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The architecture of the chloroplast psbA-trnH non-coding region in angiosperms |
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| Authors: | H ?torchová M S Olson |
| Institution: | (1) Institute of Experimental Botany v.v.i., Academy of Sciences of the Czech Republic, Rozvojová 135, 165 00 Prague 6, Lysolaje, Czech Republic;(2) Department of Biology and Wildlife, University of Alaska at Fairbanks, Fairbanks, AK, USA;(3) Institute of Arctic Biology, University of Alaska at Fairbanks, Fairbanks, AK, USA |
| 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. |
| Keywords: | chloroplast DNA psbA-trnH intergenic region Silene deletions insertions and inversions in stem-loop region psbA 3′ untranslated region RNA secondary structure |
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