| | Category for genes | Group of gene | Name of gene |
| | Photosynthesis related genes | Rubisco | rbcL | | Photosystem I | psaA, psaB, psaC, psaI, psaJ | | Assembly/stability of photosystem I | ycf3, ycf4 | | Photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | | ATP synthase | atpA, atpB, atpE, atpF, atpH, atpI | | cytochrome b/f complex | petA, petB, petD, petG, petL, petN | | Cytochrome c synthesis | ccsA | | NADPH dehydrogenase | ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK |
| | Transcription and translation related genes | Transcription | rpoA, rpoB, rpoC1, rpoC2 | | Ribosomal proteins | rps2, rps3, rps4, rps7, rps8, rps11, rps12, rps14, rps15, rps16, rps18, rps19,rpl2, rpl14, rpl16, rpl20, rpl22, rpl23, rpl32, rpl33, rpl36 | | Translation initiation factor | infA |
| | RNA genes | Ribosomal RNA | rrn5, rrn4.5, rrn16, rrn23 | | Transfer RNA | trnAUGC, trnCGCA, trnDGUC, trnEUUC, trnFGAA, trnGGCC, trnGUCC, trnHGUG, trnICAU, trnIGAU,trnKUUU, trnLCAA, trnLUAA, trnLUAG, trnfMCAUI, trnMCAU, trnNGUU, trnPUGG, trnQUUG, trnRACG, trnRUCU, trnSGCU, trnSGGA, trnSUGA, trnTGGU, trnTUGU, trnVGAC, trnVUAC, trnWCCA, trnYGUA |
| | Other genes | RNA processing | matK | | Carbon metabolism | cemA | | Fatty acid synthesis | accD | | Proteolysis | clpP |
| | Genes of unknown function | Conserved reading frames | ycf1, ycf2 |
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