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Table 2 Comparison of gene and intron content of cpDNAs from selected lycophytes and monilophytes (a)

From: Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes

  Gene/intron If Hl Oc Pn Eh Ea Ae As Ac Pa   Gene/intron If Hl Oc Pn Eh Ea Ae As Ac Pa
Transfer trnA-UGC + + + + + + + + + + ATP atpA + + + + + + + + + +
RNAs trnAUGCi38 + + + + + + + + + + synthase atpB + + + + + + + + + +
trnC-GCA + + + + + + + + + +   atpE + + + + + + + + + +
trnD-GUC + + + + + + + + + +   atpF + + + + + + + + + +
trnE-UUC + + + + + + + + + +   atpFi145 + + + + + + + + + +
trnF-GAA + + + + + + + + + +   atpH + + + + + + + + + +
trnfM-CAU + + + + + + + + + +   atpI + + + + + + + + + +
trnG-GCC + + + + + + + + + + Chlorophyll chlB + + + - + + + + + +
trnG-UCC + + + + + + + + + + biosynthesis chlL + + + - + + + + + +
trnGUCCi23 + + + + + + + + + +   chlN + + + - + + + + + +
trnH-GUG + + + + + + + + + + NADH ndhA + + + + + + + + + +
trnI-CAU + + + + + + + + + + dehydrogenase ndhAi556 + + + + + + + + + +
trnI-GAU + + + + + + + + + +   ndhB + + + + + + + + + +
trnIGAUi37 + + + + + + + + + +   ndhBi726 + + + + + + + + + +
trnK-UUU + + + + + + + - - -   ndhC + + + + + + + + + +
trnKUUUi37 + + + + + + + - - -   ndhD + + + + + + + + + +
trnL-CAA + + + + + + + Ψ Ψ Ψ   ndhE + + + + + + + + + +
trnL-UAA (b) + + + + + + + + + +   ndhF + + + + + + + + + +
trnLUAAi35 + + + + + + + + + +   ndhG + + + + + + + + + +
trnL-UAG + + + + + + + + + +   ndhH + + + + + + + + + +
trnM-CAU + + + + + + + + + +   ndhI + + + + + + + + + +
trnN-GUU + + + + + + + + + +   ndhJ + + + + + + + + + +
trnP-GGG + + + + + + + + + +   ndhK + + + + + + + + + +
trnP-UGG + + + + + + + + + + Ribosomal rpl2 + + + + + + + + + +
trnQ-UUG + + + + + + + + + + proteins rpl2i397 + + + + + + + + + +
trnR-ACG + + + + + + + + + +   rpl14 + + + + + + + + + +
trnR-CCG (c, d) + + + + + + + + + +   rpl16 + + + + + + + + + +
trnR-UCU + + + + + + + + + +   rpl16i9 + + + + - + + + + +
trnS-CGA - - + + + + + - - -   rpl20 + + + + + + + + + +
trnS-GCU + + + + + + + + + +   rpl21 + + + + + + + + + +
trnS-GGA + + + + + + + + + +   rpl22 + + + + + + + + + +
trnS-UGA + + + + + + + + + +   rpl23 + + + + + + + + + +
trnT-GGU + - + + + + + + + +   rpl32 + + + + + + + + + +
trnT-UGU + + - + + + + - - -   rpl33 + + + + + + + + + +
trnV-GAC + + + + + + + Ψ - -   rpl36 + + + + + + + + + +
trnV-UAC + + + + + + + + + +   rps2 Ψ + + + + + + + + +
trnVUACi37 + + + + + + + + + +   rps3 + + + + + + + + + +
trnW-CCA + + + + + + + + + +   rps4 + + + + + + + + + +
  trnY-GUA + + + + + + + + + +   rps7 + + + + + + + + + +
Ribosomal rrn4.5 + + + + + + + + + +   rps8 + + + + + + + + + +
RNAs rrn5 + + + + + + + + + +   rps11 + + + + + + + + + +
rrn16 + + + + + + + + + +   rps12 + + + + + + + + + +
  rrn23 + + + + + + + + + +   rps12i114 (e) t t t t t t t t t t
Photosystem I psaA + + + + + + + + + +   rps12i346 + + - - - - + + + +
psaB + + + + + + + + + +   rps14 + + + + + + + + + +
psaC + + + + + + + + + +   rps15 + + + + + + + + + +
psaI + + + + + + + + + +   rps16 Ψ + - - - - + + + +
psaJ + + + + + + + + + +   rps16i40 Ψ + - - - - + + + +
  psaM + + + + + + + + - -   rps18 + + + + + + + + + +
Photosystem II psbA + + + + + + + + + +   rps19 + + + + + + + + + +
psbB + + + + + + + + + + RNA rpoA + + + + + + + + + +
psbC + + + + + + + + + + polymerase rpoB + + + + + + + + + +
psbD + + + + + + + + + +   rpoC1 + + + + + + + + + +
psbE + + + + + + + + + +   rpoC1i432 + + + + + + + + + +
psbF + + + + + + + + + +   rpoC2 + + + + + + + + + +
psbH + + + + + + + + + + Miscellaneous infA Ψ + + + + + + + + +
psbI + + + + + + + + + + proteins ccsA + + + + + + + + + +
psbJ + + + + + + + + + +   matK + + + + + + + + + +
psbK + + + + + + + + + +   clpP + + + + + + + + + +
psbL + + + + + + + + + +   clpPi71 + + + + + + + + + +
psbM + + + + + + + + + +   cplPi363 + + + + - - + + + +
psbN + + + + + + + + + +   accD Ψ + + + + + + + + +
psbT + + + + + + + + + +   cemA + + + + + + + + + +
  psbZ + + + + + + + + + + Hypothetical ycf1 (f) + + + + + + Ψ + + +
Cytochrome petA + + + + + + + + + + proteins ycf2 + + + + + + + + + +
petB + + + + + + + + + +   ycf3 + + + + + + + + + +
petBi6 + + + + + + + + + +   ycf3i124 + + + + + + + + + +
petD + + + + + + + + + +   ycf3i354 + + + + + + + + + +
petDi8 + + + + + + + + + +   ycf4 + + + + + + + + + +
petG + + + + + + + + + +   ycf12 + + + + + + + + + +
petL + + + + + + + + + +   ycf66 + + - - Ψ Ψ + Ψ - -
  petN + + + + + + + + + +   ycf66i106 + + - - Ψ ? + Ψ - -
Rubisco rbcL + + + + + + + + + +             
  1. a) Species: Isoetes flaccida (If), Huperzia lucidula (Hl), Ophioglossum californicum (Oc), Psilotum nudum (Pn), Equisetum hyemale (Eh), Equisetum arvense (Ea), Angiopteris evecta (Ae), Alsophila spinulosa (As), Adiantum capillus-veneris (Ac) and Pteridium aquilinum (Pa).
  2. b) CAA anticodon of trnL-UAA in Adiantum capillus-veneris (Ac) is subjected to partial C-to-U RNA editing [35] and is potentially edited in Alsophila spinulosa (As).
  3. c) anticodon of trnR-CCG in Isoetes flaccida (If) is assumed to be subjected to U-to-C RNA editing [18].
  4. d) Mutations in anticodon of trnR-CCG created a UCG anticodon in Alsophila spinulosa (As) and Pteridium aquilinum (Pa) and a UCA anticodon in Adiantum capillus-veneris (Ac).
  5. e) rps12i114 intron is trans-spliced (t).
  6. f) ycf1 in Angiopteris evecta (Ae) may retain functionality as a split gene with two protein products [18].