Mycobacterial Phylogenomics: An Enhanced Method for Gene Turnover Analysis Reveals Uneven Levels of Gene Gain and Loss among Species and Gene Families

摘要: Species of the genus Mycobacterium differ in several features, from geographic ranges, and degree pathogenicity, to ecological host preferences. The recent availability fully sequenced genomes for a number these species enabled comparative study genetic determinants this wide lifestyle diversity. Here, we applied two complementary phylogenetic-based approaches using information 19 obtain more comprehensive view evolution genus. First, inferred phylogenetic relationships new approaches, one based on Mycobacterium-specific amino acid substitution matrix other gene content dissimilarity matrix. Then, utilized our recently developed gain-and-death stochastic models turnover dynamics maximum-likelihood framework. We uncovered scenario that differs markedly traditional 16S rRNA data improves upon phylogenomic approaches. also found rates gain death are high unevenly distributed both across families, further supporting utility rate heterogeneity context. Finally, functional annotation most expanded or contracted families revealed transposable elements fatty metabolism-related important drivers Mycobacterium.