Choice of stem and stern for Argonaut given a vessel (5)
I believe the answer is:
aorta
'vessel' is the definition.
(aorta is a kind of vessel)
'choice of stem and stern for argonaut given a' is the wordplay.
'choice of stem' becomes 'ao' (I am not sure about this - if you are sure you should believe this answer much more).
'and' says to put letters next to each other.
'stern' indicates one should take the final letters (I've seen 'stern of' mean this (stern can mean back)).
'given' is a charade indicator (letters next to each other).
The final letters of 'for argonaut' are 'rt'.
'ao'+'rt'+'a'='AORTA'
(Other definitions for aorta that I've seen before include "main arterial route" , "One leads from heart" , "sort of vessel" , "Large trunk artery" , "blood flows from it" .)