Functional genetic variation in / genes contributes to diversity in lineages and potential interactions with the human host.

Introduction: Around 10% of the coding potential of is constituted by two poorly understood gene families, the and loci, thought to be involved in host-pathogen interactions. Their repetitive nature and high GC content have hindered sequence analysis, leading to exclusion from whole-genome studies. Understanding the genetic diversity of families is essential to facilitate their potential translation into tools for tuberculosis prevention and treatment.

Methods: To investigate the genetic diversity of the 169 / genes, we performed a sequence analysis across 73 long-read assemblies representing seven different lineages of and BCG. Individual gene alignments were extracted and diversity and conservation across the different lineages studied.

Results: The / genes were classified into three groups based on the level of protein sequence conservation relative to H37Rv, finding that >50% were conserved, with indels in and sub-families being major drivers of structural variation. Gene rearrangements, such as duplications and gene fusions, were observed between and genes. Inter-lineage diversity revealed lineage-specific SNPs and indels.

Discussion: The high level of genes conservation, together with the lineage-specific findings, suggest their phylogenetic informativeness. However, structural variants and gene rearrangements differing from the reference were also identified, with potential implications for pathogenicity. Overall, improving our knowledge of these complex gene families may have insights into pathogenicity and inform the development of much-needed tools for tuberculosis control.