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Table 1 Substitution rates in grasses. Chloroplast genes are divided into seven groups according to the function of their product. For groups of more than one gene the top row gives the mean substitution rate, and the second and third rows show the genes, within that group, with the maximum and minimum rates respectively. ENV: Envelope membrane. MAT: maturaseK. NADH: NADH genes. PS: Photosynthetic genes. RP: ribosomal genes. RNPol: RNA polymerase genes. B: Brachypodium. W: wheat. R: rice. M: maize.

From: The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes

GENE GROUP NO. OF GENES SYNONYMOUS SUBSTITUTIONS1 NONSYNONYMOUS SUBSTITUTIONS1 NNONSYNONYMOUS/SYNONYMOUS RATIO
   B W R M B W R M B W R M
RNPol 4 0.371 0.359 0.358 0.36 0.131 0.126 0.131 0.128 0.35 0.35 0.37 0.35
Max   rpoC1 0.452 rpoC1 0.423 rpoC1 0.428 rpoC1 0.42 rpoC2 0.172 rpoC2 0.162 rpoC2 0.166 rpoC2 0.159 rpoC2 0.6 rpoC2 0.57 rpoC2 0.61 rpoC2 0.54
Min   rpoC2 0.289 rpoC2 0.286 rpoC2 0.273 rpoC2 0.296 rpoB 0.088 rpoB 0.084 rpoB 0.087 rpoB 0.089 rpoC1 0.24 rpoB 0.24 rpoC1 0.25 rpoC1 0.25
ENV 1 0.46 0.454 0.422 0.44 0.2 0.193 0.2 0.188 0.44 0.43 0.47 0.43
MAT 1 0.448 0.47 0.466 0.45 0.225 0.209 0.212 0.213 0.5 0.44 0.46 0.47
NADH 11 0.362 0.354 0.358 0.36 0.092 0.092 0.091 0.09 0.25 0.26 0.25 0.25
Max   ndhH 0.463 ndhH 0.461 ndhH 0.445 ndHA 0.448 ndhF 0.188 ndhF 0.18 ndhF 0.181 ndhF 0.172 ndhF 0.55 ndhF 0.53 ndhF 0.51 ndhF 0.49
Min   ndhB 0.062 ndhB 0.076 ndhB 0.059 ndhB 0.065 ndhB 0.028 ndhB 0.04 ndhB 0.029 ndhB 0.025 ndhC 0.125 ndhH 0.14 ndhH 0.13 ndhH 0.15
PS 32 0.370 0.362 0.353 0.36 0.039 0.041 0.039 0.039 0.11 0.12 0.11 0.11
Max   psaC 0.554 psaC 0.571 psaC 0.519 psaC 0.485 atpE 0.158 atpE 0.158 atpE 0.15 atpE 0.147 atpE 0.42 atpF 0.42 atpF 0.47 atpF 0.53
Min   psbL 0.2 psbL 0.16 psbL 0.16 psbL 0.16 petG, psbI 0 petG, psbI 0 petG psbM psbT 0 petG, psbF psbI psbT 0 petD 1.24 × 10-2 petB 9.52 × 10-3 petD 1.7 × 10-2 petD 6.83 × 10-3
PR 1 0.442 0.412 0.426 0.427 0.161 0.161 0.168 0.161 0.36 0.39 0.39 0.38
RP 22 0.312 0.297 0.302 0.287 0.121 0.121 0.127 0.121 0.39 0.41 0.42 0.42
Max   rps8 0.489 rps8 0.469 rps8 0.48 rps8 0.47 rpl22 0.251 rpl22 0.248 rpl22 0.256 rpl22 0.256 rpl2 1.1 rpl2 0.98 rpl2 1.18 rpl2 1.18
Min   rps12 0.05 rps12 0.045 rps12 0.05 rps12 0.056 rps12 0.028 rps12 0.028 rps12 0.035 rps12 0.026 rps14 0.2 rpl16 0.21 rps14 0.2 rps14 0.18
  1. 1 Rates were calculated using the method of Nei and Gojobori [27] using tobacco as an outgroup to Brachypodium, wheat, rice, and maize.