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Comparative phylogenomics of pathogenic and non-pathogenic mycobacterium.

Prasanna AN, Mehra S - PLoS ONE (2013)

Bottom Line: Phylogenetic trees were constructed using sequence of core orthologs, gene content and gene order.It is found that the genome based methods can better resolve the inter-species evolutionary distances compared to the conventional 16S based tree.It is found that while rearrangements between some Mycobacterium genomes are local within synteny blocks, few possess global rearrangements across the genomes.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.

ABSTRACT
Mycobacterium species are the source of a variety of infectious diseases in a range of hosts. Genome based methods are used to understand the adaptation of each pathogenic species to its unique niche. In this work, we report the comparison of pathogenic and non-pathogenic Mycobacterium genomes. Phylogenetic trees were constructed using sequence of core orthologs, gene content and gene order. It is found that the genome based methods can better resolve the inter-species evolutionary distances compared to the conventional 16S based tree. Phylogeny based on gene order highlights distinct evolutionary characteristics as compared to the methods based on sequence, as illustrated by the shift in the relative position of M. abscessus. This difference in gene order among the Mycobacterium species is further investigated using a detailed synteny analysis. It is found that while rearrangements between some Mycobacterium genomes are local within synteny blocks, few possess global rearrangements across the genomes. The study illustrates how a combination of different genome based methods is essential to build a robust phylogenetic relationship between closely related organisms.

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Related in: MedlinePlus

Synteny Analysis of Core Orthologs in mycobacteria.Order of blocks in few chosen mycobacteria are shown. Three representative rearrangement patterns are shown (A–C) for 22 blocks where each block had a minimum of 10 genes.
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pone-0071248-g006: Synteny Analysis of Core Orthologs in mycobacteria.Order of blocks in few chosen mycobacteria are shown. Three representative rearrangement patterns are shown (A–C) for 22 blocks where each block had a minimum of 10 genes.

Mentions: Next, a detailed analysis of gene order was performed to analyse the rearrangement pattern in the Mycobacterium genomes. The core genes are grouped into synteny blocks as described in methods. A total of 95 blocks were found with the number of genes in each block varying from 1 to 40. 22 blocks with a minimum of 10 genes are considered for visualization. Figure 6 shows the order of these blocks with respect to M. smegmatis in three representative genomes to illustrate the increasing complexity of rearrangements.


Comparative phylogenomics of pathogenic and non-pathogenic mycobacterium.

Prasanna AN, Mehra S - PLoS ONE (2013)

Synteny Analysis of Core Orthologs in mycobacteria.Order of blocks in few chosen mycobacteria are shown. Three representative rearrangement patterns are shown (A–C) for 22 blocks where each block had a minimum of 10 genes.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3756022&req=5

pone-0071248-g006: Synteny Analysis of Core Orthologs in mycobacteria.Order of blocks in few chosen mycobacteria are shown. Three representative rearrangement patterns are shown (A–C) for 22 blocks where each block had a minimum of 10 genes.
Mentions: Next, a detailed analysis of gene order was performed to analyse the rearrangement pattern in the Mycobacterium genomes. The core genes are grouped into synteny blocks as described in methods. A total of 95 blocks were found with the number of genes in each block varying from 1 to 40. 22 blocks with a minimum of 10 genes are considered for visualization. Figure 6 shows the order of these blocks with respect to M. smegmatis in three representative genomes to illustrate the increasing complexity of rearrangements.

Bottom Line: Phylogenetic trees were constructed using sequence of core orthologs, gene content and gene order.It is found that the genome based methods can better resolve the inter-species evolutionary distances compared to the conventional 16S based tree.It is found that while rearrangements between some Mycobacterium genomes are local within synteny blocks, few possess global rearrangements across the genomes.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.

ABSTRACT
Mycobacterium species are the source of a variety of infectious diseases in a range of hosts. Genome based methods are used to understand the adaptation of each pathogenic species to its unique niche. In this work, we report the comparison of pathogenic and non-pathogenic Mycobacterium genomes. Phylogenetic trees were constructed using sequence of core orthologs, gene content and gene order. It is found that the genome based methods can better resolve the inter-species evolutionary distances compared to the conventional 16S based tree. Phylogeny based on gene order highlights distinct evolutionary characteristics as compared to the methods based on sequence, as illustrated by the shift in the relative position of M. abscessus. This difference in gene order among the Mycobacterium species is further investigated using a detailed synteny analysis. It is found that while rearrangements between some Mycobacterium genomes are local within synteny blocks, few possess global rearrangements across the genomes. The study illustrates how a combination of different genome based methods is essential to build a robust phylogenetic relationship between closely related organisms.

Show MeSH
Related in: MedlinePlus