Table 2 The gene contents of 52 Gesneriaceae plastomes analyzed in this study.

From: Plastomes of limestone karst gesneriad genera Petrocodon and Primulina, and the comparative plastid phylogenomics of Gesneriaceae

Gene category

Gene name

Photosystem I

psaA, psaB, psaC, psaI, psaJ

Photosystem II

psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ

Cytochrome b/f complex

petA, petB*, petD*, petG, petL, petN

ATP synthase

atpA, atpB, atpE, atpF*, atpH, atpI

NADH dehydrogenase

ndhA*, ndhB(×2)*, ndhC, ndhD, ndhE, ndhF#, ndhG, ndhH, ndhI, ndhJ, ndhK

RubisCO large subunit

rbcL

RNA polymerase

rpoA, rpoB, rpoC1*, rpoC2

Ribosomal proteins (SSU)

rps2, rps3, rps4, rps7(×2), rps8, rps11, rps12(×1.67)*, rps142, rps15, rps16*, rps18, rps19#1

Ribosomal proteins (LSU)

rpl2(×2)*, rpl14, rpl16, rpl20, rpl22, rpl23(×2), rpl32, rpl33, rpl36

Protease, Maturase

clpP**, matK

Other genes

accD, ccs1, ccsA, infA, cemA

Hypothetical chloroplast reading frames (ycf)

ycf1#, ycf2(×2), ycf3**, ycf4, ycf15(×2)

Transfer RNAs (tRNA)

trnA-UGC(×2)*, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC, trnG-UCC, trnH-GUG, trnI-GAU(×2)*, trnK-UUU*, trnL-CAA(×2), trnL-UAA*, trnL-UAG, trnM-CAU (LSC)3, trnM-CAU(×2)(IR)3, trnfM-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

Ribosomal RNAs (rRNA)

rrn4.5(×2), rrn5(×2), rrn16(×2), rrn2(×2)

  1. (×2): gene duplicated in IRs. *Gene with one intron. **Gene with two introns. (×1.67): the trans-splicing gene, rps12, which possesses three exons with two of which duplicated in IRs, and thus the gene was marked as ×1.67 copies. #The partially duplicated genes locating on the IR/SC boundaries. 1Rps19 of some Paraboea species is not partially duplicated by IRs. 2Rps14 is loss in Oreocharis mileensis. 3The trnM-CAU gene in LSC is different in sequence from the trnM-CAU in IRs, and thus regarded as distinct genes.
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