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Mol. Biol. Evol. 20(1):105-110. 2003
DOI: 10.1093/molbev/msg008
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Base Compositions of Genes Encoding {alpha}-Actin and Lactate Dehydrogenase-A from Differently Adapted Vertebrates Show No Temperature-Adaptive Variation in G + C Content

Rachael A. Ream, Glenn C. Johns and George N. Somero

Hopkins Marine Station of Stanford University, Pacific Grove, California

There is a long-standing debate in molecular evolution concerning the putative importance of GC content in adapting the thermal stabilities of DNA and RNA. Most studies of this relationship have examined broad-scale compositional patterns, for example, total GC percentages in genomes and occurrence of GC-rich isochores. Few studies have systematically examined the GC contents of individual orthologous genes from differently thermally adapted species. When this has been done, the emphasis has been on comparing large numbers of genes in only a few species. We have approached the GC-adaptation temperature hypothesis in a different manner by examining patterns of base composition of genes encoding lactate dehydrogenase-A (ldh-a) and alpha-actin ({alpha}-actin) from 51 species of vertebrates whose adaptation temperatures ranged from -1.86°C (Antarctic fishes) to approximately 45°C (desert reptile). No significant positive correlation was found between any index of GC content (GC content of the entire sequence, GC content of the third codon position [GC3], and GC content at fourfold degenerate sites [GC4]) and any index of adaptation temperature (maximal, mean, or minimal body temperature). For {alpha}-actin, slopes of regression lines for all comparisons did not differ significantly from zero. For ldh-a, negative correlations between adaptation temperature and total GC content, GC3, and GC4 were observed but were shown to be due entirely to phylogenetic influences (as revealed by independent contrast analyses). This comparison of GC content across a wide range of ectothermic ("cold-blooded") and endothermic ("warm-blooded") vertebrates revealed that frogs of the genus Xenopus, which have commonly been used as a representative cold-blooded species, in fact are outliers among ectotherms for the {alpha}-actin analyses, raising concern about the appropriateness of choosing these amphibians as representative of ectothermic vertebrates in general. Our study indicates that, whereas GC contents of isochores may show variation among different classes of vertebrates, there is no consistent relationship between adaptation temperature and the percentage of thermal stability-enhancing G + C base pairs in protein-coding genes.

Key Words: Vertebrate genome evolution • GC content • codon bias • temperature • alpha-actin • lactate dehydrogenase-A (ldh-a)


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