Figure S1. Expression of At4g25270 in wild-type (Wt), mutant (otp70) and complemented lines. Total RNA was extracted from 3 day-old seedlings and reversed transcribed with Superscript III (Invitrogen) using 3 μg of DNA-free total RNA and the primers Salk_090845 LP and Salk_090845 RP described in Supplementary Table S1. The various complemented lines are described in Figure 6.

Figure S2. OTP70 contains a plastid targeting sequence. The first 300bp of the OTP70 coding sequence was fused N-terminally to the coding sequence of GFP. This protein fusion was expressed in cultured Arabidopsis cells (a) together with a plastid marker (Rubisco small subunit fused to RFP) (b). The overlay of the two fluorescence patterns in shown in (c).

Figure S3.otp70 is not impaired in editing of the 34 known plastid editing sites High-resolution melt curves of mixed genomic and cDNA amplification products from wild-type and otp70 plants. Each amplification product spans a specific editing site. The mixed melt curves differ from that of unmixed genomic DNA amplification products because of heterodimers formed between edited and unedited sequences. A defect in editing would be revealed by the melt curve of amplification products from otp70 following that of the unmixed genomic DNA, which is not observed in any of the tests.

Figure S4. Clustering of plastid transcript patterns. Levels of all plastid transcripts quantified by qRT-PCR were used to build a distance tree by hierarchical clustering depicting similarities between the transcript patterns. The crr mutants are defective in the chloroplast NDH complex but otherwise have a wild-type growth phenotype; ys1, clb19 and ptac2 are all affected in PEP transcription.

Figure S5. Editing of spliced rpoC1 transcripts. Editing of the rpoC1(21806) site in RNA from leaves was quantified using poisoned primer extension using ddGTP to prevent extension before the first C encountered. The primers used to amplify reverse transcribed RNA to form the template were specific for spliced transcripts. Data for unspliced transcripts is given in Figure 7. C indicates the band obtained from unedited template, U the band from edited template. H2O, no template; edited, cloned edited control template; unedited, cloned unedited control template; other lanes are labeled as in Figures 6 and 7.

Table S1. Sequences of oligonucleotide primers used in this study.

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