Table 1.
Summary of editing sites detected in the mRNAs of the 25 protein encoding genes of the I. engelmannii chondrome
| Gene | Size [bp] | Codon changes by C > U editing |
C-to-U |
Codon changes by U > C editing |
U-to-C |
Total AA changes | Total sites | Creation of |
|||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A>V | H>Y | L>F | P>F | P>L | P>S | Q>* | R>* | R>C | R>W | S>F | S>L | T>I | T>M | Total | Silent | V>A | Y>H | F>L | F>P | L>P | S>P | *>Q | *>R | C>R | W>R | F>S | L>S | I>T | M>T | Total | silent | Start | Stop | ||||
| atp1 | 1545 | 5 | 9 | 1 | 3 | 18 | 12 | 0 | 0 | 5 | 0 | 5 | 20 | 8 | 4 | 104 | 10 | 3 | 0 | 0 | 0 | 0 | 1 | 12 | 3 | 5 | 0 | 0 | 1 | 2 | 0 | 27 | 0 | 117 | 131 | Yes | No |
| atp4 | 588 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 6 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 6 | No | No |
| atp6 | 762 | 3 | 4 | 1 | 7 | 12 | 5 | 0 | 1 | 3 | 1 | 9 | 15 | 3 | 3 | 83 | 9 | 1 | 1 | 0 | 0 | 1 | 0 | 3 | 2 | 2 | 0 | 0 | 1 | 1 | 0 | 12 | 0 | 79 | 95 | Yes | Yes |
| atp8 | 489 | 0 | 3 | 0 | 1 | 6 | 1 | 0 | 0 | 1 | 1 | 0 | 6 | 1 | 1 | 31 | 9 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 25 | 35 | Yes | No |
| atp9 | 225 | 1 | 0 | 1 | 2 | 4 | 1 | 1 | 0 | 0 | 0 | 4 | 4 | 2 | 2 | 30 | 6 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 26 | 34 | Yes | Yes |
| cob | 1170 | 4 | 11 | 6 | 4 | 17 | 1 | 0 | 0 | 1 | 6 | 8 | 13 | 2 | 1 | 99 | 20 | 3 | 3 | 0 | 0 | 4 | 3 | 4 | 1 | 1 | 0 | 0 | 2 | 1 | 0 | 22 | 0 | 96 | 121 | No | No |
| cox1 | 1632 | 0 | 5 | 5 | 2 | 16 | 4 | 0 | 0 | 2 | 6 | 11 | 11 | 2 | 3 | 88 | 18 | 4 | 4 | 1 | 0 | 0 | 2 | 2 | 1 | 2 | 0 | 2 | 1 | 1 | 0 | 22 | 1 | 87 | 110 | Yes | No |
| cox2 | 753 | 0 | 0 | 2 | 0 | 1 | 0 | 0 | 0 | 1 | 2 | 0 | 1 | 0 | 1 | 10 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 12 | 14 | Yes | No |
| cox3 | 792 | 3 | 3 | 1 | 8 | 17 | 6 | 1 | 0 | 1 | 9 | 10 | 5 | 2 | 6 | 98 | 18 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 75 | 101 | Yes | Yes |
| nad1 | 987 | 1 | 1 | 1 | 2 | 8 | 5 | 1 | 0 | 1 | 3 | 1 | 7 | 1 | 5 | 48 | 9 | 0 | 0 | 0 | 0 | 1 | 2 | 3 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 9 | 0 | 46 | 57 | Yes | No |
| nad2 | 1464 | 0 | 8 | 5 | 2 | 13 | 8 | 1 | 0 | 8 | 1 | 8 | 12 | 1 | 4 | 94 | 20 | 0 | 0 | 0 | 0 | 1 | 2 | 2 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 6 | 0 | 77 | 100 | No | Yes |
| nad3 | 357 | 0 | 2 | 0 | 1 | 6 | 3 | 1 | 0 | 2 | 1 | 12 | 8 | 3 | 0 | 53 | 13 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 4 | 0 | 42 | 57 | No | Yes |
| nad4 | 1488 | 2 | 8 | 1 | 9 | 23 | 6 | 1 | 0 | 5 | 5 | 13 | 17 | 3 | 6 | 140 | 30 | 0 | 2 | 1 | 0 | 2 | 3 | 2 | 2 | 0 | 0 | 1 | 2 | 0 | 0 | 16 | 0 | 114 | 156 | Yes | Yes |
| nad4L | 303 | 0 | 0 | 0 | 0 | 2 | 4 | 1 | 0 | 0 | 0 | 3 | 6 | 2 | 4 | 26 | 4 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 23 | 27 | Yes | Yes |
| nad5 | 1986 | 2 | 7 | 6 | 7 | 15 | 13 | 0 | 0 | 8 | 8 | 19 | 25 | 4 | 7 | 152 | 22 | 1 | 1 | 0 | 0 | 0 | 0 | 3 | 3 | 0 | 0 | 0 | 3 | 2 | 0 | 14 | 1 | 134 | 166 | No | No |
| nad6 | 627 | 2 | 1 | 1 | 4 | 11 | 2 | 0 | 0 | 1 | 3 | 1 | 8 | 2 | 5 | 58 | 12 | 0 | 1 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 6 | 1 | 46 | 64 | Yes | No |
| nad7 | 1191 | 5 | 7 | 0 | 2 | 16 | 3 | 1 | 0 | 5 | 2 | 8 | 13 | 5 | 8 | 95 | 18 | 0 | 4 | 1 | 0 | 2 | 0 | 5 | 5 | 1 | 0 | 0 | 0 | 1 | 0 | 20 | 0 | 94 | 115 | No | Yes |
| nad9 | 558 | 1 | 1 | 1 | 3 | 2 | 2 | 0 | 0 | 1 | 5 | 4 | 8 | 1 | 3 | 40 | 5 | 1 | 0 | 0 | 0 | 2 | 0 | 3 | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 10 | 0 | 42 | 50 | Yes | No |
| rpl5 | 549 | 2 | 0 | 0 | 0 | 3 | 1 | 0 | 0 | 1 | 0 | 1 | 3 | 1 | 1 | 23 | 10 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 7 | 2 | 18 | 30 | No | No |
| rps2 | 699 | 0 | 0 | 0 | 0 | 2 | 2 | 0 | 0 | 3 | 0 | 0 | 8 | 0 | 0 | 23 | 8 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 5 | 0 | 20 | 28 | No | No |
| rps3 | 1200 | 2 | 4 | 0 | 1 | 5 | 4 | 0 | 0 | 3 | 2 | 6 | 8 | 1 | 0 | 56 | 19 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 0 | 42 | 62 | No | No |
| rps4 | 765 | 2 | 4 | 0 | 0 | 12 | 7 | 0 | 0 | 1 | 1 | 5 | 5 | 3 | 0 | 48 | 8 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 2 | 0 | 0 | 0 | 0 | 1 | 0 | 7 | 1 | 46 | 55 | No | No |
| sdh3 | 297 | 0 | 2 | 1 | 0 | 4 | 4 | 1 | 0 | 1 | 0 | 1 | 2 | 1 | 0 | 21 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 2 | 0 | 19 | 23 | No | Yes |
| tatC | 756 | 0 | 4 | 3 | 2 | 11 | 8 | 0 | 0 | 4 | 3 | 8 | 3 | 4 | 0 | 62 | 10 | 0 | 0 | 0 | 0 | 1 | 1 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 6 | 0 | 56 | 68 | No | No |
| mat* | 2019 | 1 | 8 | 0 | 0 | 24 | 8 | 0 | 0 | 3 | 3 | 3 | 6 | 5 | 2 | 72 | 9 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 5 | 0 | 68 | 77 | Yes | No |
| Partial | 1 | 7 | 4 | 0 | 16 | 9 | 2 | 0 | 3 | 1 | 12 | 15 | 10 | 3 | 282 | 198 | 2 | 0 | 2 | 0 | 1 | 0 | 16 | 6 | 0 | 0 | 1 | 2 | 2 | 0 | 38 | 6 | |||||
| Full | 35 | 85 | 32 | 60 | 232 | 101 | 8 | 1 | 58 | 61 | 129 | 199 | 47 | 63 | 1278 | 99 | 16 | 17 | 2 | 0 | 16 | 16 | 45 | 22 | 15 | 1 | 7 | 14 | 9 | 0 | 184 | 0 | |||||
| Total | 36 | 92 | 36 | 60 | 248 | 110 | 10 | 1 | 61 | 62 | 141 | 214 | 57 | 66 | 1560 | 297 | 18 | 17 | 4 | 0 | 17 | 16 | 61 | 28 | 15 | 1 | 8 | 16 | 11 | 0 | 222 | 6 | 1406 | 1782 | 12 | 9 | |
Codon conversions resulting from C-to-U and U-to-C editing that were observed in the complete coding sequences are listed separately from the respective silent editing events. Additionally indicated are editing events causing the creation of start and stop codons, and the fraction of sites for which either full or partial editing was observed in the respective cDNA pools. The total editing counts contain number of amino acid changes, silent editing and multiple editings affecting single codons (S>L [3], L>S [9], L>P [1], P>F [60]). The atp9i87 maturase (mat) is translated in frame with the two upstream atp9 exons and the asterisk indicates that editing sites in these exons were not included here but only counted once for the line labelled atp9.