title: Comprehensive insights in the Mycobacterium avium subsp. paratuberculosis genome using new WGS data of sheep strain JIII-386 from Germany.
abstract: Mycobacterium avium (M. a.) subsp. paratuberculosis (MAP) - the etiologic agent of Johne's disease - affects cattle, sheep and other ruminants worldwide. To decipher phenotypic differences among sheep and cattle strains (belonging to MAP-S [Type-I/III] respectively MAP-C [Type-II]) comparative genome analysis needs data from diverse isolates originating from different geographic regions of the world. The current study presents the so far best assembled genome of a MAP-S-strain: sheep isolate JIII-386 from Germany. One newly sequenced cattle isolate (JII-1961, Germany), four published MAP strains of MAP-C and MAP-S from U.S. and Australia and M. a. subsp. hominissuis (MAH) strain 104 were used for assembly improvement and comparisons. All genomes were annotated by BacProt and results compared with NCBI annotation. Corresponding protein-coding sequences (CDSs) were detected, but also CDSs that were exclusively determined either by NCBI or BacProt. A new Shine-Dalgarno sequence motif (5'AGCTGG3') was extracted. Novel CDSs including PE-PGRS family protein genes and about 80 non-coding RNAs exhibiting high sequence conservation are presented. Previously found genetic differences between MAP-types are partially revised. Four out of ten assumed MAP-S-specific large sequence polymorphism regions (LSPSs) are still present in MAP-C strains; new LSPSs were identified. Independently of the regional origin of the strains, the number of individual CDSs and single nucleotide variants confirm the strong similarity of MAP-C strains and show higher diversity among MAP-S strains. This study gives ambiguous results regarding the hypothesis that MAP-S is the evolutionary intermediate between MAH and MAP-C, but it clearly shows a higher similarity of MAP to MAH than to M. intracellulare.
authors.affiliation: NRL for Paratuberculosis, Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Naumburger Straße 96a, 07743 Jena, Germany petra.moebius@fli.bund.de.
authors.forename: Petra
authors.initials: P
authors.lastname: Möbius
authors.affiliation: RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Hölzer
authors.affiliation: Leibniz Institute for Age Research - Fritz-Lipmann-Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
authors.forename: Marius
authors.initials: M
authors.lastname: Felder
authors.affiliation: Department of Genome Analysis, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Nordsiek
authors.affiliation: Leibniz Institute for Age Research - Fritz-Lipmann-Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
authors.forename: Marco
authors.initials: M
authors.lastname: Groth
authors.affiliation: NRL for Paratuberculosis, Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Naumburger Straße 96a, 07743 Jena, Germany.
authors.forename: Heike
authors.initials: H
authors.lastname: Köhler
authors.affiliation: Leibniz Institute for Age Research - Fritz-Lipmann-Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Reichwald
authors.affiliation: Leibniz Institute for Age Research - Fritz-Lipmann-Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Platzer
authors.affiliation: RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany.
authors.forename: Manja
authors.initials: M
authors.lastname: Marz
keywords: Johne’s disease; MAP-S; SNV/SNP; Shine-Dalgarno sequence; evolution of MAP-types; ncRNA; new LSPSs