Phylogenetics of early branching eudicots: comparing phylogenetic signal accross chloroplast introns, spacers, and genes

Barniske A, Borsch T, Müller KF, Krug M, Worberg A, Neinhuis C, Quandt D

Research article (journal)


Recent phylogenetic analyses revealed a grade with Ranunculales, Sabiales, Proteales, Trochodendrales and Buxales as the first branches of the eudicots, while the respective positions of Proteales and Sabiales still lacked statistical confidence. The majority of conserved coding genes of the plastid genome has been utilized for analyses, whereas the phylogenetic signal of the about 40 percent of the plastid genome’s non-coding part remains largely unexplored. By adding further group II introns and spacers to our initial analysis, we aimed at comparing a more representative set of introns and spacers. Here we compare phylogenetic signal of a group I intron (trnL), three group II introns (in petD, rpl16, trnK), and four spacers (trnL-F, petB-petD, atpB-rbcL, rps3-rpl16), with the rapidly evolving matK and the slowly evolving atpB and rbcL genes. Similar mutational patterns with confined hotspots were found in all intron and spacer partitions, allowing for multiple sequence alignment across eudicots. Overall patterns of microstructural mutations converged across genomic regions, underscoring the existence of a general mutational pattern throughout the plastid genome. The phylogenetic structure R differed strongly between functionally and structurally different genomic regions and was highest in matK followed by spacers, group II and group I introns. The more conserved atpB and rbcL coding regions showed distinctly lower phylogenetic structure. Maximum Parsimony, Maximum Likelihood, and Bayesian tree inference of the combined data set of non-coding and rapidly evolving regions (>14,000 aligned characters) converged to a backbone topology of eudicots with Ranunculales branching first, a Proteales-Sabiales clade second, followed by Trochodendrales and Buxales. Gunnerales generally appeared as sister to all remaining core eudicots with maximum support. Our results show that a small number of intron and spacer sequences allows similar insights into phylogenetic relationships of eudicots than data sets of many combined genes. The non-coding proportion of the plastid genome thus will be an important information source in chloroplast phylogenomics.

Details zur Publikation

Pages: 24
Release year: 2012
Language in which the publication is writtenEnglish