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The architecture of the chloroplast psbA-trnH non-coding region in angiosperms

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Abstract

The psbA-trnH intergenic region is among the most variable regions in the angiosperm chloroplast genome. It is a popular tool for plant population genetics and species level phylogenetics and has been proposed as suitable for DNA barcoding studies. This region contains two parts differing in their evolutionary conservation: 1) the psbA 3′UTR (untranslated region) and 2) the psbA-trnH intergenic non-transcribed spacer. We compared the sequence and RNA secondary structure of the psbA 3′ UTR across angiosperms and found consensus motifs corresponding to the stem portions of the RNA stem-loop structures and a consensus TTAGTGTATA box. The psbA-trnH spacer exhibited patterns that can be explained by the independent evolution of large inversions in the psbA 3′UTR and mutational hot spots in the remaining portion of the psbA-trnH spacer. We conclude that a comparison of chloroplast UTRs across angiosperms offer clues to the identity of putative regulatory elements and information about selective constraints imposed on the chloroplast non-coding regions.

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Authors and Affiliations

  1. Institute of Experimental Botany v.v.i., Academy of Sciences of the Czech Republic, Rozvojová 135, 165 00, Prague 6, Lysolaje, Czech Republic

    H. Štorchová

  2. Department of Biology and Wildlife, University of Alaska at Fairbanks, Fairbanks, AK, USA

    M. S. Olson

  3. Institute of Arctic Biology, University of Alaska at Fairbanks, Fairbanks, AK, USA

    H. Štorchová & M. S. Olson

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  1. H. Štorchová
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  2. M. S. Olson
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Correspondence to H. Štorchová.

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Štorchová, H., Olson, M. The architecture of the chloroplast psbA-trnH non-coding region in angiosperms. Plant Syst. Evol. 268, 235–256 (2007). https://doi.org/10.1007/s00606-007-0582-6

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  • DOI: https://doi.org/10.1007/s00606-007-0582-6

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