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MBE Advance Access originally published online on March 24, 2004
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Mol. Biol. Evol. 21(6):1152-1159. 2004
DOI: 10.1093/molbev/msh133
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Evolution of Prokaryotic DNA: Intragenic and Extragenic Divergences Observed with Orthologs from Three Related Species

Anders Fuglsang

Danish University of Pharmaceutical Sciences, Institute of Pharmacology, Universitetsparken, Copenhagen, Denmark

E-mail anfu{at}dfh.dk.

This study compared orthologous gene pairs from Escherichia coli K12, E. coli O157:H7 EDL933, Salmonella typhimurium LT2, and Yersinia pestis CO92 using only homologs of equal length, and differing nucleotides were counted and mapped. The data showed very clearly how the rates of divergence change with intragenic and extragenic position. The rate of synonymous mutation is lowest near start codons and near stop codons, and, a little surprisingly, the opposite seemed to be true for nonsynonymous substitutions. Analysis outside genes reveals that nucleotide divergences occur less frequently upstream of start codons than downstream of stop codons, and a remarkable drop in divergences is seen for two of the data sets around N = 9 nucleotides upstream of start codons; that is, the Shine-Dalgarno region changes at a lower rate. The explanation is likely to be the link between expressivity and sequence complementarity to the 3' end of 16S ribosomal rRNA. The latter is highly conserved across many bacterial and archaebacterial species.

Key Words: Sequence alignment • Shine-Dalgarno regions • mutation • molecular evolution • codon usage bias • expressivity


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