Table 2 |
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List of plastid genes and pseudogenes annotated for Equisetum arvense and Isoetes flaccida. |
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Gene class |
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|
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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 |
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|
Photosystem I |
psaA |
psaB b |
psaC |
psaI b |
|
psaJ |
psaM |
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|
Photosystem II |
psbA |
psbB |
psbC |
psbD |
|
psbE |
psbF |
psbH b |
psbI |
|
|
psbJ |
psbK |
psbL b |
psbM |
|
|
psbN |
psbT b |
psbZ |
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|
Cytochrome |
petA |
petB* b, e |
petD* b, e |
petG b |
|
petL |
petN b |
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|
ATP synthase |
atpA |
atpB |
atpE |
atpF* |
|
atpH |
atpI b |
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|
Rubisco |
rbcL b |
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|
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 |
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|
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 |
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|
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 |
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|
Hypothetical proteins |
ycf1 b |
ycf2 i |
ycf3* |
ycf4 b |
|
ycf12 |
ycf66* ψ (Ea) |
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|
Duplicate gene fragments |
ndhB ψ in If |
ycf2 IR in If |
ndhF IR in Ea |
|
|
|
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|
* = 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. |
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|
Karol et al. BMC Evolutionary Biology 2010 10:321 doi:10.1186/1471-2148-10-321 |
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