Diversity Sequencing

Different M. tuberculosis (TB) strains have varying virulence, immunogenicity, and drug resistance. However, currently sequenced T B genomes are thought to be responsible for only a minority of global TB burden.

This project, led by Sebastien Gagneux and Peter Small in collaboration with the NIAID-funded Broad Genomic Sequencing Center for Infectious Disease, exploits recently revealed TB global population structure to re-sequence 31 rationally selected TB strains as representatives of the TB global diversity and identify sequence polymorphisms between these strains.

Polymorphisms are searchable through the links below and also displayed on each gene detail page (see here for an example)

The main strain lineages of M. tuberculosis are associated with different geographic regions. Colors indicate the dominant lineage(s) in each country; from Gagneux et al. PNAS 2006 103(8):2869-73..
[Click image to enlarge]

Maximum parsimony phylogenetic tree based on concatenates of 89 genes in 108 strains of M. tuberculosis complex (MTBC)(adapted from Hershberg et al 2008 PLoS Biology 6 (12):e311.). The 6 main lineages of human MTBC are indicated as in Gagneux & Small 2007 Lancet Infect Diseases 7(5):328-37. For comparison with other MTBC nomenclature see Comas et al 2009 PLoS ONE 12;4(11):e7815. Strains marked by a blue dot have full or partial whole-genome sequence available in the public domain. Strains marked by a red dot were sequenced (or are being sequenced) in this project. [Click image to enlarge]

Search by Strain

Search for polymorphisms that differentiate subsets of the resequenced strains

Search by Location

Search polymorphisms by genomic region

Browse Polymorphisms

Counts of SNPs pairwise between resequenced genomes, and between resequenced genomes and the reference

Coverage statistics

View coverage statistics from diversity sequencing

Multiple Genome Alignments