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Table 2 Genes present in the ten sequenced chloroplast genomes in subfamily Zingiberoideae

From: Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)

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, psbZ, 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, trnS-GCU (× 2), trnS-GGA, trnS-UGA, trnT-GGU, 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
  1. Note: (×2): gene with two copies; (×4): gene with four copies; *: gene containing one intron; **: gene containing two introns; : psbZ gene is only present in the chloroplast genomes of H. neocarneum and H. coccineum, respectively; : lhbA gene is missing in the chloroplast genomes of H. neocarneum and H. coccineum, respectively; : 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; : trnS-GGA and trnT-GGU are missing in the chloroplast genome of G. schomburgkii