Table 2.
Genes and contents in the newly assembled Carya plastomes.
| Category | Group | Genes and number | ||
|---|---|---|---|---|
| LSC | SSC | IRa/ba | ||
| Photosynthesis | Subunits of photosystem I | psaA, psaB, psaI, psaJ (4) | psaC (1) | – |
| Subunits of photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ (15) | – | – | |
| Subunits of NADH dehydrogenase | ndhC, ndhJ, ndhK (3) | ndhA*, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI (7) | ndhB* (1X2) | |
| Subunits of cytochrome b/f complex | petA, petB, petD, petG, petL, petN (6) | – | – | |
| Subunits of ATP synthase | atpA, atpB, atpE, atpF*, atpH, atpI (6) | – | – | |
| Large subunit of Rubisco | rbcL (1) | – | – | |
| Self-replication | Large subunits of ribosome | rpl14, rpl16, rpl20, rpl22, rpl33, rpl36 (6) | rpl32 (1) | rps7, rps12 * d (2X2) |
| Small subunits of ribosome | rps2, rps3, rps4, rps8, rps11, rps14, rps16*, rps18, rps19 (9) | rps15 (1) | rpl2 * , rpl23 (2X2) | |
| DNA-dependent RNA polymerase | rpoA, rpoB, rpoC1*, rpoC2 (4) | – | – | |
| Ribosomal RNAs | – | – | rrn16S, rrn23S, rrn4.5S, rrn5S (4X2) | |
| Transfer RNAs | trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC, trnH-GUG, trnK-UUU, trnL-UAA*, trnM-CAU, trnP-UGG, trnQ-UUG, trnR-UCU, trnS-CGA*, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-UAC*, trnW-CCA, trnY-GUA (22) | trnL-UAG (1) | trnA-UGC*, trnI-CAU, trnI-GAU*, trnL-CAA, trnN-GUU b , trnR-ACG b , trnV-GAC (7X2) | |
| Other genes | Maturase | matK (1) | – | – |
| Protease | clpP* (1) | – | – | |
| Envelope membrane protein | cemA (1) | – | – | |
| Acetyl-CoA carboxylase | accD (1) | – | – | |
| C-type cytochrome synthesis gene | – | ccsA (1) | – | |
| Hypothetical reading frames | Proteins of unknown function | ycf3*, ycf4 (2) | ycf1 c (1) | ycf15, ycf2 (2X2) |
a, located in IR regions with two copies; b, trnR-ACG and trnN-GUU only located in SSC region in C. tonkinensis and C. poilanei with single copy; c, ycf1 gene located in SSC region for C. tonkinensis and C. poilanei, but the most part of its genic region located in SSC and small part in IRa region for other species; d, the most part of rps12 located in IR regions and only small part in LSC region; * indicated intron-containing gene.