Table 2.
Gene content and functional classification of the 19 Ilex chloroplast genomes.
| Gene category | Gene function | Gene name |
|---|---|---|
| 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(× 2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | |
| Transcription- and translation-related genes | Transcription | rpoA, rpoB, *rpoC1, rpoC2, |
| Ribosomal protein | rps2, rps3, rps4, rps7(× 2), rps8, rps11, *rps12(× 2), rps14, rps15, *rps16, rps18, rps19, *rpl2(× 2), rpl14, *rpl16, rpl20, rpl22, rpl23(× 2), rpl32, rpl33, rpl36 | |
| Translation initiation factor | infA | |
| RNA genes | Ribosomal RNA | rrn4.5(× 2), rrn5(× 2), rrn16(× 2), rrn23(× 2) |
| Transfer RNA | *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, trnfM-CAU, trnN-GUU(× 2), trnP-UGG, *trnQ-UUG, trnR-ACG(× 2), trnR-UCU, trnS-GGA, trnS-GCU, trnS-UGA, trnT-UGU, trnT-GGU, trnV-GAC(× 2), *trnV-UAC, trnW-CCA, trnY-GUA | |
| Miscellaneous group | Maturase | matK |
| Inner membrane protein | cemA | |
| ATP-dependent protease | **clpP | |
| Acetyl-CoA carboxylase | accD | |
| Unknown functions | ycf1(× 2), ycf2(× 2), ycf15(× 2) |
Intron-containing genes are labelled with asterisks. The number of introns corresponds to the number of asterisks.