Too many genomes to count and list and go into detail. See JGI recent releases here

I’ll highlight that 3 Neocallimastigomycota  genomes from early diverging lineages have been released including updated assemblies and annotations.

• Piromyces finnis (v3.0)
• Neocallimastix californiae
• Anaeromyces robustus

Several Mucoromycota and related genomes from the Zygolife project were also released.

• Mucor heterogamus NRRL 1489
• Mycotypha africana NRRL 2978

Jason Stajich on Google+