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

Štorchová H., Olson MS.

Keywords: chloroplast DNA; psbA-trnH intergenic region; Silene; deletions, insertions and inversions in stem-loop region; psbA 3' untranslated region; RNA secondary structure
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 explicable 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 a angiosperms offer clues to the identity ofputative regulatory elements and information about selective constraints imposed on the chloroplast non-coding regions.
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IEB authors: Helena Štorchová