| Category | Gene group | Gene name |
| Photosynthesis | Subunits of photosystem I | psaA, psaB, psaC, psaI, psaJ |
| Subunits of photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | |
| Subunits of NADH dehydrogenase | ndhA*, ndhB* (2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | |
| Subunits of cytochrome b/f complex | petA, petB*, petD*, petG, petL, petN | |
| Subunits of ATP synthase | atpA, atpB, atpE, atpF*, atpH, atpI | |
| Large subunit of rubisco | rbcL | |
| Self-replication | Proteins of large ribosomal subunit | rpl14, rpl16*, rpl2* (2), rpl20, rpl22, rpl23 (2), rpl32, rpl33, rpl36 |
| Proteins of small ribosomal subunit | rps11, rps12** (2), rps14, rps15 (2), rps16*, rps18, rps19 (2), rps2, rps3, rps4, rps7 (2), rps8 | |
| Subunits of RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 | |
| Ribosomal RNAs | rrn16 (2), rrn23 (2), rrn4.5 (2), rrn5 (2) | |
| Transfer RNAs | trnA-UGC* (2), trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC, trnG-UCC*, trnH-GUG (2), trnI-CAU (2), trnI-GAU* (2), trnK-UUU*, trnL-CAA (2), trnL-UAA*, trnL-UAG, trnM-CAU, trnN-GUU (2), trnP-UGG, trnQ-UUG, trnR-ACG (2), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC (2), trnV-UAC*, trnW-CCA, trnY-GUA, trnfM-CAU | |
| Other genes | Maturase | matK |
| Protease | clpP | |
| Envelope membrane protein | cemA | |
| c-type cytochrome synthesis gene | ccsA | |
| Translation initiation factor | infA |