| | Category for genes | Group of genes | Name of genes |
| | Self-replication | Transfer RNAs | trnA-UGC, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAU, trnI-GAU, trnK-UUU, trnL-CAA, trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU, trnP-UGG, trnQ-UUG, trnR-ACG, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC, trnV-UAC, trnW-CCA, trnY-GUA | | Ribosomal RNAs | rrn4.5, rrna5, rrn16, rrn23 | | RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 | | Small subunit of ribosomal proteins (SSU) | rps2, rps3, rps4, rps7, rps8, rps11, rps12, rps14, rps15, rps16, rps18, rps19 (rps19, ψrps19) | | Large subunit of ribosomal proteins (LSU) | rpl2, rpl14, rpl16, rpl20, rpl22, rpl23, rpl32, rpl33, rpl36 |
| | Genes for photosynthesis | Subunits of NADH-dehydrogenase | ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | | 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 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 |
| | Other genes | Protease | clpP | | Maturase | matK | | Subunit of acetyl-CoA-carboxylase | accD | | Envelope membrane protein | cemA | | C-type cytochrome synthesis gene | ccsA |
| | Genes of unknown function | Hypothetical chloroplast reading frames | ycf1 (ycf1, ψycf1), ycf2, ycf3, ycf4, ψycf68 |
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