Pinus thunbergii vs pine tree

Pinus thunbergii and pine tree both are nouns.

Word	Noun	Adjective	Verb	Adverb
Pinus thunbergii	Yes	No	No	No
pine tree	Yes	No	No	No

As nouns, pine tree is a hypernym of Pinus thunbergii; that is, pine tree is a word with a broader meaning than Pinus thunbergii:

Pinus thunbergii: large Japanese ornamental having long needles in bunches of 2; widely planted in United States because of its resistance to salt and smog
pine tree: a coniferous tree

Other hypernyms of Pinus thunbergii include pine, true pine.

Pinus thunbergii (noun)	pine tree (noun)
large Japanese ornamental having long needles in bunches of 2; widely planted in United States because of its resistance to salt and smog	a coniferous tree