Limits...
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

The heatmap shows 74 HGCs absent from reference strains Mtb ATCC H37Ra and Mtb ATCC H37Rv but present in most of the clinical isolates.Predicted annotation of each of the cluster family is also represented. The genes validated using PCR are also shown adjacent to the annotations.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4390332&req=5

pone.0122979.g007: The heatmap shows 74 HGCs absent from reference strains Mtb ATCC H37Ra and Mtb ATCC H37Rv but present in most of the clinical isolates.Predicted annotation of each of the cluster family is also represented. The genes validated using PCR are also shown adjacent to the annotations.

Mentions: We further analyzed the differences in the gene pool of clinical isolates (from across the globe) and laboratory maintained strains by looking out for genes that were conspicuously missing in the genome assemblies of the laboratory strains, H37Rv and H37Ra, but were present in at-least or greater than 1/3rd of the clinical strains. We obtained 74 clusters meeting this criterion from the accessory genome of 4,725 HGCs. A cross-validation of the 74 clusters against whole genome sequences of H37Rv and H37Ra was done using BLAT [37]. We identified 10 clusters which had absolutely no match with H37Ra and H37Rv genomes, whereas the other 64 shared partial homology with H37Rv and H37Ra in variable regions of the genomes with a sequence length difference in the alignment. Fig 7 shows the 74 clusters absent from H37Ra and H37Rv (first 4 columns in Fig 7) but present in at-least 1/3rd of the clinical isolates along with their annotations.


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)

The heatmap shows 74 HGCs absent from reference strains Mtb ATCC H37Ra and Mtb ATCC H37Rv but present in most of the clinical isolates.Predicted annotation of each of the cluster family is also represented. The genes validated using PCR are also shown adjacent to the annotations.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0122979.g007: The heatmap shows 74 HGCs absent from reference strains Mtb ATCC H37Ra and Mtb ATCC H37Rv but present in most of the clinical isolates.Predicted annotation of each of the cluster family is also represented. The genes validated using PCR are also shown adjacent to the annotations.
Mentions: We further analyzed the differences in the gene pool of clinical isolates (from across the globe) and laboratory maintained strains by looking out for genes that were conspicuously missing in the genome assemblies of the laboratory strains, H37Rv and H37Ra, but were present in at-least or greater than 1/3rd of the clinical strains. We obtained 74 clusters meeting this criterion from the accessory genome of 4,725 HGCs. A cross-validation of the 74 clusters against whole genome sequences of H37Rv and H37Ra was done using BLAT [37]. We identified 10 clusters which had absolutely no match with H37Ra and H37Rv genomes, whereas the other 64 shared partial homology with H37Rv and H37Ra in variable regions of the genomes with a sequence length difference in the alignment. Fig 7 shows the 74 clusters absent from H37Ra and H37Rv (first 4 columns in Fig 7) but present in at-least 1/3rd of the clinical isolates along with their annotations.

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