Abstract
Introns and spacers are a rich and well-appreciated information source for evolutionary studies in plants. Compared to coding sequences, the mutational dynamics of introns and spacers is very different, involving frequent microstructural changes in addition to substitutions of individual nucleotides. An understanding of the biology of sequence change is required for correct application of molecular characters in phylogenetic analyses, including homology assessment, alignment coding, and tree inference. The widely used term “indel” is very general, and different kinds of microstructural mutations, such as simple sequence repeats, short tandem repeats, homonucleotide repeats, inversions, inverted repeats, and deletions, need to be distinguished. Noncoding DNA has been indispensable for analyses at the species level because coding sequences usually do not offer sufficient variability. A variety of introns and spacers has been successfully applied for phylogeny inference at deeper levels (major lineages of angiosperms and land plants) in past years, and phylogenetic structure R in intron and spacer data sets usually outperforms that of coding-sequence data sets. In order to fully utilize their potential, the molecular evolution and applicability of the most important noncoding markers (the trnT–trnF region comprising two spacers and a group I intron; the trnS–G region comprising one spacer and a group II intron in trnG; the group II introns in petD, rpl16, rps16, and trnK; and the atpB–rbcL and psbA–trnG spacers) are reviewed. The study argues for the use of noncoding DNA in a spectrum of applications from deep-level phylogenetics to speciation studies and barcoding, and aims at outlining molecular evolutionary principles needed for effective analysis.
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Acknowledgments
This work was supported by grants of the Deutsche Forschungsgemeinschaft to T.B. (BO1815/2) and D.Q. (QU153/2) for the project “Mutational dynamics of noncoding genomic regions and their potential for reconstructing eudicot evolution.” Karsten Salomo (Dresden) provided unpublished data for Fig. 5 and Kim Govers (Berlin) helped with preparing Fig. 1. Various kinds of support by Susi Wicke (Vienna/Bonn) and Markus Ackermann (Berlin) are appreciated. We kindly acknowledge helpful comments by Scot Kelchner and David Morrison to an earlier version of this manuscript.
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An erratum to this article can be found at http://dx.doi.org/10.1007/s00606-009-0233-1
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Borsch, T., Quandt, D. Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA. Plant Syst Evol 282, 169–199 (2009). https://doi.org/10.1007/s00606-009-0210-8
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DOI: https://doi.org/10.1007/s00606-009-0210-8