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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

Phylogenetic tree based on order of syntenic blocks from core ortholog genes.The number in bracket denotes the % micro-rearrangements with respect to M. smegmatis. Pathogens are shown in red whereas green denotes non-pathogens.
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pone-0071248-g007: Phylogenetic tree based on order of syntenic blocks from core ortholog genes.The number in bracket denotes the % micro-rearrangements with respect to M. smegmatis. Pathogens are shown in red whereas green denotes non-pathogens.

Mentions: To understand this further, we compared the rearrangement pattern of all 759 core orthologs with that of the synteny blocks. Percentage micro-rearrangements between any two genomes was computed based on the difference in the number of reversals for all the core orthologs considered separately and the number of reversals computed when they are considered as part of synteny blocks. Figure 7 shows the phylogenetic tree based on the synteny blocks. The computed percentages with respect to the M. smegmatis genome are also shown. Comparison of the core genes between M. avium and M. smegmatis show 24 reversals in gene order. However, the number of reversals decreases to 7 when the core genes on the two genomes are grouped into blocks; a reduction of 70% compared to the gene level rearrangements. This implies that there are more micro-rearrangements within blocks in the M. avium genome than global rearrangements. On an average, 50–60% of reversals can be classified as micro-rearrangements for most genomes. Notable exceptions are M. ulcerans and M. leprae, where only 14% and 24% rearrangements respectively are within blocks. The changes are mostly global as illustrated in Figure 6, where M. leprae blocks are shuffled across the genome. A similar scenario can be observed in the case of M. ulcerans (Figure S4).


Comparative phylogenomics of pathogenic and non-pathogenic mycobacterium.

Prasanna AN, Mehra S - PLoS ONE (2013)

Phylogenetic tree based on order of syntenic blocks from core ortholog genes.The number in bracket denotes the % micro-rearrangements with respect to M. smegmatis. Pathogens are shown in red whereas green denotes non-pathogens.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0071248-g007: Phylogenetic tree based on order of syntenic blocks from core ortholog genes.The number in bracket denotes the % micro-rearrangements with respect to M. smegmatis. Pathogens are shown in red whereas green denotes non-pathogens.
Mentions: To understand this further, we compared the rearrangement pattern of all 759 core orthologs with that of the synteny blocks. Percentage micro-rearrangements between any two genomes was computed based on the difference in the number of reversals for all the core orthologs considered separately and the number of reversals computed when they are considered as part of synteny blocks. Figure 7 shows the phylogenetic tree based on the synteny blocks. The computed percentages with respect to the M. smegmatis genome are also shown. Comparison of the core genes between M. avium and M. smegmatis show 24 reversals in gene order. However, the number of reversals decreases to 7 when the core genes on the two genomes are grouped into blocks; a reduction of 70% compared to the gene level rearrangements. This implies that there are more micro-rearrangements within blocks in the M. avium genome than global rearrangements. On an average, 50–60% of reversals can be classified as micro-rearrangements for most genomes. Notable exceptions are M. ulcerans and M. leprae, where only 14% and 24% rearrangements respectively are within blocks. The changes are mostly global as illustrated in Figure 6, where M. leprae blocks are shuffled across the genome. A similar scenario can be observed in the case of M. ulcerans (Figure S4).

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