Genomic Degeneration and Reduction in the Fish Pathogen Mycobacterium shottsii

Area of Science:

• Genomics
• Microbiology
• Fish Pathology

Background:

• Mycobacterium shottsii and Mycobacterium pseudoshottsii are novel species isolated from diseased striped bass (Morone saxatilis).
• These species belong to the Mycobacterium ulcerans/Mycobacterium marinum clade (MuMC).
• M. pseudoshottsii has been suggested as an ecovar of M. ulcerans.

Purpose of the Study:

• To describe the complete genome of Mycobacterium shottsii.
• To clarify the phylogenetic position of M. shottsii within the MuMC.
• To investigate genomic modifications indicative of evolutionary changes in M. shottsii.

Main Methods:

• Whole-genome sequencing of Mycobacterium shottsii.
• Comparative genomic analysis with related Mycobacterium species (M. ulcerans, M. marinum, M. pseudoshottsii).
• Phylogenetic analysis to determine evolutionary relationships.

Main Results:

• M. shottsii is phylogenetically distinct from M. ulcerans and not an ecovar.
• The M. shottsii genome exhibits significant degeneration, including pseudogene accumulation, insertion sequence proliferation (IS Mysh01, IS Mysh03), deletions, and reorganization.
• Genomic features parallel those of M. ulcerans, suggesting convergent evolution towards pathogenicity.

Conclusions:

• Mycobacterium shottsii represents a transitional lineage within the MuMC, basal to proposed 'Aronson' and 'M' lineages.
• Genomic degeneration in M. shottsii indicates an evolutionary trajectory towards obligate pathogenicity.
• This study clarifies the phylogeny of M. shottsii and provides insights into the genomic processes driving its evolution.