Table 2

List of plastid genes and pseudogenes annotated for Equisetum arvense and Isoetes flaccida.

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

psaB b

psaC

psaI b

psaJ

psaM

Photosystem II

psbA

psbB

psbC

psbD

psbE

psbF

psbH b

psbI

psbJ

psbK

psbL b

psbM

psbN

psbT b

psbZ

Cytochrome

petA

petB* b, e

petD* b, e

petG b

petL

petN b

ATP synthase

atpA

atpB

atpE

atpF*

atpH

atpI b

Rubisco

rbcL b

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*

rpl14 b, i, e

rpl16*

rpl20 b

rpl21 i

rpl22

rpl23

rpl32

rpl33

rpl36

rps2 ψ (If)

rps3

rps4 b

rps7 x2 in If

rps8 b

rps11 b, s

rps12 x2 tr

rps14

rps15

rps16 ψ in If

rps18

rps19

RNA polymerase

rpoA i

rpoB i

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*

ycf4 b

ycf12

ycf66* ψ (Ea)

Duplicate gene fragments

ndhB ψ in If

ycf2 IR in If

ndhF IR in Ea


* = 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.

Karol et al. BMC Evolutionary Biology 2010 10:321   doi:10.1186/1471-2148-10-321

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