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Quantitative Exploration of the Occurrence of Lateral Gene Transfer by Using Nitrogen Fixation Genes as a Case Study
Katherina J. Kechris, Jason C. Lin, Peter J. Bickel and Alexander N. Glazer
Proceedings of the National Academy of Sciences of the United States of America
Vol. 103, No. 25 (Jun. 20, 2006), pp. 9584-9589
Published by: National Academy of Sciences
Stable URL: http://www.jstor.org/stable/30050952
Page Count: 6
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Lateral gene transfer (LGT) is now accepted as an important factor in the evolution of prokaryotes. Establishment of the occurrence of LGT is typically attempted by a variety of methods that includes the comparison of reconstructed phylogenetic trees, the search for unusual GC composition or codon usage within a genome, and identification of similarities between distant species as determined by best BLAST hits. We explore quantitative assessments of these strategies to study the prokaryotic trait of nitrogen fixation, the enzyme-catalyzed reduction of N₂ to ammonia. Phylogenies constructed on nitrogen fixation genes are not in agreement with the tree-of-life based on 16S rRNA but do not conclusively distinguish between gene loss and LGT hypotheses. Using a series of analyses on a set of complete genomes, our results distinguish two structurally distinct classes of MoFe nitrogenases whose distribution cuts across lines of vertical inheritance and makes us believe that a conclusive case for LGT has been made.
Proceedings of the National Academy of Sciences of the United States of America © 2006 National Academy of Sciences