Supplementary dataset to publication: Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes.

This is the modified supplemented material to the publication “Complete genome sequence of ovine Mycobacterium avium subsp. paratuberculosis strain JIII-386 (MAP-S/type III) and its comparison to MAP-S/type I, MAP-C, and M. avium complex genomes”.

The complete circular genome of Mycobacterium avium subsp. paratuberculosis (MAP) strain JIII-386 from Germany, closed by Nanopore technology in this study, was presented and compared with the draft genome of JIII-386, previously published in [doi:10.1093/gbe/ew154], the closed genome of the MAP-S/type I strain Telford, the MAP-S/type III draft genome of strain S397, twelve closed MAP-C (type II) strains and eight closed Mycobacterium avium (M. a.) strains of subsp. hominissuis (MAH) and subsp. avium (MAA). Structural comparisons clearly revealed the mosaic nature of MAP genomes, the differences between MAP subtypes I, II and III, and the higher diversity of MAP-S compared to MAP-C genomes. 

The material provides a wealth of detailed results from these analyses and comparisons. These include a list of identified ncRNA and Riboswitches, as well as additional genes in finished JIII-386, the gene content of identified prophage regions, copy number of identified transposable elements and a list of selected virulence-associated genes in the different MAP-type (I - III) strains. The genomic islands identified and included genes along with their predicted functions were presented for six MAP genomes (belonging to MAP-S/type I and III, and MAP-C), one MAH genome and one MAA genome. One table shows the corresponding genomic islands in the genomes of JIII-386, Telford and three MAP-C genomes. Furthermore, homologous genes of known MAP-S specific Large Sequence Polymorphisms regions (LSP^S = LSP-S) were recorded in different MAP-S type strains, one MAH and one MAA strain, as well as genes of deletions #1 (LSP^A-20), #2, and s-delta-1, previously described as MAP-S-specific deletions, their presence or absence in 3 MAP-S, 12 MAP-C, 4 MAH, and 4 MAA strains were listed. Different presence or absence of genes, but also identified frameshifts or disruptions of various virulence-associated genes could lead to the different MAP-type specific phenotypic characteristics. Comprehensive core and pan genome analyses (results listed in six tables) revealed unique genes and genes likely to have been acquired by horizontal gene transfer in different MAP types and subtypes, but also emphasized the highly conserved and close relationship, and the complex evolution of M. a. strains.