Specific compositional patterns of synonymous positions in homologous mammalian genes |
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| Authors: | Serguei Zoubak Giuseppe D'Onofrio Simone Cacciò Giacomo Bernardi Giorgio Bernardi |
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| Affiliation: | (1) Laboratoire de Genetique Moleculaire, Institut Jacques Monod, 2 Place Jussieu, 75005 Paris, France;(2) Department of Biology, University of California, Santa Cruz, 95064 Santa Cruz, CA, USA;(3) Present address: Institute of Molecular Biology and Genetics, Zabolotnogo str. 150, 252627 Kiev, Ukraine;(4) Present address: Stazione Zoologica, Villa Comunale 1, 80121 Naples, Italy |
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| Abstract: | All 69 homologous coding sequences that are currently available in four mammalian orders were aligned and the synonymous (ie., third) positions of quartet (fourfold degenerate) codons were divided into three classes (that will be called conserved, intermediate, and variable), according to whether they show no change, one change, and more than one change, respectively. The three classes were analyzed in their compositional patterns. In the majority of GC-rich genes, the three classes of positions (but especially conserved positions) exhibited significantly different base compositions compared to expectations based on a  random substitution process from the ancestral (consensus) sequence to the present-day (actual) sequences. Significant differences were rare in GC-poor genes.An analysis of the present results indicates that natural selection plays a role in the synonymous nucleotide substitution process, especially in GC-rich genes which represent the vast majority of mammalian genes.This paper is dedicated to the memory of Dr. Motoo Kimura (1924–1994)Correspondence to: Giorgio Bernardi |
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| Keywords: | Homologous mammalian genes Compositional patterns Synonymous positions |
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