Journal
PLANT SYSTEMATICS AND EVOLUTION
Volume 268, Issue 1-4, Pages 235-256Publisher
SPRINGER WIEN
DOI: 10.1007/s00606-007-0582-6
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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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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