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Comparative whole-genome analysis of clinical isolates reveals characteristic architecture of Mycobacterium tuberculosis pangenome.

Periwal V, Patowary A, Vellarikkal SK, Gupta A, Singh M, Mittal A, Jeyapaul S, Chauhan RK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K, Chauhan DS, Sivasubbu S, Scaria V - PLoS ONE (2015)

Bottom Line: We identified 74 HGCs that were absent from reference strains H37Rv and H37Ra but were present in most of clinical isolates.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.

View Article: PubMed Central - PubMed

Affiliation: GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India; Academy of Scientific & Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi 110001, India.

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.

No MeSH data available.


Related in: MedlinePlus

Core-gene Tree.The un-rooted MTBC tree was created from alignment of 971 orthologous core-genes from 96 strains. A tree with Bootstrapped values is presented in S3 Fig (details in text).
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pone.0122979.g001: Core-gene Tree.The un-rooted MTBC tree was created from alignment of 971 orthologous core-genes from 96 strains. A tree with Bootstrapped values is presented in S3 Fig (details in text).

Mentions: We investigated the genetic diversity within MTBC strains by inferring phylogeny based on genes. In contrast to the single gene based trees which have low inter-species discriminatory power, multi-gene approaches offer more robust phylogenetic trees [32,33]. In order to infer phylogeny of MTBC strains, we used the hard-core component i.e. genes shared amongst all the isolates under consideration. From the 2,066 hard-core, we removed the HGCs having paralogs thus leaving 971 orthologous gene clusters (OGCs) in the hard-core. CDS translations of the 971 OGCs from all 96 strains were subjected to multiple sequence alignment followed by bootstrapping, generating a total of 100 resamples. Pairwise differences amongst sequences were estimated and the resultant distance matrix was used to build the tree. The original and the resampled trees were compared and the resultant tree referred here as the core-gene tree, is presented in Fig 1 and the tree with comparative bootstrapped values is presented in S3 Fig.


Comparative whole-genome analysis of clinical isolates reveals characteristic architecture of Mycobacterium tuberculosis pangenome.

Periwal V, Patowary A, Vellarikkal SK, Gupta A, Singh M, Mittal A, Jeyapaul S, Chauhan RK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K, Chauhan DS, Sivasubbu S, Scaria V - PLoS ONE (2015)

Core-gene Tree.The un-rooted MTBC tree was created from alignment of 971 orthologous core-genes from 96 strains. A tree with Bootstrapped values is presented in S3 Fig (details in text).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390332&req=5

pone.0122979.g001: Core-gene Tree.The un-rooted MTBC tree was created from alignment of 971 orthologous core-genes from 96 strains. A tree with Bootstrapped values is presented in S3 Fig (details in text).
Mentions: We investigated the genetic diversity within MTBC strains by inferring phylogeny based on genes. In contrast to the single gene based trees which have low inter-species discriminatory power, multi-gene approaches offer more robust phylogenetic trees [32,33]. In order to infer phylogeny of MTBC strains, we used the hard-core component i.e. genes shared amongst all the isolates under consideration. From the 2,066 hard-core, we removed the HGCs having paralogs thus leaving 971 orthologous gene clusters (OGCs) in the hard-core. CDS translations of the 971 OGCs from all 96 strains were subjected to multiple sequence alignment followed by bootstrapping, generating a total of 100 resamples. Pairwise differences amongst sequences were estimated and the resultant distance matrix was used to build the tree. The original and the resampled trees were compared and the resultant tree referred here as the core-gene tree, is presented in Fig 1 and the tree with comparative bootstrapped values is presented in S3 Fig.

Bottom Line: We identified 74 HGCs that were absent from reference strains H37Rv and H37Ra but were present in most of clinical isolates.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.

View Article: PubMed Central - PubMed

Affiliation: GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India; Academy of Scientific & Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi 110001, India.

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.

No MeSH data available.


Related in: MedlinePlus