Abstract
The definition and delineation of microbial species are of great importance and challenge due to the extent of evolution and diversity. Whole-genome DNA–DNA hybridization is the cornerstone for defining procaryotic species relatedness, but obtaining pairwise DNA–DNA reassociation values for a comprehensive phylogenetic analysis of procaryotes is tedious and time consuming. A previously described microarray format containing whole-genomic DNA (the community genome array or CGA) was rigorously evaluated as a high-throughput alternative to the traditional DNA–DNA reassociation approach for delineating procaryotic species relationships. DNA similarities for multiple bacterial strains obtained with the CGA-based hybridization were comparable to those obtained with various traditional whole-genome hybridization methods (r=0.87, P<0.01). Significant linear relationships were also observed between the CGA-based genome similarities and those derived from small subunit (SSU) rRNA gene sequences (r=0.79, P<0.0001), gyrB sequences (r=0.95, P<0.0001) or REP- and BOX-PCR fingerprinting profiles (r=0.82, P<0.0001). The CGA hybridization-revealed species relationships in several representative genera, including Pseudomonas, Azoarcus and Shewanella, were largely congruent with previous classifications based on various conventional whole-genome DNA–DNA reassociation, SSU rRNA and/or gyrB analyses. These results suggest that CGA-based DNA–DNA hybridization could serve as a powerful, high-throughput format for determining species relatedness among microorganisms.
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Acknowledgements
This research was supported by The United States Department of Energy under Genomics: GTL program through the Virtual Institute of Microbial Stress and Survival (VIMSS; http://vimss.lbl.gov), and the Environmental Remediation Science Program (ERSP), and was supported by Oklahoma Center for the Advancement of Science and Technology under Oklahoma Applied Research Support Program. A part of XL's efforts was supported by Chinese National Science Foundation (NSFC) Joint Research Fund for Overseas Chinese Young Scholars (30428014), NSFC Fund for Creative Research (code 50321402) and Chinese National Basic Research (2004CB619201).
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Wu, L., Liu, X., Fields, M. et al. Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness. ISME J 2, 642–655 (2008). https://doi.org/10.1038/ismej.2008.23
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DOI: https://doi.org/10.1038/ismej.2008.23
