Paper covers nearly bankrupt seed repository (5)
I believe the answer is:
fruit
'seed repository' is the definition.
(fruits contain seeds)
'paper covers nearly bankrupt' is the wordplay.
'paper' becomes 'FT' (newspaper the FT, Financial Times).
'covers' indicates putting letters inside.
'nearly' means to remove the last letter.
'bankrupt' becomes 'ruin' (synonyms).
'ruin' with its last letter taken away is 'rui'.
'ft' enclosing 'rui' is 'FRUIT'.
(Other definitions for fruit that I've seen before include "Kiwi, mandarin etc" , "Eg, banana or apple" , "See 9" , "Eg, bananas" , "Apples, pears etc" .)