ArticleProceedings of the National Academy of Sciences of the United States of America2004
Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 187 papers.
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187 citing papers in PubMed.
- Article
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- Alpibectir-Ethionamide combination (AlpE) for the treatment of tuberculosis.Nature communications · 2026Article
- The Pyridoxal-5'-Phosphate-Dependent Enzymes ofACS infectious diseases · 2026Review
- Article
- Unraveling Epistatic Interactions Between Sites Under Drug-Dependent Selection in the Mycobacterium tuberculosis Genome.Molecular biology and evolution · 2025Article
- Mycobacterium tuberculosis complex Lineage 1: A neglected cause of tuberculosis.PLoS neglected tropical diseases · 2025Review
- Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species.Bioinformatics (Oxford, England) · 2025Article
- Prevalence of Beijing Central Asian/Russian Cluster 94-32 among Multidrug-ResistantAntibiotics (Basel, Switzerland) · 2023Article
- Mapping the phylogeny and lineage history of geographically distinct BCG vaccine strains.Microbial genomics · 2023Article
- Genetic Diversity and Primary Drug Resistance ofMicroorganisms · 2023Article
- Large genomic deletions delineate Mycobacterium tuberculosis L4 sublineages in South American countries.PloS one · 2023Article
- CRISPRi-mediated characterization of novel anti-tuberculosis targets: Mycobacterial peptidoglycan modifications promote beta-lactam resistance and intracellular survival.Frontiers in cellular and infection microbiology · 2023Article
- Article
- Investigating the Diversity of Tuberculosis Spoligotypes with Dimensionality Reduction and Graph Theory.Genes · 2022Article
- The role of triacylglycerols and repurposing DGAT1 inhibitors for the treatment ofCell surface (Amsterdam, Netherlands) · 2022Review
- Analysis of the twenty-six largest outbreaks of tuberculosis in Aragon using whole-genome sequencing for surveillance purposes.Scientific reports · 2022Article
- In Silico Exploration ofBiomolecules · 2022Article
- Identification of region of difference and H37Rv-related deletion inFrontiers in microbiology · 2022Article
- Genomic signatures of pre-resistance in Mycobacterium tuberculosis.Nature communications · 2021Article
127 more citing papers are in PubMed but not listed here.
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10 authors.
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Abstract
To better understand genome function and evolution in Mycobacterium tuberculosis, the genomes of 100 epidemiologically well characterized clinical isolates were interrogated by DNA microarrays and sequencing. We identified 68 different large-sequence polymorphisms (comprising 186,137 bp, or 4.2% of the genome) that are present in H37Rv, but absent from one or more clinical isolates. A total of 224 genes (5.5%), including genes in all major functional categories, were found to be partially or completely deleted. Deletions are not distributed randomly throughout the genome but instead tend to be aggregated. The distinct deletions in some aggregations appear in closely related isolates, suggesting a genomically disruptive process specific to an individual mycobacterial lineage. Other genomic aggregations include distinct deletions that appear in phylogenetically unrelated isolates, suggesting that a genomic region is vulnerable throughout the species. Although the deletions identified here are evidently inessential to the causation of disease (they are found in active clinical cases), their frequency spectrum suggests that most are weakly deleterious to the pathogen. For some deletions, short-term evolutionary pressure due to the host immune system or antibiotics may favor the elimination of genes, whereas longer-term physiological requirements maintain the genes in the population.
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