Organ tonality includes one reed’s lowest note (6)
I believe the answer is:
kidney
'organ' is the definition.
(kidney is a kind of organ)
'tonality includes one reed's lowest note' is the wordplay.
'tonality' becomes 'key' (synonyms).
'includes' means one lot of letters goes inside another.
'one' becomes 'i' (Roman numeral).
'lowest' suggests the final letters (in a down clue, the bottom-most letter).
'note' becomes 'n' (abbreviation).
The final letter of 'reed' is 'd'.
'i'+'d'+'n'='idn'
'key' going around 'idn' is 'KIDNEY'.
(Other definitions for kidney that I've seen before include "Organ filtering waste with water from blood" , "temperament" , "Bodily organ" , "Organ associated with steak" , "Renal organ" .)