Codon Usage by Transposable Elements and Their Host Genes in Five Species |
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Authors: | Emmanuelle Lerat Pierre Capy Christian Biémont |
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Institution: | (1) Laboratoire Biométrie et Biologie évolutive, UMR CNRS 5558, Université Lyon 1, 69622 Villeurbanne Cedex, France, FR;(2) Laboratoire Populations, Génétique et évolution, UPR CNRS 9034, 91198 Gif/Yvette Cedex, France, FR |
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Abstract: | We compared the codon usage of sequences of transposable elements (TEs) with that of host genes from the species Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Saccharomyces cerevisiae, and Homo sapiens. Factorial correspondence analysis showed that, regardless of the base composition of the genome, the TEs differed from the
genes of their host species by their AT-richness. In all species, the percentage of A + T on the third codon position of the
TEs was higher than that on the first codon position and lower than that in the noncoding DNA of the genomes. This indicates
that the codon choice is not simply the outcome of mutational bias but is also subject to selection constraints. A tendency
toward higher A + T on the third position than on the first position was also found in the host genes of A. thaliana, C. elegans, and S. cerevisiae but not in those of D. melanogaster and H. sapiens. This strongly suggests that the AT choice is a host-independent characteristic common to all TEs. The codon usage of TEs
generally appeared to be different from the mean of the host genes. In the AT-rich genomes of Arabidopsis thaliana, Caenorhabditis elegans, and Saccharomyces cerevisiae, the codon usage bias of TEs was similar to that of weakly expressed genes. In the GC-rich genome of D. melanogaster, however, the bias in codon usage of the TEs clearly differed from that of weakly expressed genes. These findings suggest
that selection acts on TEs and that TEs may display specific behavior within the host genomes.
Received: 2 May 2001 / Accepted: 29 October 2001 |
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Keywords: | : Codon usage — Transposable elements — Retrotransposons — Transposons |
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