A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome

Abstract

H37Rv is the most widely used Mycobacterium tuberculosis strain, and its genome is globally used as the M. tuberculosis reference sequence. Here, we present Bact-Builder, a pipeline that uses consensus building to generate complete and accurate bacterial genome sequences and apply it to three independently cultured and sequenced H37Rv aliquots of a single laboratory stock. Two of the 4,417,942 base-pair long H37Rv assemblies are 100% identical, with the third differing by a single nucleotide. Compared to the existing H37Rv reference, the new sequence contains ~6.4 kb additional base pairs, encoding ten new regions that include insertions in PE/PPE genes and new paralogs of esxN and esxJ, which are differentially expressed compared to the reference genes. New sequencing and de novo assemblies with Bact-Builder confirm that all 10 regions, plus small additional polymorphisms, are also present in the commonly used H37Rv strains NR123, TMC102, and H37Rv1998. Thus, Bact-Builder shows promise as an improved method to perform accurate and reproducible de novo assemblies of bacterial genomes, and our work provides important updates to the primary M. tuberculosis reference genome.

Learning the fitness dynamics of pathogens from phylogenies

“…Mutations were then classified as synonymous, non-synonymous, or extragenic. For M. tuberculosis and B. pertussis we also classified each mutation by functional category( 36, 37 ).…”

“…Where 𝐹 is the gene functional category considered (36,37). As a sensitivity analysis, we also replicated this computation on synonymous nucleotide changes, as we expect these mutations to be neutral, and therefore not linked to any particular functional category (Figure S19).…”

“…Figure S19: Proportion of synonymous mutations that are lineage-defining, by gene functional categories, for B. pertussis and M. tuberculosis Similarly to Figure 4K-L, we plot the proportion of synonymous mutations that are lineage-defining within each functional category, for (A) B. pertussis and (B) M. tuberculosis(36,37). For M. tuberculosis, we only considered the most recent lineages 1 and 2.…”

Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies

“…We used 30 samples for benchmarking, representing genomes from a variety of Gramnegative and Gram-positive bacteria. We chose these samples as they have real hybrid read sets in combination with manually curated genome assemblies produced using either 42 The full details for each individual isolate used can be found in Supplementary Tables 1 and 2.…”

“…Trycycler or Bact-builder42 -a consensus-building pipeline based on Trycycler. These samples came from 5 different studies below.…”