-
1
-
-
0030915387
-
Expansion of the IR in the chloroplast genomes of buckwheat species is due to incorporation of an SSC sequence that could be mediated by an inversion
-
DOI 10.1007/s002940050206
-
Aii J, Kishima Y, Mikami T, Adachi T (1997) Expansion of the IR in the chloroplast genomes of buckwheat species is due to incorporation of an SSC sequence that could be mediated by an inversion. Curr Genet 31:276-279 (Pubitemid 27156502)
-
(1997)
Current Genetics
, vol.31
, Issue.3
, pp. 276-279
-
-
Aii, J.1
Kishima, Y.2
Mikami, T.3
Adachi, T.4
-
2
-
-
0037393246
-
An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II
-
APG II (2003) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot J Linn Soc 141:399-436
-
(2003)
Bot J Linn Soc
, vol.141
, pp. 399-436
-
-
Apg, I.I.1
-
3
-
-
11144263232
-
Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: A comparative analysis of four monocot chloroplast genomes
-
Asano T, Tsudzuki T, Takahashi S, Shimada H, Kadowaki K (2004) Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes. DNA Res 11:93-99
-
(2004)
DNA Res
, vol.11
, pp. 93-99
-
-
Asano, T.1
Tsudzuki, T.2
Takahashi, S.3
Shimada, H.4
Kadowaki, K.5
-
4
-
-
0029176713
-
Polyphyly of Arundinoideae (Poaceae): Evidence from rbcL sequence data
-
Barker NP, Linder HP, Harley EH (1995) Polyphyly of Arundinoideae (Poaceae): evidence from rbcL sequence data. Syst Bot 20:423-435
-
(1995)
Syst Bot
, vol.20
, pp. 423-435
-
-
Barker, N.P.1
Linder, H.P.2
Harley, E.H.3
-
5
-
-
0029895752
-
Rate of rbcL gene sequence evolution and species diversification in flowering plants (angiosperms)
-
Barraclough TG, Harvey PH, Nee S (1996) Rate of rbcL gene sequence evolution and species diversification in flowering plants (angiosperms). Proc R Soc Lond B Biol Sci 263:589-591
-
(1996)
Proc R Soc Lond B Biol Sci
, vol.263
, pp. 589-591
-
-
Barraclough, T.G.1
Harvey, P.H.2
Nee, S.3
-
6
-
-
19544374490
-
Genome rearrangement distances and gene order phylogeny in γ-proteobacteria
-
DOI 10.1093/molbev/msi134
-
Belda E, Moya A, Silva FJ (2005) Genome rearrangement distances and gene order phylogeny in gamma-Proteobacteria. Mol Biol Evol 22:1456-1467 (Pubitemid 40734196)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.6
, pp. 1456-1467
-
-
Belda, E.1
Maya, A.2
Silva, F.J.3
-
7
-
-
0001677717
-
Controlling the false discovery rate-a practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate-a practical and powerful approach to multiple testing. J R Stat Soc B Methodol 57:289-300
-
(1995)
J R Stat Soc B Methodol
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
8
-
-
77649179494
-
Structure, function, and inheritance of plastid genomes
-
Bock R (ed) Springer, Berlin/Heidelberg, pp
-
Bock R (2007) Structure, function, and inheritance of plastid genomes. In: Bock R (ed) Cell and molecular biology of plastids. Springer, Berlin/Heidelberg, pp 1610-2096
-
(2007)
Cell and Molecular Biology of Plastids
, pp. 1610-2096
-
-
Bock, R.1
-
9
-
-
58449092050
-
The complete chloroplast genome sequence of Brachypodium distachyon: Sequence comparison and phylogenetic analysis of eight grass plastomes
-
Bortiri E, Coleman-Derr D, Lazo GR, Anderson OD, Gu YQ (2008) The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes. BMC Res Notes 1:61
-
(2008)
BMC Res Notes 1
, vol.61
-
-
Bortiri, E.1
Coleman-Derr, D.2
Lazo, G.R.3
Anderson, O.D.4
Gu, Y.Q.5
-
11
-
-
0345408762
-
The location and possible evolutionary significance of small dispersed repeats in wheat ctDNA
-
Bowman CM, Dyer T (1986) The location and possible evolutionary significance of small dispersed repeats in wheat ctDNA. Curr Genet 10:931-941
-
(1986)
Curr Genet
, vol.10
, pp. 931-941
-
-
Bowman, C.M.1
Dyer, T.2
-
12
-
-
0031437324
-
The chloroplast-located homolog of bacterial DNA recombinase
-
CaoJ,CombsC,JagendorfAT(1997)Thechloroplast- locatedhomologofbacterialDNArecombinase.PlantCellPhysiol38:1319- 1325(Pubitemid28034912)
-
(1997)
Plant and Cell Physiology
, vol.38
, Issue.12
, pp. 1319-1325
-
-
Cao, J.1
Combs, C.2
Jagendorf, A.T.3
-
13
-
-
48149087802
-
Maize and sorghum: Genetic resources for bioenergy grasses
-
Carpita NC, McCann MC (2008) Maize and sorghum: Genetic resources for bioenergy grasses. Trends Plant Sci 13:415-420
-
(2008)
Trends Plant Sci
, vol.13
, pp. 415-420
-
-
Carpita, N.C.1
McCann, M.C.2
-
15
-
-
30744447444
-
The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): Comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications
-
Chang CC, Lin HC, Lin IP, Chow TY, Chen HH, Chen WH, Cheng CH, Lin CY, Liu SM, Chaw SM (2006) The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Mol Biol Evol 23:279-291
-
(2006)
Mol Biol Evol
, vol.23
, pp. 279-291
-
-
Chang, C.C.1
Lin, H.C.2
Lin, I.P.3
Chow, T.Y.4
Chen, H.H.5
Chen, W.H.6
Cheng, C.H.7
Lin, C.Y.8
Liu, S.M.9
Chaw, S.M.10
-
16
-
-
10644220870
-
Monocot relationships: An overview
-
Chase MW (2004) Monocot relationships: an overview. Am J Bot 91:1645-1655
-
(2004)
Am J Bot
, vol.91
, pp. 1645-1655
-
-
Chase, M.W.1
-
17
-
-
33749336062
-
The complete chloroplast genome sequence of Pelargonium X hortorum: Organization and evolution of the largest and most highly rearranged chloroplast genome of land plants
-
Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, Boore JL, Jansen RK (2006) The complete chloroplast genome sequence of Pelargonium X hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Mol Biol Evol 23:2175-2190
-
(2006)
Mol Biol Evol
, vol.23
, pp. 2175-2190
-
-
Chumley, T.W.1
Palmer, J.D.2
Mower, J.P.3
Fourcade, H.M.4
Calie, P.J.5
Boore, J.L.6
Jansen, R.K.7
-
18
-
-
0029188719
-
A phylogeny of the grass family (Poaceae) based on ndhF sequence data
-
Clark LG, Zhang W, Wendel JF (1995) A phylogeny of the grass family (Poaceae) based on ndhF sequence data. Syst Bot 20:436-460
-
(1995)
Syst Bot
, vol.20
, pp. 436-460
-
-
Clark, L.G.1
Zhang, W.2
Wendel, J.F.3
-
19
-
-
0030918808
-
The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): Multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families
-
Cosner ME, Jansen RK, Palmer JD, Downie SR (1997) The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families. Curr Genet 31:419-429
-
(1997)
Curr Genet
, vol.31
, pp. 419-429
-
-
Cosner, M.E.1
Jansen, R.K.2
Palmer, J.D.3
Downie, S.R.4
-
20
-
-
0030451873
-
Multiple independent losses of the rpoCl intron in angiosperm chloroplast
-
Downie SR, Lianas E, Katz-Downie DS (1996) Multiple independent losses of the rpoCl intron in angiosperm chloroplast DNA's. Syst Bot 21:135-151
-
(1996)
DNA's. Syst Bot
, vol.21
, pp. 135-151
-
-
Downie, S.R.1
Lianas, E.2
Katz-Downie, D.S.3
-
21
-
-
0026781151
-
Chloroplast DNA inversions and the origin of the grass family (Poaceae)
-
Doyle JJ, Davis JI, Soreng RJ, Garvin D, Anderson MJ (1992) Chloroplast DNA inversions and the origin of the grass family (Poaceae). Proc Natl Acad Sci USA 89:7722-7726
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 7722-7726
-
-
Doyle, J.J.1
Davis, J.I.2
Soreng, R.J.3
Garvin, D.4
Anderson, M.J.5
-
22
-
-
0036935568
-
PipTools: A computational toolkit to annotate and analyze pairwise comparisons of genomic sequences
-
DOI 10.1006/geno.2002.7018
-
Elnitski L, Riemer C, Petrykowska H, Florea L, Schwartz S, Miller W, Hardison R (2002) PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics 80:681-690 (Pubitemid 36062655)
-
(2002)
Genomics
, vol.80
, Issue.6
, pp. 681-690
-
-
Elnitski, L.1
Riemer, C.2
Petrykowska, H.3
Florea, L.4
Schwartz, S.5
Miller, W.6
Hardison, R.7
-
23
-
-
0031978181
-
Base-calling of automated sequencer traces using phred. II. Error probabilities
-
Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186-194
-
(1998)
Genome Res
, vol.8
, pp. 186-194
-
-
Ewing, B.1
Green, P.2
-
24
-
-
0031955518
-
Base-calling of automated sequencer traces using phred. I. Accuracy assessment
-
Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175-185
-
(1998)
Genome Res
, vol.8
, pp. 175-185
-
-
Ewing, B.1
Hillier, L.2
Wendl, M.C.3
Green, P.4
-
25
-
-
42449097595
-
Development of genetic and genomic research resources for Brachypodium distachyon, a new model system, for grass crop research
-
Garvin DF, Gu Y-Q, Hasterok R, Hazen SP, Jenkins G, Mockler TC, Mur LAJ, Vogel JP (2008) Development of genetic and genomic research resources for Brachypodium distachyon, a new model system, for grass crop research. Crop Sci 48:S-69-S-84
-
(2008)
Crop Sci
, vol.48
-
-
Garvin, D.F.1
Gu, Y.-Q.2
Hasterok, R.3
Hazen, S.P.4
Jenkins, G.5
Mockler, T.C.6
Mur, L.A.J.7
Vogel, J.P.8
-
26
-
-
0027611630
-
Relative rates of nucleotide substitution in the chloroplast genome
-
Gaut BS, Muse SV, Clegg MT (1993) Relative rates of nucleotide substitution in the chloroplast genome. Mol Phylogenet Evol 2:89-96
-
(1993)
Mol Phylogenet Evol
, vol.2
, pp. 89-96
-
-
Gaut, B.S.1
Muse, S.V.2
Clegg, M.T.3
-
27
-
-
0031955116
-
Consed: A graphical tool for sequence finishing
-
GordonD,AbajianC,GreenP(1998)Consed:agraphicaltoolforsequencefinishing. GenomeRes8:195-202(Pubitemid28177231)
-
(1998)
Genome Research
, vol.8
, Issue.3
, pp. 195-202
-
-
Gordon, D.1
Abajian, C.2
Green, P.3
-
28
-
-
0029905884
-
Ebb and flow of the chloroplast inverted repeat
-
GouldingSE,OlmsteadRG,MordenCW,WolfeKH(1996) Ebbandflowofthechloroplastinvertedrepeat.MolGenGenet252:195- 206(Pubitemid126451142)
-
(1996)
Molecular Genetics and Genomics
, vol.252
, Issue.1-2
, pp. 195-206
-
-
Goulding, S.E.1
Olmstead, R.G.2
Morden, C.W.3
Wolfe, K.H.4
-
29
-
-
0034800508
-
Phylogeny and subfamilial classification of the grasses
-
GPWG
-
GPWG (2001) Phylogeny and subfamilial classification of the grasses. Ann Mo Bot Gard 88:373-457
-
(2001)
Ann Mo Bot Gard
, vol.88
, pp. 373-457
-
-
-
30
-
-
38949143348
-
Robust inference of monocot deep phylogeny using an expanded multigene plastid data set
-
Graham SW, Zgurski JM., McPherson MA, Cherniawsky DM, Saarela JM, Home ESC, Smith SY, Wong WA, O'Brien HE, Biron VL, Pires JC, Olmstead RG, Chase MW, Rai HS (2006) Robust inference of monocot deep phylogeny using an expanded multigene plastid data set. Aliso 22:3-20
-
(2006)
Aliso
, vol.22
, pp. 3-20
-
-
Graham, S.W.1
Zgurski, J.M.2
McPherson, Ma.3
Cherniawsky, D.M.4
Saarela, J.M.5
Home, E.S.C.6
Smith, S.Y.7
Wong, W.A.8
O'Brien, H.E.9
Biron, V.L.10
Pires, J.C.11
Olmstead, R.G.12
Chase, M.W.13
Rai, H.S.14
-
31
-
-
57449097796
-
Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions
-
Guisinger MM, Kuehl JV, Boore JL, Jansen RK (2008) Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions. Proc Natl Acad Sci USA 105:18424-18429
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 18424-18429
-
-
Guisinger, M.M.1
Kuehl, J.V.2
Boore, J.L.3
Jansen, R.K.4
-
32
-
-
43149125849
-
Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes
-
Haberle RC, Fourcade HM, Boore JL, Jansen RK (2008) Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. J Mol Evol 66:350-361
-
(2008)
J Mol Evol
, vol.66
, pp. 350-361
-
-
Haberle, R.C.1
Fourcade, H.M.2
Boore, J.L.3
Jansen, R.K.4
-
33
-
-
47749095118
-
Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees
-
Heath TA, Zwickl DJ, Kim J, Hills DM (2008) Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Syst Biol 57:160-166
-
(2008)
Syst Biol
, vol.57
, pp. 160-166
-
-
Heath, T.A.1
Zwickl, D.J.2
Kim, J.3
Hills, D.M.4
-
34
-
-
0024674380
-
The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals
-
Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY, Li YQ, Kanno A, Nishizawa Y, Hirai A, Shinozaki K, Sugiura M (1989) The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol Gen Genet 217:185-194
-
(1989)
Mol Gen Genet
, vol.217
, pp. 185-194
-
-
Hiratsuka, J.1
Shimada, H.2
Whittier, R.3
Ishibashi, T.4
Sakamoto, M.5
Mori, M.6
Kondo, C.7
Honji, Y.8
Sun, C.R.9
Meng, B.Y.10
Li, Y.Q.11
Kanno, A.12
Nishizawa, Y.13
Hirai, A.14
Shinozaki, K.15
Sugiura, M.16
-
35
-
-
0002294347
-
A simple sequential rejective multiple test procedure
-
Holm S (1979) A simple sequential rejective multiple test procedure. Scand J Stat 6:65-70
-
(1979)
Scand J Stat
, vol.6
, pp. 65-70
-
-
Holm, S.1
-
36
-
-
0022167389
-
The endpoints of an inversion in wheat chloroplast DNA are associated with short repeated sequences containing homology to aff-lambda
-
Howe CJ (1985) The endpoints of an inversion in wheat chloroplast DNA are associated with short repeated sequences containing homology to aff-lambda. Curr Genet 10:139-145
-
(1985)
Curr Genet
, vol.10
, pp. 139-145
-
-
Howe, C.J.1
-
37
-
-
0023990181
-
Common features of three inversions in wheat chloroplast DNA
-
Howe CJ, Barker RF, Bowman CM, Dyer TA (1988) Common features of three inversions in wheat chloroplast DNA, Curr Genet 13:343-349
-
(1988)
Curr Genet
, vol.13
, pp. 343-349
-
-
Howe, C.J.1
Barker, R.F.2
Bowman, C.M.3
Dyer, T.A.4
-
38
-
-
19944424442
-
Methods for obtaining and analyzing whole chloroplast genome sequences
-
Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ, Fourcade HM, Kuehl JV, McNeal JR, Leebens-Mack J, Cui L (2005) Methods for obtaining and analyzing whole chloroplast genome sequences. Methods Enzymol 395:348-384
-
(2005)
Methods Enzymol
, vol.395
, pp. 348-384
-
-
Jansen, R.K.1
Raubeson, L.A.2
Boore, J.L.3
Depamphilis, C.W.4
Chumley, T.W.5
Haberle, R.C.6
Wyman, S.K.7
Alverson, A.J.8
Peery, R.9
Herman, S.J.10
Fourcade, H.M.11
Kuehl, J.V.12
McNeal, J.R.13
Leebens-Mack, J.14
Cui, L.15
-
39
-
-
37649007931
-
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
-
Jansen RK, Cai Z, Raubeson LA, Danieli H, dePamphilis CW, Leebens-Mack J, Muller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee SB, Peery R, McNeal JR, Kuehl JV, Boore JL (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci USA 104:19369-19374
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 19369-19374
-
-
Jansen, R.K.1
Cai, Z.2
Raubeson, L.A.3
Danieli, H.4
Depamphilis, C.W.5
Leebens-Mack, J.6
Muller, K.F.7
Guisinger-Bellian, M.8
Haberle, R.C.9
Hansen, A.K.10
Chumley, T.W.11
Lee, S.B.12
Peery, R.13
McNeal, J.R.14
Kuehl, J.V.15
Boore, J.L.16
-
40
-
-
0027462277
-
Structural alterations of the chloroplast genome found in grasses are not common in monocots
-
DOI 10.1007/BF00352016
-
Katayama H, Ogihara Y (1993) Structural alterations of the chloroplast genome found in grasses are not common in monocots. Curr Genet 23:160-165 (Pubitemid 23045018)
-
(1993)
Current Genetics
, vol.23
, Issue.2
, pp. 160-165
-
-
Katayama, H.1
Ogihara, Y.2
-
41
-
-
0027134478
-
Phylogenetic studies of a large data set. I. Bambusoideae, Andropogonodae, and Pooideae (Gramineae)
-
Kellogg EA, Watson L (1993) Phylogenetic studies of a large data set. I. Bambusoideae, Andropogonodae, and Pooideae (Gramineae). Bot Rev 59:273-343
-
(1993)
Bot Rev
, vol.59
, pp. 273-343
-
-
Kellogg, E.A.1
Watson, L.2
-
42
-
-
33646835562
-
Elimination of deleterious mutations in plastid genomes by gene conversion
-
DOI 10.1111/j.1365-313X.2006.02673.x
-
Khakhlova O, Bock R (2006) Elimination of deleterious mutations in plastid genomes by gene conversion. Plant J 46:85-94 (Pubitemid 43773580)
-
(2006)
Plant Journal
, vol.46
, Issue.1
, pp. 85-94
-
-
Khakhlova, O.1
Bock, R.2
-
43
-
-
0043124413
-
An arabidopsis homologue of bacterial RecA that complements an E. coli recA deletion is targeted to plant mitochondria
-
Khazi FR, Edmondson AC, Nielsen BL (2003) An Arabidopsis homologue of bacterial RecA that complements an E. coli recA deletion is targeted to plant mitochondria. Mol Genet Genomics 269:454-463
-
(2003)
Mol Genet Genomics
, vol.269
, pp. 454-463
-
-
Khazi, F.R.1
Edmondson, A.C.2
Nielsen, B.L.3
-
44
-
-
0032904367
-
The chloroplast genome arrangement of Lobelia thuliniana (Lobeliaceae): Expansion of the inverted repeat in an ancestor of the Campanulales
-
Knox EB, Palmer JD (1999) The chloroplast genome arrangement of Lobelia thuliniana (Lobeliaceae): expansion of the inverted repeat in an ancestor of the Campanulales. Plant Syst Evol 214:49-64
-
(1999)
Plant Syst Evol
, vol.214
, pp. 49-64
-
-
Knox, E.B.1
Palmer, J.D.2
-
45
-
-
24744449757
-
Identifying the basal angiosperm node in chloroplast genome phylogenies: Sampling one's way out of the Felsenstein zone
-
DOI 10.1093/molbev/msi191
-
Leebens-Mack J, Raubeson LA, Cui L, Kuehl JV, Fourcade MH, Chumley TW, Boore JL, Jansen RK, dePamphilis CW (2005) Identifying the basal angiosperm node in chloroplast genome phytogenies: sampling one's way out of the Felsenstein zone. Mol Biol Evol 22:1948-1963 (Pubitemid 41298063)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.10
, pp. 1948-1963
-
-
Leebens-Mack, J.1
Raubeson, L.A.2
Cui, L.3
Kuehl, J.V.4
Fourcade, M.H.5
Chumley, T.W.6
Boore, J.L.7
Jansen, R.K.8
Depamphilis, C.W.9
-
46
-
-
33745874687
-
Origins and evolution of the recA/RAD51 gene family: Evidence for ancient gene duplication and endosymbiotic gene transfer
-
Lin Z, Kong H, Nei M, Ma H (2006) Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer. Proc Natl Acad Sci USA 103:10328-10333
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 10328-10333
-
-
Lin, Z.1
Kong, H.2
Nei, M.3
Ma, H.4
-
47
-
-
37649009007
-
Phylogeny of flowering plants by the chloroplast genome sequences: In search of a "lucky gene"
-
Logacheva MD, Penin AA, Samigullin TH, Vallejo-Roman CM, Antonov AS (2007) Phylogeny of flowering plants by the chloroplast genome sequences: in search of a "lucky gene". Biochem (Mose) 72:1324-1330
-
(2007)
Biochem (Mose)
, vol.72
, pp. 1324-1330
-
-
Logacheva, M.D.1
Penin, A.A.2
Samigullin, T.H.3
Vallejo-Roman, C.M.4
Antonov, A.S.5
-
48
-
-
47249126308
-
Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale-a wild ancestor of cultivated buckwheat
-
Logacheva MD, Samigullin TH, Dhingra A, Penin AA (2008) Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale-a wild ancestor of cultivated buckwheat. BMC Plant Biol 8:59
-
(2008)
BMC Plant Biol
, vol.8
, pp. 59
-
-
Logacheva, M.D.1
Samigullin, T.H.2
Dhingra, A.3
Penin, A.A.4
-
49
-
-
0029160870
-
Complete sequence of the maize chloroplast genome: Gene content, hotspots of divergence and fine tuning of genetic information by transcript editing
-
Maier RM, Neckermann K, Igloi GL, Kossel H (1995) Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J Mol Biol 251:614-628
-
(1995)
J Mol Biol
, vol.251
, pp. 614-628
-
-
Maier, R.M.1
Neckermann, K.2
Igloi, G.L.3
Kossel, H.4
-
50
-
-
0036899796
-
Whole chloroplast genome comparison of rice, maize, and wheat: Implications for chloroplast gene diversification and phylogeny of cereals
-
MatsuokaY,YamazakiY,OgiharaY,TsunewakiK(2002) Wholechloroplastgenomecomparisonofrice,maize,andwheat: Implicationsforchloroplastgenediversificationandphylogenyofcereals. MolBiolEvol19:2084-2091(Pubitemid35440444)
-
(2002)
Molecular Biology and Evolution
, vol.19
, Issue.12
, pp. 2084-2091
-
-
Matsuoka, Y.1
Yamazaki, Y.2
Ogihara, Y.3
Tsunewaki, K.4
-
51
-
-
37549054628
-
Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms
-
Moore MJ, Bell CD, Soltis PS, Soltis DE (2007) Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc Natl Acad Sci USA 104:19363-19368
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 19363-19368
-
-
Moore, M.J.1
Bell, C.D.2
Soltis, P.S.3
Soltis, D.E.4
-
52
-
-
0037403391
-
The role of context-dependent mutations in generating compositional and codon usage bias in grass chloroplast DNA
-
Morton BR (2003) The role of context-dependent mutations in generating compositional and codon usage bias in grass chloroplast DNA. J Mol Evol 56:616-629
-
(2003)
J Mol Evol
, vol.56
, pp. 616-629
-
-
Morton, B.R.1
-
53
-
-
0028834672
-
Neighboring base composition is strongly correlated with base substitution bias in a region of the chloroplast genome
-
Morton BR, Clegg MT (1995) Neighboring base composition is strongly correlated with base substitution bias in a region of the chloroplast genome. J Mol Evol 41:597-603
-
(1995)
J Mol Evol
, vol.41
, pp. 597-603
-
-
Morton, B.R.1
Clegg, M.T.2
-
54
-
-
0028024626
-
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
-
Muse SV, Gaut BS (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11:715-724
-
(1994)
Mol Biol Evol
, vol.11
, pp. 715-724
-
-
Muse, S.V.1
Gaut, B.S.2
-
55
-
-
0030984551
-
Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test
-
Muse SV, Gaut BS (1997) Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test. Genet 146:393-399
-
(1997)
Genet
, vol.146
, pp. 393-399
-
-
Muse, S.V.1
Gaut, B.S.2
-
56
-
-
0034560807
-
Chinese spring wheat (Triticum aestivum L.) chloroplast genome: Complete sequence and contig clones
-
Ogihara Y, Isono K, Kojima T, Endo A, Hanaoka M, Shiina T, Terachi T, Utsugi S, Murate M, Mori N, Takumi S, Ikeo K, Gojobori T, Murai R, Murai K, Matsuoka Y, Ohnishi Y, Tajiri H, Tsunewaki K (2000) Chinese spring wheat (Triticum aestivum L.) chloroplast genome: complete sequence and contig clones. Plant Mol Biol Rep 18:243-253
-
(2000)
Plant Mol Biol Rep
, vol.18
, pp. 243-253
-
-
Ogihara, Y.1
Isono, K.2
Kojima, T.3
Endo, A.4
Hanaoka, M.5
Shiina, T.6
Terachi, T.7
Utsugi, S.8
Murate, M.9
Mori, N.10
Takumi, S.11
Ikeo, K.12
Gojobori, T.13
Murai, R.14
Murai, K.15
Matsuoka, Y.16
Ohnishi, Y.17
Tajiri, H.18
Tsunewaki, K.19
-
57
-
-
77957046363
-
Isolation and structural analysis of chloroplast DNA
-
Palmer JD (1986) Isolation and structural analysis of chloroplast DNA. Methods Enzymol 118:167-186
-
(1986)
Methods Enzymol
, vol.118
, pp. 167-186
-
-
Palmer, J.D.1
-
59
-
-
0001695670
-
Unusual structure of geranium chloroplast DNA: A triple-sized repeat, extensive gene duplications, multiple inversions, and new repeat families
-
Palmer JD, Nugent JM, Herbon LA (1987) Unusual structure of geranium chloroplast DNA: a triple-sized repeat, extensive gene duplications, multiple inversions, and new repeat families. Proc Natl Acad Sci USA 84:769-773
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, pp. 769-773
-
-
Palmer, J.D.1
Nugent, J.M.2
Herbon, L.A.3
-
60
-
-
0034475496
-
Expansion and contraction of the chloroplast inverted repeat in Apiaceae subfamily Apioideae
-
Plunkett GM, Downie SR (2000) Expansion and contraction of the chloroplast inverted repeat in Apiaceae subfamily Apioideae. Syst Bot 25:648-667
-
(2000)
Syst Bot
, vol.25
, pp. 648-667
-
-
Plunkett, G.M.1
Downie, S.R.2
-
61
-
-
0024971786
-
A new rearrangement of angiosperm chloroplast DNA in rye (Secale cereale) involving translocation and duplication of the ribosomal rpslS gene
-
Prombona A, Subramanian AR (1989) A new rearrangement of angiosperm chloroplast DNA in rye (Secale cereale) involving translocation and duplication of the ribosomal rpslS gene. J Biol Chem 264:19060-19065
-
(1989)
J Biol Chem
, vol.264
, pp. 19060-19065
-
-
Prombona, A.1
Subramanian, A.R.2
-
62
-
-
0022169885
-
Organization and sequence of five tRNA genes and of an unidentified reading frame in the wheat chloroplast genome: Evidence for gene rearrangements during the evolution of chloroplast genomes
-
Quigley F, Weil JH (1985) Organization and sequence of five tRNA genes and of an unidentified reading frame in the wheat chloroplast genome: Evidence for gene rearrangements during the evolution of chloroplast genomes. Curr Genet 9:495-503
-
(1985)
Curr Genet
, vol.9
, pp. 495-503
-
-
Quigley, F.1
Weil, J.H.2
-
63
-
-
5444244910
-
Chloroplast genomes of plants
-
Henry RJ (ed) CABI Publishing, Cambridge, MA, pp
-
Raubeson LA, Jansen RK (2005) Chloroplast genomes of plants. In: Henry RJ (ed) Plant diversity and evolution: genotypic and phenotypic variation in higher plants. CABI Publishing, Cambridge, MA, pp 45-68
-
(2005)
Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants.
, pp. 45-68
-
-
Raubeson, L.A.1
Jansen, R.K.2
-
64
-
-
34447635560
-
Comparative chloroplast genomics: Analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus
-
DOI 10.1186/1471-2164-8-174
-
Raubeson LA, Peery R, Chumley TW, Dziubek C, Fourcade HM, Boore JL, Jansen RK (2007) Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8:174 (Pubitemid 47090617)
-
(2007)
BMC Genomics
, vol.8
, pp. 174
-
-
Raubeson, L.A.1
Peery, R.2
Chumley, T.W.3
Dziubek, C.4
Fourcade, H.M.5
Boore, J.L.6
Jansen, R.K.7
-
65
-
-
49649106060
-
Genomics of cellulosic biofuels
-
Rubin EM (2008) Genomics of cellulosic biofuels. Nature 454:841-845
-
(2008)
Nature
, vol.454
, pp. 841-845
-
-
Rubin, E.M.1
-
66
-
-
27144516495
-
Complete chloroplast genome sequence of Gycine max and comparative analyses with other legume genomes
-
Saski C, Lee SB, Danieli H, Wood TC, Tomkins J, Kim HG, Jansen RK (2005) Complete chloroplast genome sequence of Gycine max and comparative analyses with other legume genomes. Plant Mol Biol 59:309-322
-
(2005)
Plant Mol Biol
, vol.59
, pp. 309-322
-
-
Saski, C.1
Lee, S.B.2
Danieli, H.3
Wood, T.C.4
Tomkins, J.5
Kim, H.G.6
Jansen, R.K.7
-
67
-
-
34547793573
-
Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes
-
Saski C, Lee SB, Fjellheim S, Guda C, Jansen RK, Luo H, Tomkins J, Rognli OA, Danieli H, Clarke JL (2007) Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. Theor Appl Genet 115:571-590
-
(2007)
Theor Appl Genet
, vol.115
, pp. 571-590
-
-
Saski, C.1
Lee, S.B.2
Fjellheim, S.3
Guda, C.4
Jansen, R.K.5
Luo, H.6
Tomkins, J.7
Rognli, O.A.8
Danieli, H.9
Clarke, J.L.10
-
68
-
-
0042490659
-
MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences
-
DOI 10.1093/nar/gkg579
-
Schwartz S, Elnitski L, Li M, Weirauch M, Riemer C, Smit A, Program NCS, Green ED, Hardison RC, Miller W (2003) MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res 31:3518-3524 (Pubitemid 37442189)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3518-3524
-
-
Schwartz, S.1
Elnitski, L.2
Li, M.3
Weirauch, M.4
Riemer, C.5
Smit, A.6
Thomas, J.7
Touchman, J.8
Blakesley, B.9
Bouffard, G.10
Beckstrom-Sternberg, S.11
Thomas, P.12
McDowell, J.13
Maskeri, B.14
Hansen, N.15
Margulies, E.16
Green, E.D.17
Hardison, R.C.18
Miller, W.19
-
69
-
-
2542462934
-
Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects
-
DOI 10.1093/molbev/msg176
-
Shao R, Dowton M, Murrell A, Barker SC (2003) Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects. Mol Biol Evol 20:1612-1619 (Pubitemid 41070822)
-
(2003)
Molecular Biology and Evolution
, vol.20
, Issue.10
, pp. 1612-1619
-
-
Shao, R.1
Dowton, M.2
Murrell, A.3
Barker, S.C.4
-
70
-
-
0024311019
-
Pseudogenes and short repeated sequences in the rice chloroplast genome
-
DOI 10.1007/BF00422116
-
Shimada H, Sugiura M (1989) Pseudogenes and short repeated sequences in the rice chloroplast genome. Curr Genet 16:293-301 (Pubitemid 20000961)
-
(1989)
Current Genetics
, vol.16
, Issue.4
, pp. 293-301
-
-
Shimada, H.1
Sugiura, M.2
-
71
-
-
53349160132
-
Rates of molecular evolution are linked to life history in flowering plants
-
Smith SA, Donoghue MJ (2008) Rates of molecular evolution are linked to life history in flowering plants. Science 322:86-89
-
(2008)
Science
, vol.322
, pp. 86-89
-
-
Smith, S.A.1
Donoghue, M.J.2
-
72
-
-
4644250777
-
Amborella not a "basal angiosperm"? Not so fast
-
Soltis DE, Soltis PS (2004) Amborella not a "basal angiosperm"? Not so fast. Am J Bot 91:997-1001
-
(2004)
Am J Bot
, vol.91
, pp. 997-1001
-
-
Soltis, D.E.1
Soltis, P.S.2
-
73
-
-
10644253746
-
Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
-
Stefanovic S, Rice DW, Palmer JD (2004) Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots? BMC Evol Biol 4:35
-
(2004)
BMC Evol Biol
, vol.4
, pp. 35
-
-
Stefanovic, S.1
Rice, D.W.2
Palmer, J.D.3
-
75
-
-
37249014420
-
Chloroplast vector systems for biotechnology applications
-
DOI 10.1104/pp.107.106690
-
Verma D, Danieli H (2007) Chloroplast vector systems for biotechnology applications. Plant Physiol 145:1129-1143 (Pubitemid 350276732)
-
(2007)
Plant Physiology
, vol.145
, Issue.4
, pp. 1129-1143
-
-
Verma, D.1
Daniell, H.2
-
76
-
-
43549096694
-
Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots
-
Wang RJ, Cheng CL, Chang CC, Wu CL, Su TM, Chaw SM (2008) Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Evol Biol 8:36
-
(2008)
BMC Evol Biol
, vol.8
, pp. 36
-
-
Wang, R.J.1
Cheng, C.L.2
Chang, C.C.3
Wu, C.L.4
Su, T.M.5
Chaw, S.M.6
-
77
-
-
0023462635
-
Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs
-
Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl. Acad Sci USA. 84:9054-9058
-
(1987)
Proc Natl. Acad Sci USA.
, vol.84
, pp. 9054-9058
-
-
Wolfe, K.H.1
Li, W.H.2
Sharp, P.M.3
-
78
-
-
69149092980
-
Complete nucleotide sequence of Dendrocalamus latiflorus and Bambusa oldhamii chloroplast genomes
-
Wu F, Kan D, Lee S, Daniel! H, Lee Y, Lin C, Lin N, Lin C (2009) Complete nucleotide sequence of Dendrocalamus latiflorus and Bambusa oldhamii chloroplast genomes. Tree Physiol 29:847-856
-
(2009)
Tree Physiol
, vol.29
, pp. 847-856
-
-
Wu, F.1
Kan, D.2
Lee, S.3
Daniel, H.4
Lee, Y.5
Lin, C.6
Lin, N.7
Lin, C.8
-
79
-
-
10244240599
-
Automatic annotation of organellar genomes with DOGMA
-
Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252-3255
-
(2004)
Bioinformatics
, vol.20
, pp. 3252-3255
-
-
Wyman, S.K.1
Jansen, R.K.2
Boore, J.L.3
-
80
-
-
33748969002
-
The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes
-
DOI 10.1007/s00239-005-0246-5
-
Xu W, Jameson D, Tang B, Higgs PG (2006) The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes. J Mol Evol 63:375-392 (Pubitemid 44440479)
-
(2006)
Journal of Molecular Evolution
, vol.63
, Issue.3
, pp. 375-392
-
-
Xu, W.1
Jameson, D.2
Tang, B.3
Higgs, P.G.4
-
81
-
-
0031897964
-
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
-
Yang Z (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 15:568-573
-
(1998)
Mol Biol Evol
, vol.15
, pp. 568-573
-
-
Yang, Z.1
-
82
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586-1591
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
83
-
-
0036270185
-
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
-
YangZ,NielsenR(2002)Codon- substitutionmodelsfordetectingmolecularadaptationatindividualsitesalong specificlineages.MolBiolEvol19:908-917(Pubitemid34602960)
-
(2002)
Molecular Biology and Evolution
, vol.19
, Issue.6
, pp. 908-917
-
-
Yang, Z.1
Nielsent, R.2
-
84
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
YangZ,NielsenR,GoldmanN,PedersenAM(2000) Codonsubstitutionmodelsforheterogeneousselectionpressureataminoacidsites. Genet155:431-449(Pubitemid30257141)
-
(2000)
Genetics
, vol.155
, Issue.1
, pp. 431-449
-
-
Yang, Z.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.-M.K.4
-
85
-
-
0037023384
-
A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
-
DOI 10.1126/science.1068037
-
Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79-92 (Pubitemid 34280064)
-
(2002)
Science
, vol.296
, Issue.5565
, pp. 79-92
-
-
Yu, J.1
Hu, S.2
Wang, J.3
Wong, G.K.-S.4
Li, S.5
Liu, B.6
Deng, Y.7
Dai, L.8
Zhou, Y.9
Zhang, X.10
Cao, M.11
Liu, J.12
Sun, J.13
Tang, J.14
Chen, Y.15
Huang, X.16
Lin, W.17
Ye, C.18
Tong, W.19
Cong, L.20
Geng, J.21
Han, Y.22
Li, L.23
Li, W.24
Hu, G.25
Huang, X.26
Li, W.27
Li, J.28
Liu, Z.29
Li, L.30
Liu, J.31
Qi, Q.32
Liu, J.33
Li, L.34
Li, T.35
Wang, X.36
Lu, H.37
Wu, T.38
Zhu, M.39
Ni, P.40
Han, H.41
Dong, W.42
Ren, X.43
Feng, X.44
Cui, P.45
Li, X.46
Wang, H.47
Xu, X.48
Zhai, W.49
Xu, Z.50
Zhang, J.51
He, S.52
Zhang, J.53
Xu, J.54
Zhang, K.55
Zheng, X.56
Dong, J.57
Zeng, W.58
Tao, L.59
Ye, J.60
Tan, J.61
Ren, X.62
Chen, X.63
He, J.64
Liu, D.65
Tian, W.66
Tian, C.67
Xia, H.68
Bao, Q.69
Li, G.70
Gao, H.71
Cao, T.72
Wang, J.73
Zhao, W.74
Li, P.75
Chen, W.76
Wang, X.77
Zhang, Y.78
Hu, J.79
Wang, J.80
Liu, S.81
Yang, J.82
Zhang, G.83
Xiong, Y.84
Li, Z.85
Mao, L.86
Zhou, C.87
Zhu, Z.88
Chen, R.89
Hao, B.90
Zheng, W.91
Chen, S.92
Guo, W.93
Li, G.94
Liu, S.95
Tao, M.96
Wang, J.97
Zhu, L.98
Yang, H.99
more..
-
86
-
-
34247176936
-
GARLI: Genetic algorithm for rapid likelihood inference
-
version 0.951. version 0.951. Available at
-
Zwickl DJ (2006) GARLI: genetic algorithm for rapid likelihood inference, version 0.951. GARLI: genetic algorithm for rapid likelihood inference, version 0.951. Available at http://www.bio. utexas.edu/faculty/antisense/garli/Garli. html
-
(2006)
GARLI: Genetic Algorithm for Rapid Likelihood Inference
-
-
Zwickl, D.J.1
|