Bugeraenun procerae (fictional)
season 5, episode 5: Fallen Idols
Sam finds some seeds in the victims’ stomachs that came from a Balkan forest once inhabited by the pagan god Leshi. Despite previously having recognized an extinct plant species, Sam initially describes the seeds as “unlike anything I’ve ever seen before.” He figures it out eventually.
At around 28:45, Sam's laptop screen is briefly shown, displaying an image of a seed labeled “bugeraenun procerae” (which is not a real species) and text describing the corresponding plant as shrublike, producing “starlike minute flowers that bloom only once a year at midnight.” Many plants only bloom once a year, but the specificity of "at midnight" suggests that the supposed flowers only open for a short time in the middle of a single night, sort of like night-blooming cereus cacti, although there is no reason why every bud should bloom on the same night. A longer flowering period is much more practical, facilitating the simultaneity of flowering across individuals. I am not certain whether plants can control or coordinate when they bloom. In any case, the seeds shown on screen look a lot like peach pits, being relatively large, dark, and textured.
There are two shrubs which bear some small resemblance to the fictional plant. The first is similar in name, the second only in description.
Subreddit r/destiel user xain_the_idiot points out the existence of Calotropis procera, commonly called giant milkweed or Apple of Sodom. The latter name and its Biblical significance fit very well with the show's themes. Like other milkweeds, this species does produce small starlike flowers and rounded seed pods which can be a few inches long (bigger than the seeds in the show). The pods are meant to split open to release the actual seeds, which are tiny, flat, and attached to white fluff which carries them off in the wind. Apple of Sodom does not strictly bloom at night, nor is it endemic to Balkan forests. It is native to Africa and Asia, and is not rare or endangered.
Cestrum nocturnum, the night-scented cestrum or night-blooming jasmine, bears flowers composed of pale green tubes nearly one inch long, ending in white five-pointed star shapes. The flowers bloom at night and release a strong scent. The seeds are round, but smaller than those in the show, and are white and smooth when fresh. Night-scented cestrum is native to Central and South America but has spread to other continents and is considered invasive in New Zealand.
I'm not sure why the writers decided to invent a plant (or change up the name and description of one) instead of simply using a real species, especially when they've previously used real plants to great effect.