Complete Genome Sequence of Mycobacterium avium subsp. paratuberculosis Strain 42-13-1, Isolated in Japan.

Here, we report the complete genome sequence of Mycobacterium avium subsp. paratuberculosis strain 42-13-1, isolated from cattle presenting with chronic diarrhea caused by Johne's disease in Japan, which was assembled via long- and short-read hybrid assembly.