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Table 2 List of plastid genes and pseudogenes annotated for Equisetum arvense and Isoetes flaccid a.

From: Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

Gene class

    

Ribosomal RNAs

rrn4.5 x2

rrn5 x2

rrn16 x2

rrn23 x2

Transfer RNAs

trnA-UGC* x2

trnC-GCA

trnD-GUC

trnE-UUC

 

trnF-GAA

trnG-GCC

trnG-UCC*

trnH-GUG

 

trnI-CAU

trnI-GAU* x2

trnK-UUU*

trnL-CAA

 

trnL-UAA*

trnL-UAG

trnM-CAU

trnfM-CAU

 

trnN-GUU x2

trnP-GGG

trnP-UGG

trnQ-UUG

 

trnR-ACG x2

trnR-CCG c

trnR-UCU

trnS-CGA in Ea

 

trnS-GCU

trnS-GGA

trnS-UGA

trnT-GGU

 

trnT-UGU

trnV-GAC x2

trnV-UAC*

trnW-CCA

 

trnY-GUA

   

Photosystem I

psaA

psaBb

psaC

psaIb

 

psaJ

psaM

  

Photosystem II

psbA

psbB

psbC

psbD

 

psbE

psbF

psbHb

psbI

 

psbJ

psbK

psbLb

psbM

 

psbN

psbTb

psbZ

 

Cytochrome

petA

petB* b, e

petD* b, e

petGb

 

petL

petN b

  

ATP synthase

atpA

atpB

atpE

atpF*

 

atpH

atpIb

  

Rubisco

rbcLb

   

Chlorophyll biosynthesis

chlB

chlL b

chlN

 

NADH dehydrogenase

ndhA* b

ndhB*

ndhC

ndhD b, i

 

ndhE

ndhF i

ndhG

ndhH b

 

ndhI

ndhJ i, e

ndhK

 

Ribosomal proteins

rpl2*

rpl14b, i, e

rpl16*

rpl20b

 

rpl21 i

rpl22

rpl23

rpl32

 

rpl33

rpl36

rps2 ψ (If)

rps3

 

rps4b

rps7x2 in If

rps8b

rps11b, s

 

rps12 x2 tr

rps14

rps15

rps16 ψ in If

 

rps18

rps19

  

RNA polymerase

rpoA i

rpoBi

rpoC1* i

rpoC2 i

Miscellaneous proteins

infA ψ (If)

ccsA b

matK

clpP*

 

accD ψ (If), ss

cemA i

tufA ψ in If

 

Hypothetical proteins

ycf1 b

ycf2 i

ycf3*

ycf4b

 

ycf12

ycf66* ψ (Ea)

  

Duplicate gene fragments

ndhB ψ in If

ycf2 IR in If

ndhF IR in Ea

 
  1. * = intron-containing gene; tr = trans-spliced. In If = gene in I. flaccida but not E. arvense; in Ea = gene in E. arvense but not I. flaccida. Hypothesized RNA editing in I. flaccida: b = start edited; i = internal stop codon; e = stop codon edited; c = anticodon of tRNA edited. In E. arvense: s = start edited; ss = start and stop edited. ψ (If) = pseudogene in I. flaccida and gene present in E. arvense but not as pseudogene. ψ in If = pseudogene in I. flaccida but gene absent in E. arvense. ψ (Ea) = pseudogene in E. arvense and gene present in I. flaccida but not as pseudogene. Note that rps7 is in the IR in I. flaccida so has two copies (x2) but only one copy in E. arvense. Genes in bold were those used for phylogenetic analyses.