Table 2.
Genes present in the ten sequenced chloroplast genomes in subfamily Zingiberoideae
| Category for genes | Group of genes | Name of genes |
|---|---|---|
| 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, ① psbZ, ② lhbA | |
| Subunits of cytochrome b/f complex | petA, petB*, petD*, petG, petL, petN | |
| Subunits of ATP synthase | atpA, atpB, atpE, atpF*, atpH, atpI | |
| Subunits of NADH dehydrogenase | ndhA*, ndhB (×2)*, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | |
| Subunit of rubisco | rbcL | |
| Self-replication | RNA polymerase | rpoA, rpoB, rpoC1*, rpoC2 |
| Large subunit of ribosomal proteins | rpl2 (×2)*, rpl14, rpl16*, rpl20, rpl22, rpl23 (× 2), rpl32, rpl33, rpl36 | |
| Small subunit of ribosomal proteins | rps2, rps3, rps4, rps7 (×2), rps8, rps11, rps12 (× 2)*, rps14, rps15, rps16*, rps18, rps19 (× 2) | |
| Ribosomal RNAs | rrn4.5 (×2), rrn5 (× 2), rrn16 (× 2), rrn23 (× 2) | |
| Transfer RNAs | trnA-UGC (×4)*, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC (×2)*, trnG-UCC, trnH-GUG (× 2), trnI-CAU (× 2), trnI-GAU (×4)*, trnK-UUU (× 2)*, trnL-CAA (× 2), trnL-UAA (× 2)*, trnL-UAG, trnM-CAU, trnN-GUU (× 2), trnP-UGG, trnQ-UUG, trnR-ACG (× 2), trnR-UCU, ③ trnS-GCU (× 2), ④ trnS-GGA, trnS-UGA, ④ trnT-GGU, ③ trnT-UGU (× 2), trnV-GAC (× 2), trnV-UAC (× 2)*, trnW-CCA, trnY-GUA | |
| Other genes | Subunit of acetyl-coA-carboxylase | accD* |
| c-type cytochrome synthesis gene | ccsA | |
| Envelop membrane protein | cemA | |
| Protease | clpP** | |
| Translational initiation factor | infA | |
| Maturase | matK | |
| Unknown function | Conserved open reading frames | ycf1 (×2), ycf2 (×2), ycf3**, ycf4 |
Note: (×2): gene with two copies; (×4): gene with four copies; *: gene containing one intron; **: gene containing two introns; ①: psbZ gene is only present in the chloroplast genomes of H. neocarneum and H. coccineum, respectively; ②: lhbA gene is missing in the chloroplast genomes of H. neocarneum and H. coccineum, respectively; ③: trnS-GCU and trnT-UGU exist two gene copies only in the chloroplast genome of G. schomburgkii, and only once in other 9 sequenced chloroplast genomes in this study; ④: trnS-GGA and trnT-GGU are missing in the chloroplast genome of G. schomburgkii