Table 1.
Proteins showing differences in amino acid sequence between C3 and C4 Flaveria species and the relative changes in their cognate transcripts.
| Ortholog in A. thaliana | Genes encoding proteins involved in | Mean FPKM (C4 )/mean FPKM (C3 ) | FDR (EdgeR) | Length in Fcro (Frob)α | Protein length in A. thaliana (aa) | aa changes | Stage of key change(s) in sequence | Stage of key change(s) in FPKMβ | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total aa change(s) | Before N 5 | At N5 | At N6 | At N7 | After N7 | ||||||||
| Gene in C4 pathway | |||||||||||||
| AT3G14940 | PEPC | 85.58 | 2.78E−06 | 966 | 968 | 41 | 1 | >=34 | N7 | N7 | |||
| AT4G15530 | PPDK | 123.6 | 9.10E−09 | 958 | 963 | 31 | 2 + 6-aa REP | >=15 | N7 | N7 | |||
| AT1G79750 | NADP-ME | 26.64 | 6.64E−08 | 647 | 646 | 27 | 1 | 8 | 18 | N7 | N3 and N6 | ||
| AT4G21210 | PPDK-RP | 7.57 | 1.63E−03 | 402 | 403 | 13 | 1 | 4 | 7 | N7 | N7 | ||
| AT3G04530 | PEPC-k | 88.78 | 2.93E−03 | 281 | 278 | 12 | 3 | 2 | 7 | N7 | N7 | ||
| AT1G72330 | AlaAT | 9.63 | 1.57E−04 | 544 | 553 | 9 | 2 | 7 | N7 | N3 an N6 | |||
| AT4G31990 | AspAT5 | 36.67 | 4.34E−06 | 459 | 453 | 3 | 1 | 1 | 1 | N7 | N3 and N7 | ||
| AT2G26900 | BASS2 | 39.12 | 5.30E−07 | 415 | 409 | 14 | 2 | 12 | N7 | N7 | |||
| AT3G19490 | NHD1 | 51.19 | 8.49E−07 | 576 | 576 | 15 | 2 | 13 | N7 | N7 | |||
| Gene related to electron transport chain | |||||||||||||
| AT4G22890 | PGR5-like | 7.1 | 4.70E−02 | 328 | 324 | 10+17-aa INS | 1 | 2+17-aa INS | 7 | N6 | N7 | ||
| AT1G14150 | NdhL2/PnsL2 | 3.71 | 2.13E−02 | 190 | 190 | 4 | 2 | 1 | 1 | before N5 | N7 | ||
| AT2G04039 | NdhV | 9.17 | 1.73E−02 | 227 | 199 | 8 | 1 | 6 | 1 | N6 | N3 | ||
| AT5G43750 | Ndh18/PnsB5 | 6.8 | 6.27E−02 | 224 | 212 | 3 | 2 | 1 | N6 | N8 | |||
| AT5G21430 | NdhU/CRRL | 8.55 | 3.11E−03 | 215 | 218 | 4 | 4 | N6 | N7 | ||||
| AT4G37925 | NdhM | 7.01 | 5.24E−02 | 209 | 217 | 3 | 1 | 2 | N7 | N8 | |||
| AT1G15980 | Ndh48/PnsB1 | 8.6 | 1.77E−02 | 465 | 461 | 7 | 1 | 4 | 2 | N6 | N7 | ||
| AT1G18730 | NdhB4/PnsB4 | 8.8 | 9.57E−03 | 182 | 174 | 5 | 1 | 2 | 2 | N6 and N7 | N7 | ||
| AT5G52100 | CRR1 | 4.05 | 6.78E−03 | 302 | 298 | 5 | 1 | 1 | 3 | after N7 | N3 | ||
| Gene in photorespiration pathway | |||||||||||||
| AT5G35630 | GSL1 | 0.08 | 2.15E−02 | 430 | 430 | 8 | 3 | 1 | 2 | 1 | N7 | N7 | |
| AT1G32470 | GDC-H | 0.23 | 7.29E−01 | 162 | 166 | 6+2-aa INS + 1-aa INS | 5 + 2-aa INS + 1-aa INS | 1 | N7 | N7 | |||
| AT4G37930 | SHM | 0.16 | 4.08E−01 | 517 | 517 | 8 | 3 | 5 | 1 | N7 | N7 | ||
| AT1G80380 | GLYK | 0.49 | 3.61E−01 | 443 | 456 | 8 | 2 | 6 | 1 | N7 | N7 | ||
| AT5G04140 | GOGAT | 0.57 | 1.32E−01 | 1616 | 1648 | 18 | 4 | >=1 | >=5 | 2 | N7 | N7 | |