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Genome dynamics and evolution of Salmonella Typhi strains from the typhoid-endemic zones.

Baddam R, Kumar N, Shaik S, Lankapalli AK, Ahmed N - Sci Rep (2014)

Bottom Line: We observed a decline in core functional gene content and a significant increase in accessory pseudogene content.Thus, the study highlights the existence of heterogeneous strains in a population with varying metabolic potential and that S.Typhi possibly resorts to metabolic fine tuning for its adaptation.

View Article: PubMed Central - PubMed

Affiliation: Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India.

ABSTRACT
Typhoid fever poses significant burden on healthcare systems in Southeast Asia and other endemic countries. Several epidemiological and genomic studies have attributed pseudogenisation to be the major driving force for the evolution of Salmonella Typhi although its real potential remains elusive. In the present study, we analyzed genomes of S. Typhi from different parts of Southeast Asia and Oceania, comprising of isolates from outbreak, sporadic and carrier cases. The genomes showed high genetic relatedness with limited opportunity for gene acquisition as evident from pan-genome structure. Given that pseudogenisation is an active process in S. Typhi, we further investigated core and pan-genome profiles of functional and pseudogenes separately. We observed a decline in core functional gene content and a significant increase in accessory pseudogene content. Upon functional classification, genes encoding metabolic functions formed a major constituent of pseudogenes as well as core functional gene clusters with SNPs. Further, an in-depth analysis of accessory pseudogene content revealed the existence of heterogeneous complements of functional and pseudogenes among the strains. In addition, these polymorphic genes were also enriched in metabolism related functions. Thus, the study highlights the existence of heterogeneous strains in a population with varying metabolic potential and that S. Typhi possibly resorts to metabolic fine tuning for its adaptation.

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Related in: MedlinePlus

Pan and Core Genome Distribution.(a). Pan and core genome developments using median values of the combinations of all eight genomes. (b). Pan and core genome developments of functional genes of these eight isolates. Here it can be observed that core genome is decreasing sharply. (c). Pan and core genome developments of pseudogenes of these eight isolates. It can be seen that pan genome of pseudogenes is highly non conservative with a steep increase in accessory content while the core genome reached convergence.
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f3: Pan and Core Genome Distribution.(a). Pan and core genome developments using median values of the combinations of all eight genomes. (b). Pan and core genome developments of functional genes of these eight isolates. Here it can be observed that core genome is decreasing sharply. (c). Pan and core genome developments of pseudogenes of these eight isolates. It can be seen that pan genome of pseudogenes is highly non conservative with a steep increase in accessory content while the core genome reached convergence.

Mentions: The exponential term α determines whether pan-genome of a bacterial species is closed or open. For α > 1 (γ < 0) the pan-genome is considered closed i.e. sampling more genomes will not affect the pan-genome size, whereas for α < 1 (0 < γ > 1) the pan-genome remains open and addition of more genomes would increase its size. In this study, the k and γ values were determined as 4486 and 0.087 respectively. The pan-genome analysis of S. Typhi strains revealed an α value of 0.913 implying a highly conservative nature of these endemic isolates (Figure 3a).


Genome dynamics and evolution of Salmonella Typhi strains from the typhoid-endemic zones.

Baddam R, Kumar N, Shaik S, Lankapalli AK, Ahmed N - Sci Rep (2014)

Pan and Core Genome Distribution.(a). Pan and core genome developments using median values of the combinations of all eight genomes. (b). Pan and core genome developments of functional genes of these eight isolates. Here it can be observed that core genome is decreasing sharply. (c). Pan and core genome developments of pseudogenes of these eight isolates. It can be seen that pan genome of pseudogenes is highly non conservative with a steep increase in accessory content while the core genome reached convergence.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4264004&req=5

f3: Pan and Core Genome Distribution.(a). Pan and core genome developments using median values of the combinations of all eight genomes. (b). Pan and core genome developments of functional genes of these eight isolates. Here it can be observed that core genome is decreasing sharply. (c). Pan and core genome developments of pseudogenes of these eight isolates. It can be seen that pan genome of pseudogenes is highly non conservative with a steep increase in accessory content while the core genome reached convergence.
Mentions: The exponential term α determines whether pan-genome of a bacterial species is closed or open. For α > 1 (γ < 0) the pan-genome is considered closed i.e. sampling more genomes will not affect the pan-genome size, whereas for α < 1 (0 < γ > 1) the pan-genome remains open and addition of more genomes would increase its size. In this study, the k and γ values were determined as 4486 and 0.087 respectively. The pan-genome analysis of S. Typhi strains revealed an α value of 0.913 implying a highly conservative nature of these endemic isolates (Figure 3a).

Bottom Line: We observed a decline in core functional gene content and a significant increase in accessory pseudogene content.Thus, the study highlights the existence of heterogeneous strains in a population with varying metabolic potential and that S.Typhi possibly resorts to metabolic fine tuning for its adaptation.

View Article: PubMed Central - PubMed

Affiliation: Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India.

ABSTRACT
Typhoid fever poses significant burden on healthcare systems in Southeast Asia and other endemic countries. Several epidemiological and genomic studies have attributed pseudogenisation to be the major driving force for the evolution of Salmonella Typhi although its real potential remains elusive. In the present study, we analyzed genomes of S. Typhi from different parts of Southeast Asia and Oceania, comprising of isolates from outbreak, sporadic and carrier cases. The genomes showed high genetic relatedness with limited opportunity for gene acquisition as evident from pan-genome structure. Given that pseudogenisation is an active process in S. Typhi, we further investigated core and pan-genome profiles of functional and pseudogenes separately. We observed a decline in core functional gene content and a significant increase in accessory pseudogene content. Upon functional classification, genes encoding metabolic functions formed a major constituent of pseudogenes as well as core functional gene clusters with SNPs. Further, an in-depth analysis of accessory pseudogene content revealed the existence of heterogeneous complements of functional and pseudogenes among the strains. In addition, these polymorphic genes were also enriched in metabolism related functions. Thus, the study highlights the existence of heterogeneous strains in a population with varying metabolic potential and that S. Typhi possibly resorts to metabolic fine tuning for its adaptation.

Show MeSH
Related in: MedlinePlus