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Nonneutral GC3 and Retroelement Codon Mimicry in Phytophthora

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Abstract

Phytophthora is a genus entirely comprised of destructive plant pathogens. It belongs to the Stramenopila, a unique branch of eukaryotes, phylogenetically distinct from plants, animals, or fungi. Phytophthora genes show a strong preference for usage of codons ending with G or C (high GC3). The presence of high GC3 in genes can be utilized to differentiate coding regions from noncoding regions in the genome. We found that both selective pressure and mutation bias drive codon bias in Phytophthora. Indicative for selection pressure is the higher GC3 value of highly expressed genes in different Phytophthora species. Lineage specific GC increase of noncoding regions is reminiscent of whole-genome mutation bias, whereas the elevated Phytophthora GC3 is primarily a result of translation efficiency-driven selection. Heterogeneous retrotransposons exist in Phytophthora genomes and many of them vary in their GC content. Interestingly, the most widespread groups of retroelements in Phytophthora show high GC3 and a codon bias that is similar to host genes. Apparently, selection pressure has been exerted on the retroelement’s codon usage, and such mimicry of host codon bias might be beneficial for the propagation of retrotransposons.

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Acknowledgments

We thank Martijn Staats for his advice concerning the statistical analyses, Brett Tyler for helpful suggestions and discussions, and the DOE-Joint Genome Institute (http://www.jgi.doe.gov/index.html), in particular, Brett Tyler, Jeff Boore, and Dan Rokhsar, for P. sojae and P. ramorum genome sequences. This work was financially supported by an Aspasia grant from the Netherlands Organisation for Scientific Research (NWO-Aspasia 015.000.057).

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  1. Laboratory of Phytopathology, Plant Sciences Group, and Graduate School of Experimental Plant Sciences, Wageningen University, Binnenhaven 5, NL-6709 PD, Wageningen, The Netherlands

    Rays H. Y. Jiang & Francine Govers

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  1. Rays H. Y. Jiang
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  2. Francine Govers
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Correspondence to Francine Govers.

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Reviewing Editor: Dr. Yves van de Peer

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Jiang, R.H.Y., Govers, F. Nonneutral GC3 and Retroelement Codon Mimicry in Phytophthora . J Mol Evol 63, 458–472 (2006). https://doi.org/10.1007/s00239-005-0211-3

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