Initially tree's open root system omitted trunk (5)
I believe the answer is:
torso
'trunk' is the definition.
('torso' can be a synonym of 'trunk')
'initially tree's open root system omitted' is the wordplay.
'initially' suggests taking the first letters.
The initial letters of 'tree open root system omitted' is 'TORSO'.
(Other definitions for torso that I've seen before include "part of body will be found" , "Piece of bronze" , "Body's core" , "Body's trunk" , "Roost on trunk?" .)