cup' is the wordplay.
'in' indicates putting letters inside.
'a' becomes 'an'.
'cup' becomes 'cor' (I can't explain this - if you can you should give a lot more credence to this answer).
'an' placed around 'cor' is 'ACORN'.
'comes' acts as a link.
Can you help me to learn more?
(Other definitions for acorn that I've seen before include "mast" , "Potentially future tree" , "oak's fruit" , "Fruit of the oak tree" , "Tree seed" .)