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

H. Štorchová, M. S. Olson

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56 Scopus citations


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.

Original languageEnglish
Pages (from-to)235-256
Number of pages22
JournalPlant Systematics and Evolution
Issue number1-4
StatePublished - Oct 2007


  • Chloroplast DNA
  • Deletions, insertions and inversions in stem-loop region
  • RNA secondary structure
  • Silene
  • psbA 3′ untranslated region
  • psbA-trnH intergenic region


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