Characterisation of the Chloroplast DNA psbT-H Region and the Influence of Dyad Symmetrical Elements on Phylogenetic Reconstructions

D. Quandt; K. Müller; S. Huttunen

doi:10.1055/s-2003-42715

Plant Biology, Table of Contents

Plant Biol (Stuttg) 2003; 5(4): 400-410
DOI: 10.1055/s-2003-42715

Original Paper

Georg Thieme Verlag Stuttgart · New York

Characterisation of the Chloroplast DNA psbT-H Region and the Influence of Dyad Symmetrical Elements on Phylogenetic Reconstructions

D. Quandt¹ , K. Müller¹ , S. Huttunen²

¹Botanisches Institut und Botanischer Garten, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
²Botanical Museum, University of Helsinki, Helsinki, Finland

Abstract

The tandemly arranged genes psbT, psbN, and psbH code for proteins of photosystem II and are located in the large single copy region (LSC) of the chloroplast genome, downstream of psbB. So far, most of the studies dealing with this region have been interested in the organization and transcription of the psbB operon, while less is known about the transcription of psbN or the phylogenetic utility of this region. In the current study we discuss a sigma⁷⁰-type bacterial promoter motif upstream of psbN and present its consensus sequence for bryophytes. An analysis of the 3′ flanking inverted repeat sequences revealed a dyad symmetrical element, which is able to form a stable stem-loop structure. This hairpin structure is characterised for land plants, with an emphasis on bryophytes. Furthermore, we observed an inversion of up to 9 bases in the loop region of the hairpin structure, which occasionally occurred in different unrelated bryophyte families, orders and classes. Small inversions are frequently obscured in the alignment since, during automatic alignment, many gap-weighting schemes may not introduce gaps, nor does a manual insertion of gaps always seem needed at first glance. In subsequent phylogenetic analyses, minute inversion may overweight a particular mutation by interpreting the single inversion event as multiple apomorphic substitutions, which is particularly problematic since such inversion events are known to often be highly homoplastic. In the present study we use the psbT-N spacer as an example to quantify the effect of such small inversions, contrasting the phylogenetic structure obtained with and without information from the hairpin loop. We show that obscured minute inversions can highly significantly reduce the robustness of the phylogenetic hypothesis inferred from the data set.

Key words

Dyad symmetrical elements - inversions - repeats - noncoding chloroplast DNA - molecular evolution - phylogenetics - promoter - 3′ UTR.

Full Text

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D. Quandt

Rheinische Friedrich-Wilhelms-Universität Bonn
Botanisches Institut und Botanischer Garten, AG Bryologie

Meckenheimer Allee 170

53115 Bonn

Germany

Email: d.quandt@uni-bonn.de

Section Editor: F. Salamini