Malus pumila vs apple tree

Malus pumila and apple tree both are nouns.

Word	Noun	Adjective	Verb	Adverb
Malus pumila	Yes	No	No	No
apple tree	Yes	No	No	No

As nouns, apple tree is a hypernym of Malus pumila; that is, apple tree is a word with a broader meaning than Malus pumila:

Malus pumila: native Eurasian tree widely cultivated in many varieties for its firm rounded edible fruits
apple tree: any tree of the genus Malus especially those bearing firm rounded edible fruits

Malus pumila (noun)	apple tree (noun)
native Eurasian tree widely cultivated in many varieties for its firm rounded edible fruits	any tree of the genus Malus especially those bearing firm rounded edible fruits