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Right now (when I wrote this post), there is no wildcard support from dokku-letsencrypt plugin. Luckily, Dokku itself can use certificates from other sources.
Wildcard certificates are handy and this was the first time when I needed to use them with Dokku. It was a little bit harder than I expected, but luckily, it is doable even with automatic renewal.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.