1 and 2 are both fine, and there is no difference in meaning.
There is a slight difference in feeling between "precious, endangered" and "precious and endangered." Most formally, you would want "precious and endangered." A list of two things normally needs a conjunction like "and" or "or." But there are some "rules" that are ok to break. When you list two adjectives, you don't always need a comma. Sometimes it gives the feeling of informality, and sometimes it gives an almost poetic feeling. And it's also more efficient, which I like. Sounds smoother. So the first one is my preference.
And "some rare species of plants" and "some rare plant species" are both fine. I prefer the more economical, less wordy version: "some rare plant species."