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The Variation of Base Composition in Plant Genomes

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Plant Genome Diversity Volume 1

Abstract

The proportions of the four nucleotides in DNA may vary significantly in various genome components and with different selective forces or mutation biases acting on particular sequences. Most frequently, DNA base composition is expressed as the percentage of guanine (G) and cytosine (C) bases (i.e., GC content). The study of GC content has a long tradition in prokaryotic biology and systematics, and has been widely discussed in animal genomics namely, in the consequences of the evolution of the isochore structure of humans and other warm-blooded vertebrates. However, less attention has been paid to the GC content of plant genomes. Here, we survey existing research concerning GC content of plant nuclear genomes and outline some directions for possible interpretations of the biological relevance of variation in GC content viewed in the context of work done on bacterial and animal genomes. We briefly discuss major physical and chemical differences between GC and AT base pair and summarize existing opinions on the mechanisms of local or genome-wide GC content variation, including namely compositional variation, neutral mutational biases, and various selective reasons. In addition to the brief survey of plant genomic GC contents, most frequent methods for GC content measurements in plants are also outlined.

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Notes

  1. 1.

    The relatively small increase in genome size may be due to the combined effect of genome downsizing and the massive proliferation of GC-rich retrotransposons.

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Acknowledgements

The work of authors was supported by the Czech Ministry of Education, Youth and Sports (grants MSM 0021622416 and LC06073) and the Czech Science Foundation (grants GACR206/08/P222 and GACR506/11/0890).

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Authors and Affiliations

  1. Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic

    Petr Šmarda

  2. Faculty of Science, Department of Botany and Zoology, Masaryk University, Brno, Czech Republic

    Petr Bureš

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Correspondence to Petr Šmarda .

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Editors and Affiliations

  1. Dept. Botany, Iowa State University, Ames, 50011-1024, Iowa, USA

    Jonathan F. Wendel

  2. Inst. Botanik und Botanischer Garten, Universität Wien, Rennweg 14, Wien, 1030, Austria

    Johann Greilhuber

  3. Inst. Experimental Botany, Dept. Plant Biotechnology, ASCR Olomouc, Sokolovska 6, Olomouc, 772 00, Czech Republic

    Jaroslav Dolezel

  4. Dept. Jodrell Lab., Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, United Kingdom

    Ilia J. Leitch

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Šmarda, P., Bureš, P. (2012). The Variation of Base Composition in Plant Genomes. In: Wendel, J., Greilhuber, J., Dolezel, J., Leitch, I. (eds) Plant Genome Diversity Volume 1. Springer, Vienna. https://doi.org/10.1007/978-3-7091-1130-7_14

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