The Mycobacterium avium complex (MAC) is a group of nontuberculous mycobacteria (NTM) responsible of infections in humans and animals. Diagnostic and treatments of pulmonary MAC infections are challenging. These bacteria are commonly resistant to first line antituberculosis drugs and current treatments consist of a lengthy multi-drug therapy which represents a burden for the patients who often experience adverse effects and treatment failure. Therefore, new candidates for the design of alternative diagnostic methods and therapies are needed, which requires a better understanding of MAC virulence and pathogenesis. Several NTM, including M. avium can reversibly switch between smooth transparent (SmT) and smooth opaque (SmO) colony morphologies, discernible on agar plates. Interestingly, these two forms differ in virulence and antibiotic resistance. The virulent SmT, commonly isolated from patients, is more resistant to antibiotics and if grown repeatedly under laboratory conditions, gives rise to isogenic derived avirulent SmO colonies. Although they could be targeted for therapy, the underlying regulatory processes of the SmO/SmT reversible switch in NTM are still unknown. Phenotypic switching is described in numerous bacteria and can be regulated by reversible DNA rearrangements, such as sequence inversion or insertion/excision of short sequence repeats, or via epigenetic mechanisms (ex: DNA methylation). These changes likely result in changes in gene expression specifically related to the phenotype. Therefore, the aim of this project is to compare the genome sequences and transcriptomic profiles of SmO and SmT M. avium morphotypes to identify the regulatory networks involved in the phenotypic switching and variability in virulence. This will be accomplished in the following objectives: 1. Generation of high-quality genome assemblies SmO and SmT morphotypes using reference-guided and de novo methods (DNA already sequenced) 2. Genome annotation of SmO and SmT morphotypes and comparison with reference genomes 3. Structural comparison of genome assemblies to identify sequence inversions, gene duplications, gene inactivation or genome rearrangements.