Evolutionary implications of microbial genome tetranucleotide frequency biases

David T Pride¹, Richard J Meinersmann, Trudy M Wassenaar

¹Department of Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee 37235, USA. Prided01@med.nyu.edu

|February 5, 2003

Summary

Tetranucleotide usage patterns (TUDs) in prokaryotic genomes reveal evolutionary relationships. These DNA sequence patterns offer a complementary perspective to traditional phylogenetic methods like 16S rRNA analysis.

Area of Science:

Genomics
Bioinformatics
Evolutionary Biology

Background:

Nucleotide usage patterns, specifically tetranucleotide usage departures (TUDs), are conserved within prokaryotic genomes.
Understanding these patterns can provide insights into microbial evolution and relationships.

Purpose of the Study:

To compare nucleotide usage pattern conservation across related prokaryotes.
To assess the phylogenetic signal within tetranucleotide usage profiles.
To evaluate the congruence of TUD-based phylogenies with established methods.

Main Methods:

Analysis of DNA tetranucleotide combinations in 27 microbial genomes.
Application of Markov chain analysis and a zero-order Markov method to identify shared TUDs.
Construction of phylogenetic trees using TUD profiles and comparison with 16S rRNA, RpoA, and RecA trees.

Main Results:

Tetranucleotide usage departures (TUDs) are shared within species across chromosomes, plasmids, and bacteriophages.
TUDs differ between coding and noncoding DNA.
Prokaryotic groupings based on TUD profiles show differences from 16S rRNA phylogenies, suggesting varying evolutionary rates.
Phylogenetic trees derived from TUD profiles exhibit congruence with 16S rRNA, RpoA, and RecA trees, indicating phylogenetic signal, particularly in coding DNA.

Conclusions:

Tetranucleotide usage patterns contain significant phylogenetic information, especially within coding regions.
Whole-genome TUD-based analyses provide a complementary approach to single-gene phylogenies for understanding microbial relationships.
Discrepancies between TUD and 16S rRNA phylogenies may reflect differential evolutionary rates of nucleotide usage patterns.

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Evolutionary implications of microbial genome tetranucleotide frequency biases

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Purpose of the Study:

Main Methods:

Main Results:

Conclusions:

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