Sequence characteristics and divergent evolution of the chloroplast psbA-trnH noncoding region in gymnosperms

The psbA-trnH intergenic region is among the most variable regions in the gymnosperm chloroplast genome. It is proposed as suitable for DNA barcoding studies and is useful in phylogenetics at the species level. This region consists of two parts differing in their evolutionary characteristics: 1) the psbA 3'UTR (untranslated region) and 2) the psbA-trnH intergenic spacer. We compared the sequence and RNA secondary structure of the psbA 3' UTR across gymnosperms and found consensus motifs corresponding to the stem portions of the RNA stem-loop structures and a consensus TGGATTGTTATGT box. The psbA-trnH spacer is highly variable in length and composition. Tandem repeats that form stem loop structures were detected in both the psbA 3 UTR and the psbA-mill spacer. The presence of promoters and stem loop structures in the psbA-trnH spacer and high sequence variation in this region suggest that psbA and trnH in some gymnosperms are independently transcribed. A comparison of chloroplast UTRs across gymnosperms offer clues to the identity of putative regulatory elements and information on selective constraints imposed on the chloroplast non-coding regions. The present study should inspire researchers to explore the full potential of the psbA-trnH non-coding sequence and to further stimulate its application in a broader spectrum of studies, not limited to phylogenetics and DNA barcoding.