Table 2.
RNA Editing Sites Discovered in the Selaginella moellendorffii (Smoe) Transcriptome Are Listed for Comparison with Data from Similarly Comprehensive Transcriptome Studies in the Moss Physcomitrella patens (Ppat, Rüdinger et al. 2009), the Lycophyte Isoetes engelmannii (Ieng, Grewe et al. 2011), the Flowering Plants Beta vulgaris (Bvul, Mower and Palmer 2006), Silene noctiflora and Silene latifolia (Snoc and Slat, Sloan, MacQueen, et al. 2010), Arabidopsis thaliana (Atha, Giegé and Brennicke 1999), Brassica napus (Bnap, Handa 2003), and Oryza sativa (Osat, Notsu et al. 2002)
| Genes | Ppat | Ieng | Smoe | Bvul | Slat | Snoc | Bnap | Atha | Osat |
| Numbers of editing sites | |||||||||
| nad1 | 0 | 57 | 137 | 20 | 19 | 11 | 23 | 24 | 23 |
| nad2 | 0 | 100 | 249 | 24 | 21 | 18 | 25 | 32 | 30 |
| nad3 | 1 | 57 | 77 | 12 | 8 | 5 | 10 | 12 | 15 |
| nad4 | 1 | 156 | 237 | 19 | 16 | 11 | 35 | 32 | 20 |
| nad4L | 0 | 27 | 47 | 10 | 9 | 6 | 9 | 9 | 10 |
| nad5 | 2 | 166 | 143 | 17 | 18 | 15 | 29 | 27 | 11 |
| nad6 | 0 | 64 | 89 | 11 | 10 | 6 | 11 | 10 | 18 |
| nad7 | 0 | 115 | 103 | 20 | 19 | 9 | 28 | 27 | 32 |
| nad9 | 0 | 50 | 72 | 5 | 5 | 1 | 8 | 7 | 12 |
| sdh3 | 0 | 23 | |||||||
| sdh4 | 0 | 4 | |||||||
| cob | 0 | 121 | 122 | 13 | 9 | 6 | 8 | 7 | 19 |
| cox1 | 1 | 110 | 181 | 0 | 0 | 0 | 1 | 0 | 4 |
| cox2 | 1 | 14 | 97 | 9 | 3 | 2 | 13 | 15 | 19 |
| cox3 | 1 | 101 | 133 | 4 | 1 | 1 | 7 | 8 | 1 |
| atp1 | 0 | 131 | 160 | 3 | 3 | 0 | 5 | 5 | 5 |
| atp4 | 0 | 6 | 12 | 11 | 6 | 8 | 8 | 9 | |
| atp6 | 0 | 95 | 80 | 12 | 11 | 7 | 1 | 1 | 17 |
| atp8 | 0 | 35 | 35 | 2 | 2 | 2 | 3 | 0 | 4 |
| atp9 | 1 | 34 | 44 | 5 | 4 | 1 | 4 | 4 | 8 |
| ccmB | 0 | 30 | 27 | 19 | 39 | 39 | 35 | ||
| ccmC | 0 | 28 | 23 | 15 | 25 | 28 | 36 | ||
| ccmFN(1) | 0 | 23 | 22 | 16 | 15 | 22 | 31 | ||
| ccmFN(2) | 10 | 12 | |||||||
| ccmFC | 2 | 13 | 12 | 8 | 13 | 16 | 27 | ||
| rpl2 | 0 | 2 | 1 | 1 | |||||
| rpl5 | 0 | 30 | 5 | 6 | 4 | 9 | 10 | 1 | |
| rpl6 | 0 | ||||||||
| rpl10 | 0 | n.i. | n.i. | ||||||
| rpl16 | 0 | 6 | 5 | 12 | |||||
| rps1 | 0 | 3 | |||||||
| rps2 | 0 | 28 | 10 | ||||||
| rps3 | 0 | 62 | 6 | 4 | 3 | 8 | 13 | 10 | |
| rps4 | 0 | 55 | 11 | 19 | 15 | 15 | |||
| rps7 | 0 | 3 | 1 | 0 | 2 | ||||
| rps8 | 0 | ||||||||
| rps10 | |||||||||
| rps11 | 0 | 4 | |||||||
| rps12 | 0 | 6 | 7 | 8 | 0 | ||||
| rps13 | 0 | 2 | 1 | 0 | 8 | ||||
| rps14 | 1 | 0 | 0 | ||||||
| rps19 | 0 | ||||||||
| tatC | 0 | 68 | 133 | 19 | 15 | 11 | 27 | 24 | 33 |
| matR | 9 | 8 | 6 | 8 | 9 | n.i. | |||
| Total | 11 | 1,705 | 2,139 | 357 | 287 | 189 | 417 | 430 | 491 |
NOTE.—Dark gray shading indicates that a given gene is absent from the respective mtDNA, light shading indicates gene overlaps where editing has been counted once only (rpl16, rps3 in Arabidopsis) or pseudogenes (sdh4 in Beta, rps11 and rps14 in Oryza), matR is the nad1i728g2 intron-borne maturase present in seed plants (n.i. = not investigated). The four top-scoring genes with more than 160 editing sites each in the respective mRNAs are indicated in bold.