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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].