Fig. 3

Visualization of the Reduced Set of H37Ra-specific Variants and Their Effect on Phenotype. Our assembly contradicts many variants previously thought to be H37Ra-specific, reducing the number of genes that may contribute to H37Ra’s virulence attenuation. Several of these genes have been reassigned function since the first published assembly of the H37Ra genome [5], which is reflected in the figure. a The set of genes identified to carry H37Ra-specific polymorphisms in the original H37Ra genome publication [5] and their contribution to phenotype as understood at that time. 56 genes are affected, the majority of which were PE_PPE genes or were of unknown function. b The set of genes with H37Ra-specific variants confirmed by our assembly is reduced markedly, particularly in PE_PPE genes, highlighting the strength of single-molecule sequencing in resolving GC-rich and repetitive stretches of DNA. Genes with functions not yet characterized were also reduced significantly.*Though in a few instances this was because these genes’ function was characterized between 2008 and now, most were due to our assembly showing that they matched that of H37Rv and, therefore, are not H37Ra-specific. **For lpdA, the altered copy number in H37Ra was found not to be specific to the avirulent phenotype. However, the observed altered expression of lpdA in H37Ra may be due to altered regulation from PhoP. blue\(\bigstar \)The H37Ra-specific variant(s) in these genes have been shown to confer a phenotypic change in H37Ra relative to H37Rv in wet-lab studies. For these genes, the mechanisms affected by the H37Ra-specific variant are illustrated in detail (see Fig. 4 for hadC and phoP). For other genes, their general function is described or briefly illustrated