Supplemental Data

Files in this Data Supplement:

• Supplemental Table 1 - A comparison between our ORF models (ICBMs) and those of the AGI (TIGR Release 5 annotations). The columns of the table give, respectively, our code names for our models (based on the chromosome and the position on the chromosome), the closest AGI model, the AGI-annotated PPR genes in the vicinity, the percentage sequence identity between the two models, the length of the region that matches between the two models, the bit score of the BLAST comparison, the start and end coordinates of the ICBM and AGI models in the alignment, the length in amino acids of the protein predicted from our model, the length in amino acids of the AGI-predicted protein, an indication (true or false) of whether or not the two models are identical, and finally notes that explain the cases where models are lacking completely from one or other of the annotations.
• Supplemental Table 2 - The motif structure of Arabidopsis PPR proteins. Using the HMMER matrices defined for the different variants of the PPR motif, the highest-scoring arrangement of motifs was retained for each predicted protein. Intervening figures give the length in amino acids of gaps between the detected motifs. Based on the types of motifs present, the proteins have been classed into five subclasses: P, P-L-S, E, E+, and DYW.
• Supplemental Table 3 - Putative PPR proteins from non-plant organisms. The table lists 51 proteins detected as containing at least two putative PPR motifs at an E-value of <10 using HMMER.
• Supplemental Table 4 - Targeting predictions for Arabidopsis PPR proteins. The proteins predicted from our ORF models were tested by Predotar (Small et al., 2004) and TargetP (Emanuelsson et al., 2000). The scores from each program are given for predictions of mitochondrial targeting peptides (mTP), plastid targeting peptides (cTP), or secretory pathway signal peptides (SP) as well as the subsequent conclusion. RC indicates the degree of confidence in the TargetP prediction (Emanuelsson et al., 2000).
• Supplemental Table 5 - Expression of PPR genes. The EST column gives the number of ESTs or cDNAs listed in FLAGdb++; the RT columns give the results of amplification with 372 primer pairs from the CATMA collection on leaf or flower mRNAS (0 = no amplification, 1 = amplification). CATMA microarrays were hybridized with labeled leaf and flower RNA and the 384 spots corresponding to PPR genes were analysed; the figures given are the mean signal intensity averaged over the two dye swaps.