ArticlePloS one2015
Comparative whole-genome analysis of clinical isolates reveals characteristic architecture of Mycobacterium tuberculosis pangenome.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 58 citations in OpenAlex.
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- The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples.PLoS computational biology · 2023Article
- Pangenome Reconstruction ofMicroorganisms · 2023Article
- Synthesis and Structure-Activity Relationship of 2,6-Disubstituted Thiosemicarbazone Derivatives of Pyridine as Potential Antituberculosis Agents.Materials (Basel, Switzerland) · 2023Article
- Whole genome sequencing ofFrontiers in microbiology · 2023Article
- Comparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador.BMC genomics · 2022Article
- Pan-genome association study ofFrontiers in microbiology · 2022Article
- The open pan-genome architecture and virulence landscape ofMicrobial genomics · 2021Article
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- Pan and Core Genome Analysis of 183Antibiotics (Basel, Switzerland) · 2021Article
- Comparative genomic analysis of Mycobacterium intracellulare: implications for clinical taxonomic classification in pulmonary Mycobacterium avium-intracellulare complex disease.BMC microbiology · 2021Article
- Article
- Genomic variant-identification methods may alterMicrobial genomics · 2020Article
- Review
- PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.PLoS computational biology · 2020Article
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Authors and funding
16 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The tubercle complex consists of closely related mycobacterium species which appear to be variants of a single species. Comparative genome analysis of different strains could provide useful clues and insights into the genetic diversity of the species. We integrated genome assemblies of 96 strains from Mycobacterium tuberculosis complex (MTBC), which included 8 Indian clinical isolates sequenced and assembled in this study, to understand its pangenome architecture. We predicted genes for all the 96 strains and clustered their respective CDSs into homologous gene clusters (HGCs) to reveal a hard-core, soft-core and accessory genome component of MTBC. The hard-core (HGCs shared amongst 100% of the strains) was comprised of 2,066 gene clusters whereas the soft-core (HGCs shared amongst at least 95% of the strains) comprised of 3,374 gene clusters. The change in the core and accessory genome components when observed as a function of their size revealed that MTBC has an open pangenome. We identified 74 HGCs that were absent from reference strains H37Rv and H37Ra but were present in most of clinical isolates. We report PCR validation on 9 candidate genes depicting 7 genes completely absent from H37Rv and H37Ra whereas 2 genes shared partial homology with them accounting to probable insertion and deletion events. The pangenome approach is a promising tool for studying strain specific genetic differences occurring within species. We also suggest that since selecting appropriate target genes for typing purposes requires the expected target gene be present in all isolates being typed, therefore estimating the core-component of the species becomes a subject of prime importance.
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