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We report the genome sequence of  Frankia  sp. strain ArI3, recovered as a single contig from one run of the Oxford Nanopore Technologies (ONT) MinION instrument. The genome has a G+C content of 72%, is 7,541,222 bp long, and contains 5,427 predicted protein-coding genes.

Contiguous Genome Sequence of Frankia sp. Strain ArI3, Isolated from Root Nodules of Alnus rubra Bong