Table 3.
Gene classification of the chloroplast genomes of four Quercus section Cyclobalanopsis species. Genes marked with the * or ** sign are the genes with single or double introns, respectively. The duplicated genes located in IR regions are marked as (×2).
| Category | Gene Group | Gene Name |
|---|---|---|
| Photosynthesis | Photosystem I | psaA, psaB, psaC, psaI, psaJ |
| Photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | |
| NADH dehydrogenase | ndhA*, ndhB*(×2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | |
| Cytochrome b/f complex | petA, petB*, petD*, petG, petL, petN | |
| ATP synthase | atpA, atpB, atpE, atpF*, atpH, atpI | |
| Rubisco of Large subunit | rbcL | |
| Transcription and translation | Translation initiation factor | infA |
| Ribosomal Proteins (LSU) |
rpl14, rpl16*, rpl2*(×2), rpl20, rpl22, rpl23(×2), rpl32, rpl33, rpl36 |
|
| Ribosomal Proteins (SSU) | rps11, rps12**(×2), rps14, rps15, rps16*, rps18, rps19, rps2, rps3, rps4, rps7(×2), rps8 | |
| 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, 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 | |
| Biosynthesis | Maturase | matK |
| ATP-dependendent Protease | clpP1** | |
| Acetyl-CoA carboxylase | accD | |
| Envelope membrane protein | cemA | |
| C-type cytochrome synthesis gene | ccsA | |
| Unknown | Conserved hypothetical chloroplast ORF | ycf1(×2), ycf2(×2), ycf3 **, ycf4 |