Virginia pine vs pine tree

Virginia pine and pine tree both are nouns.

Word	Noun	Adjective	Verb	Adverb
Virginia pine	Yes	No	No	No
pine tree	Yes	No	No	No

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

Virginia pine: common small shrubby pine of the eastern United States having straggling often twisted or branches and short needles in bunches of 2
pine tree: a coniferous tree

Other hypernyms of Virginia pine include pine, true pine.

Virginia pine (noun)	pine tree (noun)
common small shrubby pine of the eastern United States having straggling often twisted or branches and short needles in bunches of 2	a coniferous tree