Classification and regression tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria.
Classification and regression tree (CART) analysis was applied to genome-wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. Although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. Temperature optima for most of the organisms examined could be distinguished by CART analyses of tetranucleotide frequencies. This suggests that pervasive (nonlinear) qualities of genomes may reflect certain environmental conditions (such as temperature) in which those genomes evolved. The predominant use of GAGA and AGGA as the discriminating tetramers in CART models suggests that purine-loading and codon biases of thermophiles may explain some of the results.
Dyer
Betsey Dexter
BD
Department of Biology, Wheaton College, Norton, MA 02766, USA.
Kahn
Michael J
MJ
Leblanc
Mark D
MD
D001105:Archaea / Q000145:classification / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D023281:Genomics; D006358:Hot Temperature; D012044:Regression Analysis; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D013696:Temperature