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Background  RNA editing in chloroplasts of angiosperms proceeds by C-to-U conversions at specific sites. Nuclear-encoded factors are required for the recognition of  cis -elements located immediately upstream of editing sites. The ensemble of editing sites in a chloroplast genome differs widely between species, and editing sites are thought to evolve rapidly. However, large-scale analyses of the evolution of individual editing sites have not yet been undertaken.    Results  Here, we analyzed the evolution of two chloroplast editing sites,  matK -2 and  matK -3, for which DNA sequences from thousands of angiosperm species are available. Both sites are found in most major taxa, including deep-branching families such as the nymphaeaceae. However, 36 isolated taxa scattered across the entire tree lack a C at one of the two  matK  editing sites. Tests of several exemplary species from this  in silico  analysis of  matK  processing unexpectedly revealed that one of the two sites remain unedited in almost half of all species examined. A comparison of sequences between editors and non-editors showed that specific nucleotides co-evolve with the C at the  matK  editing sites, suggesting that these nucleotides are critical for editing-site recognition.    Conclusion  (i) Both  matK  editing sites were present in the common ancestor of all angiosperms and have been independently lost multiple times during angiosperm evolution.  (ii) The editing activities corresponding to  matK -2 and  matK -3 are unstable.  (iii) A small number of third-codon positions in the vicinity of editing sites are selectively constrained independent of the presence of the editing site, most likely because of interacting RNA-binding proteins.

Loss of matKRNA editing in seed plant chloroplasts