Japanese lime vs lime tree

Japanese lime and lime tree both are nouns.

Word	Noun	Adjective	Verb	Adverb
Japanese lime	Yes	No	No	No
lime tree	Yes	No	No	No

As nouns, lime tree is a hypernym of Japanese lime; that is, lime tree is a word with a broader meaning than Japanese lime:

Japanese lime: medium-sized tree of Japan used as an ornamental
lime tree: any of various deciduous trees of the genus Tilia with heart-shaped leaves and drooping cymose clusters of yellowish often fragrant flowers; several yield valuable timber

Other hypernyms of Japanese lime include basswood, lime, linden, linden tree.

Japanese lime (noun)	lime tree (noun)
medium-sized tree of Japan used as an ornamental	any of various related trees bearing limes
	any of various deciduous trees of the genus Tilia with heart-shaped leaves and drooping cymose clusters of yellowish often fragrant flowers; several yield valuable timber