Genome sequence of <i>Gilbertella persicaria</i> strain SHK1000 isolated from fig fruit

<i>Gilbertella persicaria</i> is a phytopathogenic fungus that causes soft rot in several fruit crops. Here, I report the draft genome sequence of <i>G. persicaria</i> strain SHK1000 isolated from fig fruit, and consisting of total length 30.9 Mbp across 60 contigs with N₅₀ 3.6 Mbp and 99.2% BUSCO completeness.