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.
| Original language | English |
|---|---|
| Pages (from-to) | 235-256 |
| Number of pages | 22 |
| Journal | Plant Systematics and Evolution |
| Volume | 268 |
| Issue number | 1-4 |
| DOIs | |
| State | Published - Oct 2007 |
Keywords
- Chloroplast DNA
- Deletions, insertions and inversions in stem-loop region
- RNA secondary structure
- Silene
- psbA 3′ untranslated region
- psbA-trnH intergenic region