And a fourth option may be that the other group publishes their paper describing the new reference genome as a preprint on bioRxiv. As such you can reference that paper and they can still submit their paper to a ""real"" journal.
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WouterDeCoster
By not published, you mean there is no paper, but it is available for download? Or it is not published and also not available? If the genome is available on the internet, you can reference the link.
Was the genome assembly and annotation performed by you or your research group? Another group made it available to you?
There is no paper regarding this particular genome and it is not available for download to the best of my knowledge. It was assembled by people I collaborate with, but as far as I understood their idea is to publish it in another paper in some time. The only information I have is that it was assembled using the same method they presented in their recent paper. I must admit I am confused on how to approach this :)
First of all, be sure you have their permission to publish data based on their genome.
However, you may have a problem in your hands, as 1) I guess some reviewers would like / demand the genome at hand to be available, 2) providing variants without a reference genome isn't very helpful.