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Wibberg, Daniel; Price-Carter, Marian; Rückert, Christian ; Blom, Jochen; Möbius, Petra: 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, [...]. In: Microorganisms. Vol.9 Issue 1. 2021
Content
Materials and Methods
Strain Cultivation and DNA Isolation
Nanopore Library Preparation and MinION® Sequencing
Base Calling, Reads Processing, Assembly, Quality Control, and Deposition of New Genome Sequence
Genome Annotation and Comparative Analysis
Reference Genome Sequences
Results and Discussion
Genome Sequencing, Assembly, and Finishing of Strain JIII-386
General Genomic Features of JIII-386
Shine–Delgarno Motif
Chromosomal Organization
SNPs and INDELs
Taxonomic Calculations
Specific Genomic Elements
CRISPR
Prophages and Prophage-Like Elements
Insertion Sequences
Putative Virulence Associated Genes and Gene Clusters
Mce Genes
Membrane Protein and Transporter Genes
PE/PPE/PGRS Genes
Mycobactin Gene Cluster
Secondary Metabolite and Antibiotic Resistance Genes Clusters
Secondary Metabolite Genes
Antibiotic Resistance (AR) Genes
Genomic Islands
Phylogenetic Analysis based on Extended Panel of MAC Genomes
Validation of MAP-S Specific LSPS Regions and Deletions Based on the Core Genome Analysis
Core and Pan Genome Analysis
Summary
References