Chromosomes cut with stone instrument (9)
I believe the answer is:
xylophone
'instrument' is the definition.
(xylophone is a kind of instrument)
'chromosomes cut with stone' is the wordplay.
'chromosomes' becomes 'xy' (pair of sex chromosomes).
'cut' becomes 'lop' (lopping is a kind of cutting**).
'with' is a charade indicator (letters next to each other).
'stone' becomes 'hone' (hone is a kind of stone).
'xy'+'lop'+'hone'='XYLOPHONE'
(Other definitions for xylophone that I've seen before include "Percussion instrument played with small mallets" , "Instrument with wooden bars to be struck" , "Percussion instrument with wooden bars" , "Oxyphenol (anag.)" , "Patrick Moore's instrument" .)