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

By D. Quandt, Kai F. Müller, S. Huttunen. 2003

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The evolution of the plastid chromosome in land plants: gene content, gene order, gene function (2011, background): “SDRs mainly occur in non-coding DNA fractions (spacer, introns; Raubeson et al. 2007), where they are often associated with small hairpin structures (Quandt et al. 2003; Kim and Lee 2005).”
Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA (2009, methodology): “Second, the inverted element could be re-inverted, and thus gaining the substitution information prior to the inversion event secondary structure estimates (e.g., Kelchner and Wendel 1996; Quandt et al. 2003; Hernández-Maqueda et al. 2008).”
Phylogenetic analysis of Nymphaeales using fast-evolving and noncoding chloroplast markers (2007, background): “…the assessment of phylogenetic utility can be confined to the evaluation of sequence divergence, number of informative characters, frequency of length mutations and hotspots, as well as the phylogenetic structure R (Quandt et al., 2003; Müller et al., 2006) inherent in each data partition.”
Phylogeny of Nymphaea (Nymphaeaceae): Evidence from Substitutions and Microstructural Changes in the Chloroplast trnT‐trnF Region (2007, background): “Using trnL sequences from different tracheophyte, fern, and bryophyte lineages, Quandt et al. (2004) and Quandt and Stech (2005) hypothesized that the P8 stem loop has been independently prolongating in different land plant lineages.”