Abstract
Horizontal Gene Transfer (HGT) events, initially thought to be rare in Mycobacterium tuberculosis, have recently been shown to be involved in the acquisition of virulence operons in M. tuberculosis. We have developed a new partitioning framework based HGT prediction algorithm, called Grid3M, and applied the same for the prediction of HGTs in Mycobacteria. Validation and testing using simulated and real microbial genomes indicated better performance of Grid3M as compared with other widely used HGT prediction methods. Specific analysis of the genes belonging to dormancy/reactivation regulons across 14 mycobacterial genomes indicated that horizontal acquisition is specifically restricted to important accessory proteins. The results also revealed Burkholderia species to be a probable source of HGT genes belonging to these regulons. The current study provides a basis for similar analyses investigating the functional/evolutionary aspects of HGT genes in other pathogens. A database of Grid3M predicted HGTs in completely sequenced genomes is available at https://metagenomics.atc.tcs.com/Grid3M/ .
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Acknowledgements
We thank Dr RK Azad and Dr JG Lawrence for providing artificial genome sequences for our validation studies. We also thank Mr Purnachander Gajjalla for his help in creating the simulated genomes. VM is also a Junior Research Fellow of the Department of Chemical Engineering, Indian Institute of Technology (IIT), Bombay, and would like to acknowledge Department of Chemical Engineering, IIT Bombay, for its support.
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Corresponding editor: SEYED E HASNAIN
[Mehra V, Ghosh TS and Mande SS 2016 Insights into horizontal acquisition patterns of dormancy and reactivation regulon genes in mycobacterial species using a partitioning-based framework. J. Biosci.]
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Mehra, V., Ghosh, T.S. & Mande, S.S. Insights into horizontal acquisition patterns of dormancy and reactivation regulon genes in mycobacterial species using a partitioning-based framework. J Biosci 41, 475–485 (2016). https://doi.org/10.1007/s12038-016-9622-0
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DOI: https://doi.org/10.1007/s12038-016-9622-0