Bond contracted to leave port shortly with plant (6)
I believe the answer is:
bonsai
'plant' is the definition.
The answer is an example.
I can't explain the rest of the clue.
Can you help me to learn more?
(Other definitions for bonsai that I've seen before include "Japanese method of cultivating miniature trees" , "specimen with restricted roots?" , "(Cultivation of) dwarf trees" , "Mini-tree growing" , "Japanese shrub" .)