A post-marriage gender change does not invalidate the marriage: once a marriage is properly and legally formed, the couple remains married until the the marriage is dissolved by divorce or annulment.
The gender change would not alter the grounds for or process of divorce. It MAY give the other spouse the ability to seek an annulment rather than a divorce, on the grounds that since the transgendered spouse was clearly not the (mentally or psychologically at least) gender he or she professed to be before marriage, that in essence a fundamental marital "fraud" was committed and the marriage was void from the beginning. If you wish to explore that option, consult with a family law attorney.
However, it does not appear that you want to explore that option, not if you and your spouse have worked out what appears to be a mutually agreeable and amicable resolution to your marriage. In that case, simply file for divorce as if the gender change had not occured, simply providing proof of any legal name change to make sure that the transgendered person is properly connected to the name on the marriage license.
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