Hi Gianina!
Section 1.4 in the Gardening FAQ covers seeds from the original plant system, bonsai seeds and Naturalist Quest seeds, with one addition - if you visit the additional nest to get a fire seed, you now get a chance to get a white or black seed instead.
This thread discusses the NEW seeds and where they come from. There are some great charts further into the thread.
Flax has also been added to the Peculiar seed group dropped by Tsuki Wolves/Dryads/Titans.
Sorry that this info is so choppy - now that discovery seems to be finished for the new seeds/plants for a while, I clearly need to update the FAQ