Evolutionary Implications of Microbial Genome Tetranucleotide Frequency Biases
Open Access
- 14 January 2003
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 13 (2) , 145-158
- https://doi.org/10.1101/gr.335003
Abstract
We compared nucleotide usage pattern conservation for related prokaryotes by examining the representation of DNA tetranucleotide combinations in 27 representative microbial genomes. For each of the organisms studied, tetranucleotide usage departures from expectations (TUD) were shared between related organisms using both Markov chain analysis and a zero-order Markov method. Individual strains, multiple chromosomes, plasmids, and bacteriophages share TUDs within a species. TUDs varied between coding and noncoding DNA. Grouping prokaryotes based on TUD profiles resulted in relationships with important differences from those based on 16S rRNA phylogenies, which may reflect unequal rates of evolution of nucleotide usage patterns following divergence of particular organisms from a common ancestor. By both symmetrical tree distance and likelihood analysis, phylogenetic trees based on TUD profiles demonstrate a level of congruence with 16S rRNA trees similar to that of both RpoA and RecA trees. Congruence of these trees indicates that there exists phylogenetic signal in TUD patterns, most prominent in coding region DNA. Because relationships demonstrated in TUD-based analyses utilize whole genomes, they should be considered complementary to phylogenies based on single genetic elements, such as 16S rRNA.Keywords
This publication has 44 references indexed in Scilit:
- Identification of Horizontally Acquired Genetic Elements in Helicobacter pylori and Other Prokaryotes Using Oligonucleotide Difference AnalysisGenome Letters, 2002
- Genome sequence of enterohaemorrhagic Escherichia coli O157:H7Nature, 2001
- COMPARATIVE DNA ANALYSIS ACROSS DIVERSE GENOMESAnnual Review of Genetics, 1998
- Tree View: An application to display phylogenetic trees on personal computersBioinformatics, 1996
- Uneven Distribution of GATC Motifs in theEscherichia coliChromosome, its Plasmids and its PhagesJournal of Molecular Biology, 1996
- Over- and Underrepresentation of Short DNA Words in Herpesvirus GenomesJournal of Computational Biology, 1996
- Exceptional Motifs in Different Markov Chain Models for a Statistical Analysis of DNA SequencesJournal of Computational Biology, 1995
- COMPUTATIONAL DNA SEQUENCE ANALYSISAnnual Review of Microbiology, 1994
- The Use of Tree Comparison MetricsSystematic Zoology, 1985
- Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genesGene, 1982