How did you not know they had a penis if you were together for half a year?

I think she should have told you OP. I don't know when, it might not be something she would feel comfortable mentioning on a first date, but before six months definitely

That's what you get for assuming gender.

Chances are she doesn't want that bit of anatomy there anymore than you do, OP. As for why she waited this long to tell you, chances are that she was afraid, given the absurd risks of being the victim of violence that trans women face, particularly right after coming out to romantic partners. Anxiety is another big cause, because gender dysphoria is hard enough for a lot of trans people to deal with without bringing how other people view their body into the matter. That said, it sounds like your relationship had pretty much no issues aside from this and was pretty serious. So if the anatomy thing is really the only issue, it may be worth talking to her and discussing whether she intends to surgically transition. Research before you do, and know what all that would mean- because it would mean no biological kids unless you use a surrogate, for example- and if cost is the issue, consider helping her save up for it, if you do decide to stay with her. If you do break up with her, regardless of your reason why, please don't be a jerk about it. If it's the anatomy issue, fine, admit that contributed to it when you break up with her. If it's that she didn't tell you sooner, fine, give her that as a reason. But don't make her feel like shit for having a body that she already doesn't want, and PLEASE don't out her to anyone- it can LITERALLY get her killed. Even if the only reason you don't do it is because, yes, you can in fact be included in the charges if someone kills her for being trans.