Rhubarb he bottled in spirit (5)
I believe the answer is:
rheum
'rhubarb' is the definition.
The answer and definition can be both plants as well as being singular nouns.
Perhaps there's an association between them I don't understand?
'he bottled in spirit' is the wordplay.
'bottled in' means one lot of letters goes inside another.
'spirit' becomes 'rum' (alcoholic spirit).
'he' put into 'rum' is 'RHEUM'.
Can you help me to learn more?
(Other definitions for rheum that I've seen before include "Watery fluid" , "Catarrh" , "sign of illness" , "Flowing water" , "nasal drops" .)