An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows.

ABSTRACT: Reference-based alignment of short-reads is a widely used technique in genomic analysis of the Mycobacterium tuberculosis complex (MTBC) and the choice of reference sequence impacts the interpretation of analyses. The most widely used reference genomes include the ATCC type strain (H37Rv) and the putative MTBC ancestral sequence of Comas et al. both of which are based on a lineage 4 sequence. As such, these reference sequences do not capture all of the structural variation known to be present in the ancestor of the MTBC. To better represent the base of the MTBC, we generated an imputed ancestral genomic sequence, termed MTBC₀ from reference-free alignments of closed MTBC genomes. When used as a reference sequence in alignment workflows, MTBC₀ mapped more

SUBMITTER: Harrison LB 

PROVIDER: S-EPMC10868604 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature