-
1
-
-
79956309501
-
The Selaginella genome identifies genetic changes associated with the evolution of vascular plants
-
Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, Depamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, et al. 2011. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332: 960-963.
-
(2011)
Science
, vol.332
, pp. 960-963
-
-
Banks, J.A.1
Nishiyama, T.2
Hasebe, M.3
Bowman, J.L.4
Gribskov, M.5
Depamphilis, C.6
Albert, V.A.7
Aono, N.8
Aoyama, T.9
Ambrose, B.A.10
-
2
-
-
84866145891
-
A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins
-
Barkan A, Rojas M, Fujii S, Yap A, Chong YS, Bond CS, Small I. 2012. A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins. PLoS Genet 8: e1002910.
-
(2012)
PLoS Genet
, vol.8
-
-
Barkan, A.1
Rojas, M.2
Fujii, S.3
Yap, A.4
Chong, Y.S.5
Bond, C.S.6
Small, I.7
-
3
-
-
80054688192
-
RNA editing restores critical domains of a group i intron in fern mitochondria
-
Bégu D, Castandet B, Araya A. 2011. RNA editing restores critical domains of a group I intron in fern mitochondria. Curr Genet 57: 317-325.
-
(2011)
Curr Genet
, vol.57
, pp. 317-325
-
-
Bégu, D.1
Castandet, B.2
Araya, A.3
-
4
-
-
0028899208
-
RNA editing of a group II intron in Oenothera as a prerequisite for splicing
-
Börner GV, Mörl M, Wissinger B, Brennicke A, Schmelzer C. 1995. RNA editing of a group II intron in Oenothera as a prerequisite for splicing. Mol Gen Genet 246: 739-744.
-
(1995)
Mol Gen Genet
, vol.246
, pp. 739-744
-
-
Börner, G.V.1
Mörl, M.2
Wissinger, B.3
Brennicke, A.4
Schmelzer, C.5
-
5
-
-
0030736590
-
RNA editing status of nad7 intron domains in wheat mitochondria
-
Carrillo C, Bonen L. 1997. RNA editing status of nad7 intron domains in wheat mitochondria. Nucleic Acids Res 25: 403-409.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 403-409
-
-
Carrillo, C.1
Bonen, L.2
-
6
-
-
0035145548
-
Variation in sequence and RNA editing within core domains of mitochondrial group II introns among plants
-
Carrillo C, Chapdelaine Y, Bonen L. 2001. Variation in sequence and RNA editing within core domains of mitochondrial group II introns among plants. Mol Gen Genet 264: 595-603.
-
(2001)
Mol Gen Genet
, vol.264
, pp. 595-603
-
-
Carrillo, C.1
Chapdelaine, Y.2
Bonen, L.3
-
7
-
-
78651295848
-
Intron RNA editing is essential for splicing in plant mitochondria
-
Castandet B, Choury D, Bégu D, Jordana X, Araya A. 2010. Intron RNA editing is essential for splicing in plant mitochondria. Nucleic Acids Res 38: 7112-7121.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 7112-7121
-
-
Castandet, B.1
Choury, D.2
Bégu, D.3
Jordana, X.4
Araya, A.5
-
9
-
-
3042698703
-
Distribution of introns in the mitochondrial gene nad1 in land plants: Phylogenetic and molecular evolutionary implications
-
Dombrovska E, Qiu YL. 2004. Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications. Mol Phylogenet Evol 32: 246-263.
-
(2004)
Mol Phylogenet Evol
, vol.32
, pp. 246-263
-
-
Dombrovska, E.1
Qiu, Y.L.2
-
10
-
-
84871445428
-
RNA editing in mitochondrial trans-introns is required for splicing
-
Farré JC, Aknin C, Araya A, Castandet B. 2012. RNA editing in mitochondrial trans-introns is required for splicing. PLoS One 7: e52644.
-
(2012)
PLoS One
, vol.7
-
-
Farré, J.C.1
Aknin, C.2
Araya, A.3
Castandet, B.4
-
11
-
-
84876220942
-
Land plant RNA editing or: Don't be fooled by plant organellar DNA sequences
-
(ed. Bock R, Knoop V), Springer Netherlands
-
Finster S, Legen J, Qu Y, Schmitz-Linneweber C. 2012. Land plant RNA editing or: Don't be fooled by plant organellar DNA sequences. In Genomics of Chloroplasts and Mitochrondria (ed. Bock R, Knoop V), pp. 293-321. Springer Netherlands.
-
(2012)
Genomics of Chloroplasts and Mitochrondria
, pp. 293-321
-
-
Finster, S.1
Legen, J.2
Qu, Y.3
Schmitz-Linneweber, C.4
-
12
-
-
0028348197
-
Intron loss from the NADH dehydrogenase subunit 4 gene of lettuce mitochondrial DNA: Evidence for homologous recombination of a cDNA intermediate
-
Geiss KT, Abbas GM, Makaroff CA. 1994. Intron loss from the NADH dehydrogenase subunit 4 gene of lettuce mitochondrial DNA: evidence for homologous recombination of a cDNA intermediate. Mol Gen Genet 243: 97-105.
-
(1994)
Mol Gen Genet
, vol.243
, pp. 97-105
-
-
Geiss, K.T.1
Abbas, G.M.2
Makaroff, C.A.3
-
13
-
-
79954584259
-
A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii
-
Grewe F, Herres S, Viehöver P, Polsakiewicz M, Weisshaar B, Knoop V. 2011. A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii. Nucleic Acids Res 39: 2890-2902.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 2890-2902
-
-
Grewe, F.1
Herres, S.2
Viehöver, P.3
Polsakiewicz, M.4
Weisshaar, B.5
Knoop, V.6
-
14
-
-
79960100341
-
ExtremeRNAediting in coding islands and abundant microsatellites in repeat sequences of Selaginella moellendorffii mitochondria: The root of frequent plant mtDNA recombination in early tracheophytes
-
Hecht J, Grewe F, KnoopV. 2011. ExtremeRNAediting in coding islands and abundant microsatellites in repeat sequences of Selaginella moellendorffii mitochondria: the root of frequent plant mtDNA recombination in early tracheophytes. Genome Biol Evol 3: 344-358.
-
(2011)
Genome Biol Evol
, vol.3
, pp. 344-358
-
-
Hecht, J.1
Grewe, F.2
Knoop, V.3
-
15
-
-
84866954298
-
Loss of two introns from the Magnolia tripetala mitochondrial cox2 gene implicates horizontal gene transfer and gene conversion as a novel mechanism of intron loss
-
Hepburn NJ, Schmidt DW, Mower JP. 2012. Loss of two introns from the Magnolia tripetala mitochondrial cox2 gene implicates horizontal gene transfer and gene conversion as a novel mechanism of intron loss. Mol Biol Evol 29: 3111-3120.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 3111-3120
-
-
Hepburn, N.J.1
Schmidt, D.W.2
Mower, J.P.3
-
16
-
-
84887919741
-
Two DYW subclass PPR proteins are involved in RNA editing of ccmFc and atp9 transcripts in the moss Physcomitrella patens: First complete set of PPR editing factors in plant mitochondria
-
Ichinose M, Sugita C, Yagi Y, Nakamura T, Sugita M. 2013. Two DYW subclass PPR proteins are involved in RNA editing of ccmFc and atp9 transcripts in the moss Physcomitrella patens: first complete set of PPR editing factors in plant mitochondria. Plant Cell Physiol 54: 1907-1916.
-
(2013)
Plant Cell Physiol
, vol.54
, pp. 1907-1916
-
-
Ichinose, M.1
Sugita, C.2
Yagi, Y.3
Nakamura, T.4
Sugita, M.5
-
17
-
-
0036942767
-
The sugar beet mitochondrial nad4 gene: An intron loss and its phylogenetic implication in the Caryophyllales
-
Itchoda N, Nishizawa S, Nagano H, Kubo T, Mikami T. 2002. The sugar beet mitochondrial nad4 gene: an intron loss and its phylogenetic implication in the Caryophyllales. Theor Appl Genet 104: 209-213.
-
(2002)
Theor Appl Genet
, vol.104
, pp. 209-213
-
-
Itchoda, N.1
Nishizawa, S.2
Nagano, H.3
Kubo, T.4
Mikami, T.5
-
18
-
-
83755172749
-
Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems
-
Iyer LM, Zhang D, Rogozin IB, Aravind L. 2011. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Nucleic Acids Res 39: 9473-9497.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 9473-9497
-
-
Iyer, L.M.1
Zhang, D.2
Rogozin, I.B.3
Aravind, L.4
-
19
-
-
84856048359
-
Is RNA editing implicated in group II intron survival in the angiosperm mitochondrial genome?
-
Kagami H, Nagano H, Takahashi Y, Mikami T, Kubo T. 2012. Is RNA editing implicated in group II intron survival in the angiosperm mitochondrial genome? Genome 55: 75-79.
-
(2012)
Genome
, vol.55
, pp. 75-79
-
-
Kagami, H.1
Nagano, H.2
Takahashi, Y.3
Mikami, T.4
Kubo, T.5
-
20
-
-
77958040395
-
Complete plastome sequences of Equisetum arvense and Isoetes flaccida: Implications for phylogeny and plastid genome evolution of early land plant lineages
-
Karol KG, Arumuganathan K, Boore JL, Duffy AM, Everett KD, Hall JD, Hansen SK, Kuehl JV, Mandoli DF, Mishler BD, et al. 2010. Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages. BMC Evol Biol 10: 321.
-
(2010)
BMC Evol Biol
, vol.10
, pp. 321
-
-
Karol, K.G.1
Arumuganathan, K.2
Boore, J.L.3
Duffy, A.M.4
Everett, K.D.5
Hall, J.D.6
Hansen, S.K.7
Kuehl, J.V.8
Mandoli, D.F.9
Mishler, B.D.10
-
21
-
-
4744343662
-
The mitochondrial DNA of land plants: Peculiarities in phylogenetic perspective
-
Knoop V. 2004. The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Curr Genet 46: 123-139.
-
(2004)
Curr Genet
, vol.46
, pp. 123-139
-
-
Knoop, V.1
-
22
-
-
79951578730
-
When you can't trust the DNA: RNA editing changes transcript sequences
-
Knoop V. 2011. When you can't trust the DNA: RNA editing changes transcript sequences. Cell Mol Life Sci 68: 567-586.
-
(2011)
Cell Mol Life Sci
, vol.68
, pp. 567-586
-
-
Knoop, V.1
-
23
-
-
12744253474
-
Apentatricopeptide repeat protein is essential for RNA editing in chloroplasts
-
Kotera E, Tasaka M, Shikanai T. 2005. Apentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature 433: 326-330.
-
(2005)
Nature
, vol.433
, pp. 326-330
-
-
Kotera, E.1
Tasaka, M.2
Shikanai, T.3
-
24
-
-
84872537549
-
PREPACT 2.0: Predicting C-to-U and U-to-C RNA editing in organelle genome sequences with multiple references and curated RNA editing annotation
-
Lenz H, Knoop V. 2013. PREPACT 2.0: predicting C-to-U and U-to-C RNA editing in organelle genome sequences with multiple references and curated RNA editing annotation. Bioinform Biol Insights 7: 1-19.
-
(2013)
Bioinform Biol Insights
, vol.7
, pp. 1-19
-
-
Lenz, H.1
Knoop, V.2
-
25
-
-
77950867407
-
Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature
-
Lenz H, Rüdinger M, Volkmar U, Fischer S, Herres S, Grewe F, Knoop V. 2010. Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature. Curr Genet 56: 189-201.
-
(2010)
Curr Genet
, vol.56
, pp. 189-201
-
-
Lenz, H.1
Rüdinger, M.2
Volkmar, U.3
Fischer, S.4
Herres, S.5
Grewe, F.6
Knoop, V.7
-
26
-
-
0028329182
-
Differential RNA editing in closely related introns in Oenothera mitochondria
-
Lippok B, Brennicke A, Wissinger B. 1994. Differential RNA editing in closely related introns in Oenothera mitochondria. Mol Gen Genet 243: 39-46.
-
(1994)
Mol Gen Genet
, vol.243
, pp. 39-46
-
-
Lippok, B.1
Brennicke, A.2
Wissinger, B.3
-
28
-
-
36048989002
-
Organellar Genome DRAW (OGDRAW): A tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes
-
Lohse M, Drechsel O, Bock R. 2007. Organellar Genome DRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52: 267-274.
-
(2007)
Curr Genet
, vol.52
, pp. 267-274
-
-
Lohse, M.1
Drechsel, O.2
Bock, R.3
-
29
-
-
33845672553
-
RNA editing has been lost in the mitochondrial cox3 and rps13 mRNAs in Asparagales
-
Lopez L, Picardi E, Quagliariello C. 2007. RNA editing has been lost in the mitochondrial cox3 and rps13 mRNAs in Asparagales. Biochim 89: 159-167.
-
(2007)
Biochim
, vol.89
, pp. 159-167
-
-
Lopez, L.1
Picardi, E.2
Quagliariello, C.3
-
30
-
-
0030854739
-
TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
31
-
-
70649103857
-
Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms
-
Ran JH, Gao H, Wang XQ. 2010. Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms. Mol Phylogenet Evol 54: 136-149.
-
(2010)
Mol Phylogenet Evol
, vol.54
, pp. 136-149
-
-
Ran, J.H.1
Gao, H.2
Wang, X.Q.3
-
32
-
-
45849098234
-
Organellar RNA editing and plant-specific extensions of pentatricopeptide repeat (PPR) proteins in jungermanniid but not in marchantiid liverworts
-
Rüdinger M, Polsakiewicz M, Knoop V. 2008. Organellar RNA editing and plant-specific extensions of pentatricopeptide repeat (PPR) proteins in jungermanniid but not in marchantiid liverworts. Mol Biol Evol 25: 1405-1414.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1405-1414
-
-
Rüdinger, M.1
Polsakiewicz, M.2
Knoop, V.3
-
33
-
-
84862674523
-
Nuclear DYW-type PPR gene families diversify with increasing RNA editing frequencies in liverwort and moss mitochondria
-
Rüdinger M, Volkmar U, Lenz H, Groth-Malonek M, Knoop V. 2012. Nuclear DYW-type PPR gene families diversify with increasing RNA editing frequencies in liverwort and moss mitochondria. J Mol Evol 74: 37-51.
-
(2012)
J Mol Evol
, vol.74
, pp. 37-51
-
-
Rüdinger, M.1
Volkmar, U.2
Lenz, H.3
Groth-Malonek, M.4
Knoop, V.5
-
34
-
-
34548133226
-
A hypothesis on the identification of the editing enzyme in plant organelles
-
Salone V, Rüdinger M, Polsakiewicz M, Hoffmann B, Groth-Malonek M, Szurek B, Small I, Knoop V, Lurin C. 2007. A hypothesis on the identification of the editing enzyme in plant organelles. FEBS Lett 581: 4132-4138.
-
(2007)
FEBS Lett
, vol.581
, pp. 4132-4138
-
-
Salone, V.1
Rüdinger, M.2
Polsakiewicz, M.3
Hoffmann, B.4
Groth-Malonek, M.5
Szurek, B.6
Small, I.7
Knoop, V.8
Lurin, C.9
-
35
-
-
84885661266
-
A DYW-protein knockout in Physcomitrella affects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype
-
Schallenberg-Rüdinger M, Kindgren P, Zehrmann A, Small I, Knoop V. 2013. A DYW-protein knockout in Physcomitrella affects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype. Plant J 76: 420-432.
-
(2013)
Plant J
, vol.76
, pp. 420-432
-
-
Schallenberg-Rüdinger, M.1
Kindgren, P.2
Zehrmann, A.3
Small, I.4
Knoop, V.5
-
36
-
-
23144460836
-
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
-
Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33: W686-W689.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. W686-W689
-
-
Schattner, P.1
Brooks, A.N.2
Lowe, T.M.3
-
37
-
-
70849112619
-
Unparalleled GC content in the plastid DNA of Selaginella
-
Smith DR. 2009. Unparalleled GC content in the plastid DNA of Selaginella. Plant Mol Biol 71: 627-639.
-
(2009)
Plant Mol Biol
, vol.71
, pp. 627-639
-
-
Smith, D.R.1
-
38
-
-
84885110105
-
Architecture of thePPRgene family in the moss Physcomitrella patens
-
SugitaM,Ichinose M,IdeM,Sugita C. 2013. Architecture of thePPRgene family in the moss Physcomitrella patens. RNA Biol 10: 1256-1262.
-
(2013)
RNA Biol
, vol.10
, pp. 1256-1262
-
-
Sugita, M.1
Ichinose, M.2
Ide, M.3
Sugita, C.4
-
39
-
-
84878784240
-
Improved computational target site prediction for pentatricopeptide repeat RNA editing factors
-
Takenaka M, Zehrmann A, Brennicke A, Graichen K. 2013. Improved computational target site prediction for pentatricopeptide repeat RNA editing factors. PLoS One 8: e65343.
-
(2013)
PLoS One
, vol.8
-
-
Takenaka, M.1
Zehrmann, A.2
Brennicke, A.3
Graichen, K.4
-
40
-
-
79957613599
-
MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
-
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2731-2739
-
-
Tamura, K.1
Peterson, D.2
Peterson, N.3
Stecher, G.4
Nei, M.5
Kumar, S.6
-
41
-
-
33947218312
-
The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses
-
Tsuji S, Ueda K, Nishiyama T, Hasebe M, Yoshikawa S, Konagaya A, Nishiuchi T, Yamaguchi K. 2007. The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses. J Plant Res 120: 281-290.
-
(2007)
J Plant Res
, vol.120
, pp. 281-290
-
-
Tsuji, S.1
Ueda, K.2
Nishiyama, T.3
Hasebe, M.4
Yoshikawa, S.5
Konagaya, A.6
Nishiuchi, T.7
Yamaguchi, K.8
-
42
-
-
21144458976
-
The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae)
-
Wolf PG, Karol KG, Mandoli DF, Kuehl J, Arumuganathan K, EllisMW, Mishler BD, Kelch DG, Olmstead RG, Boore JL. 2005. The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae). Gene 350: 117-128.
-
(2005)
Gene
, vol.350
, pp. 117-128
-
-
Wolf, P.G.1
Karol, K.G.2
Mandoli, D.F.3
Kuehl, J.4
Arumuganathan, K.5
Ellismw Mishler, B.D.6
Kelch, D.G.7
Olmstead, R.G.8
Boore, J.L.9
-
43
-
-
84874588115
-
Elucidation of the RNA recognition code for pentatricopeptide repeat proteins involved in organelle RNA editing in plants
-
Yagi Y, Hayashi S, Kobayashi K, Hirayama T, Nakamura T. 2013. Elucidation of the RNA recognition code for pentatricopeptide repeat proteins involved in organelle RNA editing in plants. PLoS One 8: e57286.
-
(2013)
PLoS One
, vol.8
-
-
Yagi, Y.1
Hayashi, S.2
Kobayashi, K.3
Hirayama, T.4
Nakamura, T.5
-
44
-
-
64749105292
-
A DYW domain-containing pentatricopeptide repeat protein is required for RNA editing at multiple sites in mitochondria of Arabidopsis thaliana
-
Zehrmann A, Verbitskiy D, van der Merwe JA, Brennicke A, Takenaka M. 2009. A DYW domain-containing pentatricopeptide repeat protein is required for RNA editing at multiple sites in mitochondria of Arabidopsis thaliana. Plant Cell 21: 558-567.
-
(2009)
Plant Cell
, vol.21
, pp. 558-567
-
-
Zehrmann, A.1
Verbitskiy, D.2
Van Der Merwe, J.A.3
Brennicke, A.4
Takenaka, M.5
|