Fig. 1

Cladograms for a sampling of 117 angiosperm species according to the current understanding of flowering plant phylogeny. The large clades of Asterids, Caryophyllales and Liliopsida (monocots) are collapsed in the left cladogram and, vice versa, the large clade of Rosids is collapsed in the right cladogram. Species marked with asterisks lack complete chloroplast genome data. Closely related cpDNAs were inspected in these cases or chloroplast targets have been individually investigated in this study (here e.g. ndhB and ndhD sequences of Rauvolfia and Diospyros). Black downward triangles indicate simultaneous losses of editing site accDeU794SL and editing factor RARE1. The black circles indicate loss of the accDeU794SL editing site in Quercus and Castanea (Fagaceae, Fagales) or of the accD gene altogether (Trifolium) while RARE1 orthologues remain present. Blue circles indicate independent losses of editing site ndhBeU467PL owing to a plastomic C-to-T conversion in Linum, Vicia, Trifolium, a Fabales subclade including Cicer, and in Citrus sinensis. Red circles indicate loss of the ndhDeU878SL editing site in Arecales (Phoenix and Elaeis), in Dianthus, Silene and Bienertia among Caryophyllales, in Ipomoea and Nicotiana tabacum (Solanales), in Cicer, Fragaria, Cannabis and Humulus, in Eucalyptus and in Azadirachta. CRR28 orthologues were identified in all taxa except in chickpea (Cicer arietinum) were both editing sites are lost (green downward triangle). The green upward triangle indicates truncation of CRR28 behind the E2 domain in Cynara and Lactuca. Phylograms of CRR28 and RARE1 orthologues are available as Additional files 1 and 2, respectively