Genetic relationships among 527 Gram-negative bacterial plasmids

Plasmid
Yunyun ZhouShira L Broschat

Abstract

Plasmids are mosaic in composition with a maintenance "backbone" as well as "accessory" genes obtained via horizontal gene transfer. This horizontal gene transfer complicates the study of their genetic relationships. We describe a method for relating a large number of Gram-negative (GN) bacterial plasmids based on their genetic sequences. Complete coding gene sequences of 527 GN bacterial plasmids were obtained from NCBI. Initial classification of their genetic relationships was accomplished using a computational approach analogous to hybridization of "mixed-genome microarrays." Because of this similarity, the phrase "virtual hybridization" is used to describe this approach. Protein sequences generated from the gene sequences were randomly chosen to serve as "probes" for the virtual arrays, and virtual hybridization for each GN plasmid was achieved using BLASTp. Each resulting intensity matrix was used to generate a distance matrix from which an initial tree was constructed. Relationships were refined for several clusters by identifying conserved proteins within a cluster. Multiple-sequence alignment was applied to the concatenated conserved proteins, and maximum likelihood was used to generate relationships from the results of...Continue Reading

References

Jul 1, 1995·Trends in Genetics : TIG·S Karlin, C Burge
Aug 4, 1999·Proceedings of the National Academy of Sciences of the United States of America·A CampbellS Karlin
Dec 6, 2000·Proceedings of the National Academy of Sciences of the United States of America·J E Purser, S J Norris
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Jan 9, 2007·Applied and Environmental Microbiology·Yan WanDouglas R Call
May 16, 2007·PLoS Pathogens·Stephen BakerGordon Dougan

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Citations

Mar 20, 2013·Advances in Bioinformatics·Yunyun ZhouShira L Broschat
May 21, 2014·Microbial Drug Resistance : MDR : Mechanisms, Epidemiology, and Disease·Christopher J Harmer, Ruth M Hall
Apr 26, 2015·Plasmid·Christopher J Harmer, Ruth M Hall
Jun 25, 2015·Microbiology Spectrum·Clarence I Kado

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