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. 2015 May 13;16(1):155.
doi: 10.1186/s12859-015-0603-3.

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis

Ernest D Benavente  1   2 , Francesc Coll  3 , Nick Furnham  4 , Ruth McNerney  5 , Judith R Glynn  6 , Susana Campino  7 , Arnab Pain  8 , Fady R Mohareb  9 , Taane G Clark  10   11
Affiliations

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis

Ernest D Benavente et al. BMC Bioinformatics. .

Abstract

Background: Phylogenetic-based classification of M. tuberculosis and other bacterial genomes is a core analysis for studying evolutionary hypotheses, disease outbreaks and transmission events. Whole genome sequencing is providing new insights into the genomic variation underlying intra- and inter-strain diversity, thereby assisting with the classification and molecular barcoding of the bacteria. One roadblock to strain investigation is the lack of user-interactive solutions to interrogate and visualise variation within a phylogenetic tree setting.

Results: We have developed a web-based tool called PhyTB ( http://pathogenseq.lshtm.ac.uk/phytblive/index.php ) to assist phylogenetic tree visualisation and identification of M. tuberculosis clade-informative polymorphism. Variant Call Format files can be uploaded to determine a sample position within the tree. A map view summarises the geographical distribution of alleles and strain-types. The utility of the PhyTB is demonstrated on sequence data from 1,601 M. tuberculosis isolates.

Conclusion: PhyTB contextualises M. tuberculosis genomic variation within epidemiological, geographical and phylogenic settings. Further tool utility is possible by incorporating large variants and phenotypic data (e.g. drug-resistance profiles), and an assessment of genotype-phenotype associations. Source code is available to develop similar websites for other organisms ( http://sourceforge.net/projects/phylotrack ).

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Figures

Figure 1
Figure 1
PhyTB screenshot: A phylogenetic tree for the 1,601 M. tuberculosis isolates (A), with each lineage colour coded (B). A selected SNP R463L in the katG gene (associated with isoniazid resistance) (C), is located at position 2,152,224, (D) and present across all but one lineage (4) (E).
Figure 2
Figure 2
PhyTB screenshot: A map view showing the frequency of the G876G SNP in the rpoB gene (searchable from (A)) and its association with lineage 3 strain-types in Malawi. Pie chart (B) shows the non-reference allele frequency (red segment, inner circle) is linked to the CAS spoligotype (blue segment, outer circle).
Figure 3
Figure 3
PhyTB screenshot: A Russian sample (ERR019571) is located in a Beijing clade in lineage 2.2.1 (C), established using variants uploaded in a Variant Call Format file.
See this image and copyright information in PMC

References

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