Synonymous and Nonsynonymous Substitutions in Genes from Gramineae: Intragenic Correlations |
| |
| Authors: | Fernando Alvarez-Valin Kamel Jabbari Nicolas Carels Giorgio Bernardi |
| |
| Affiliation: | (1) Laboratoire de Génétique Moléculaire, Institut Jacques Monod, 2 Place Jussieu, F-75005 Paris, France, FR;(2) Stazione Zoologica Anton Dohrn, Laboratorio de Evoluzione Molecolare, Villa Comunale I, 80121 Napoli, Italy, IT;(3) Sección Biomatemática, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay, UY |
| |
| Abstract: | In this work, we have investigated the relationships between synonymous and nonsynonymous rates and base composition in coding sequences from Gramineae to analyze the factors underlying the variation in substitutional rates. We have shown that in these genes the rates of nucleotide divergence, both synonymous and nonsynonymous, are, to some extent, dependent on each other and on the base composition. In the first place, the variation in nonsynonymous rate is related to the GC level at the second codon position (the higher the GC2 level, the higher the amino acid replacement rate). The correlation is especially strong with T2, the coefficients being significant in the three data sets analyzed. This correlation between nonsynonymous rate and base composition at the second codon position is also detectable at the intragenic level, which implies that the factors that tend to increase the intergenic variance in nonsynonymous rates also affect the intragenic variance. On the other hand, we have shown that the synonymous rate is strongly correlated with the GC3 level. This correlation is observed both across genes and at the intragenic level. Similarly, the nonsynonymous rate is also affected at the intragenic level by GC3 level, like the silent rate. In fact, synonymous and nonsynonymous rates exhibit a parallel behavior in relation to GC3 level, indicating that the intragenic patterns of both silent and amino acid divergence rates are influenced in a similar way by the intragenic variation of GC3. This result, taken together with the fact that the number of genes displaying intragenic correlation coefficients between synonymous and nonsynonymous rates is not very high, but higher than random expectation (in the three data sets analyzed), strongly suggests that the processes of silent and amino acid replacement divergence are, at least in part, driven by common evolutionary forces in genes from Gramineae. Received: 2 July 1998 / Accepted: 18 April 1999 |
| |
| Keywords: | : Nucleotide substitutions — Nonsynonymous substitutions — Monocots — Base composition |
| 本文献已被 SpringerLink 等数据库收录！ |
|
