-
1
-
-
0033452726
-
Phylogeny of rice genomes with emphasis on origins of allotetraploid species
-
USA
-
Ge, S., Sang, T., Lu, B.-R. and Hong, D.-Y. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc. Natl. Acad. Sci. USA 96, 14400-14405 (1999).
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 14400-14405
-
-
Ge, S.1
Sang, T.2
Lu, B.-R.3
Hong, D.-Y.4
-
2
-
-
34250389706
-
The origin, evolution, cultivation, dissemination, and diversification of Asian and African rices
-
Chang, T.-T. The origin, evolution, cultivation, dissemination, and diversification of Asian and African rices. Euphytica 25, 425-441 (1976).
-
(1976)
Euphytica
, vol.25
, pp. 425-441
-
-
Chang, T.-T.1
-
3
-
-
84887274539
-
Conservation and utilization of African Oryza genetic resources
-
Wambugu, P., Furtado, A., Waters, D., Nyamongo, D. and Henry, R. Conservation and utilization of African Oryza genetic resources. Rice 6, 29 (2013).
-
(2013)
Rice
, vol.6
, pp. 29
-
-
Wambugu, P.1
Furtado, A.2
Waters, D.3
Nyamongo, D.4
Henry, R.5
-
4
-
-
84887121031
-
Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions
-
Zhu, T. et al. Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions. Mol. Phylogenet. Evol. 70, 348-361 (2014).
-
(2014)
Mol. Phylogenet. Evol.
, vol.70
, pp. 348-361
-
-
Zhu, T.1
-
5
-
-
21244501403
-
Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes
-
Zhu, Q. and Ge, S. Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol. 167, 249-265 (2005).
-
(2005)
New Phytol.
, vol.167
, pp. 249-265
-
-
Zhu, Q.1
Ge, S.2
-
6
-
-
79952305603
-
Chloroplast genome sequences from total DNA for plant identification
-
Nock, C. J. et al. Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnol. J. 9, 328-333 (2011).
-
(2011)
Plant Biotechnol. J.
, vol.9
, pp. 328-333
-
-
Nock, C.J.1
-
7
-
-
0346091308
-
Use of nuclear genes for phylogeny reconstruction in plants
-
Small, R. L., Cronn, R. C. and Wendel, J. F. Use of nuclear genes for phylogeny reconstruction in plants. Aust. Syst. Bot. 17, 145-170 (2004).
-
(2004)
Aust. Syst. Bot.
, vol.17
, pp. 145-170
-
-
Small, R.L.1
Cronn, R.C.2
Wendel, J.F.3
-
8
-
-
84869778772
-
Re-Mind the Gap! Insertion - Deletion data reveal neglected phylogenetic potential of the nuclear ribosomal internal transcribed spacer (ITS) of fungi
-
Nagy, L. G. et al. Re-Mind the Gap! Insertion - Deletion Data Reveal Neglected Phylogenetic Potential of the Nuclear Ribosomal Internal Transcribed Spacer (ITS) of Fungi. PloS one 7, e49794 (2012).
-
(2012)
PloS One
, vol.7
, pp. e49794
-
-
Nagy, L.G.1
-
9
-
-
33847312692
-
How should gaps be treated in parsimony? A comparison of approaches using simulation
-
Ogden, T. H. and Rosenberg, M. S. How should gaps be treated in parsimony? A comparison of approaches using simulation. Mol. Phylogenet. Evol. 42, 817-826(2007).
-
(2007)
Mol. Phylogenet. Evol.
, vol.42
, pp. 817-826
-
-
Ogden, T.H.1
Rosenberg, M.S.2
-
10
-
-
77950538424
-
Phylogenetic assessment of alignments reveals neglected tree signal in gaps
-
Dessimoz, C. and Gil, M. Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biol. 11, R37-R37(2010).
-
(2010)
Genome Biol.
, vol.11
, pp. R37-R37
-
-
Dessimoz, C.1
Gil, M.2
-
11
-
-
84941279245
-
-
[The History of the Problem] [Wlma, G. and Rene, L. (eds)] [1-7] (Oxford university press, Oxford)
-
Wood, A. E. [The History of the Problem] The Africa-South America Connection [Wlma, G. and Rene, L. (eds)] [1-7] (Oxford university press, Oxford, 1993).
-
(1993)
The Africa-South America Connection
-
-
Wood, A.E.1
-
12
-
-
84880171500
-
Plate tectonic evolution of the Caribbean region in the mantle reference frame
-
[Bonini, W. E. and Hargraves, R. S. (eds)] (Geological Society of America)
-
Duncan, R. A. and Hargraves, R. B. [Plate tectonic evolution of the Caribbean region in the mantle reference frame] The Caribbean- South American Plate Boundary and Regional Tectonics Vol. Memoir 162 [Bonini, W. E. and Hargraves, R. S. (eds)] [81-95] (Geological Society of America, 1984).
-
(1984)
The Caribbean- South American Plate Boundary and Regional Tectonics Memoir
, vol.162
, pp. 81-95
-
-
Duncan, R.A.1
Hargraves, R.B.2
-
13
-
-
33751247345
-
Convergent evolution of gigantism in damselflies of Africa and South America? Evidence from nuclear and mitochondrial sequence data
-
Groeneveld, L. F., Clausnitzer, V. and Hadrys, H. Convergent evolution of gigantism in damselflies of Africa and South America? Evidence from nuclear and mitochondrial sequence data. Mol. Phylogenet. Evol. 42, 339-346 (2007).
-
(2007)
Mol. Phylogenet. Evol.
, vol.42
, pp. 339-346
-
-
Groeneveld, L.F.1
Clausnitzer, V.2
Hadrys, H.3
-
14
-
-
4944224427
-
Ancient vicariance or recent long-distance dispersal? Inferences about phylogeny and South American-African disjunctions in Rapateaceae and Bromeliaceae based on ndhF sequence data
-
Givnish, T. J. et al. Ancient vicariance or recent long-distance dispersal? Inferences about phylogeny and South American-African disjunctions in Rapateaceae and Bromeliaceae based on ndhF sequence data. Int. J. Plant Sci. 165, S35-S54 (2004).
-
(2004)
Int. J. Plant Sci.
, vol.165
, pp. S35-S54
-
-
Givnish, T.J.1
-
15
-
-
0034712861
-
Early Cretaceous lineages of monocot flowering plants
-
USA
-
Bremer, K. Early Cretaceous lineages of monocot flowering plants. Proc. Natl. Acad. Sci. USA 97, 4707-4711 (2000).
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, pp. 4707-4711
-
-
Bremer, K.1
-
16
-
-
80053362389
-
Rate variation and estimation of divergence times using strict and relaxed clocks
-
Brown, R. P. and Yang, Z. Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evol. Biol. 11, 271-271(2011).
-
(2011)
BMC Evol. Biol.
, vol.11
, pp. 271-271
-
-
Brown, R.P.1
Yang, Z.2
-
17
-
-
84897556789
-
Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe
-
Middleton, C. P. et al. Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PloS One 9, e85761 (2014).
-
(2014)
PloS One
, vol.9
, pp. e85761
-
-
Middleton, C.P.1
-
18
-
-
0032580152
-
A molecular timescale for vertebrate evolution
-
Kumar, S. and Hedges, S. B. A molecular timescale for vertebrate evolution. Nature 392, 917-920 (1998).
-
(1998)
Nature
, vol.392
, pp. 917-920
-
-
Kumar, S.1
Hedges, S.B.2
-
19
-
-
0033059511
-
P-SINE1-like intron of the CatA catalase homologs and phylogenetic relationships among AA-genome Oryza and related species
-
Iwamoto, M., Nagashima, H., Nagamine, T., Higo, H. and Higo, K. p-SINE1-like intron of the CatA catalase homologs and phylogenetic relationships among AA-genome Oryza and related species. Theor. Appl. Genet. 98, 853-861 (1999).
-
(1999)
Theor. Appl. Genet.
, vol.98
, pp. 853-861
-
-
Iwamoto, M.1
Nagashima, H.2
Nagamine, T.3
Higo, H.4
Higo, K.5
-
20
-
-
0036814150
-
Evolutionary relationships among rice species with AA genome based on SINE insertion analysis
-
Cheng, C., Tsuchimoto, S., Ohtsubo, H. and Ohtsubo, E. Evolutionary relationships among rice species with AA genome based on SINE insertion analysis. Genes Genet. Syst. 77, 323-334 (2002).
-
(2002)
Genes Genet. Syst.
, vol.77
, pp. 323-334
-
-
Cheng, C.1
Tsuchimoto, S.2
Ohtsubo, H.3
Ohtsubo, E.4
-
21
-
-
20844443346
-
On the phylogeny and biogeography of the genus Oryza
-
Vaughan, D. A., Kadowaki, K.-I., Kaga, A. and Tomooka, N. On the phylogeny and biogeography of the genus Oryza. Breeding Sci. 55, 113-122 (2005).
-
(2005)
Breeding Sci.
, vol.55
, pp. 113-122
-
-
Vaughan, D.A.1
Kadowaki, K.-I.2
Kaga, A.3
Tomooka, N.4
-
22
-
-
85015386763
-
-
[Phylogeny and Biogeography of the Genus Oryza] [Hirano, H.-Y., Hirai, A., Sano, Y. and Sasaki, T. (eds)] (Springer, Berlin Heidelberg)
-
Vaughan, D. A., Ge, S., Kaga, A. and Tomooka, N. [Phylogeny and Biogeography of the Genus Oryza] Rice Biology in the Genomics Era [Hirano, H.-Y., Hirai, A., Sano, Y. and Sasaki, T. (eds)] [219-234] (Springer, Berlin Heidelberg, 2008).
-
(2008)
Rice Biology in the Genomics Era
, pp. 219-234
-
-
Vaughan, D.A.1
Ge, S.2
Kaga, A.3
Tomooka, N.4
-
23
-
-
4344616881
-
Rapid recent growth and divergence of rice nuclear genomes
-
USA
-
Ma, J. and Bennetzen, J. L. Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl. Acad. Sci. USA 101, 12404-12410 (2004).
-
(2004)
Proc. Natl. Acad. Sci.
, vol.101
, pp. 12404-12410
-
-
Ma, J.1
Bennetzen, J.L.2
-
24
-
-
79957761306
-
Molecular evidence for a single evolutionary origin of domesticated rice
-
USA
-
Molina, J. et al. Molecular evidence for a single evolutionary origin of domesticated rice. Proc. Natl. Acad. Sci. USA 108, 8351-8356 (2011).
-
(2011)
Proc. Natl. Acad. Sci.
, vol.108
, pp. 8351-8356
-
-
Molina, J.1
-
25
-
-
0033916763
-
Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza
-
Joshi, S. P., Gupta, V. S., Aggarwal, R. K., Ranjekar, P. K. and Brar, D. S. Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor. Appl. Genet. 100, 1311-1320 (2000).
-
(2000)
Theor. Appl. Genet.
, vol.100
, pp. 1311-1320
-
-
Joshi, S.P.1
Gupta, V.S.2
Aggarwal, R.K.3
Ranjekar, P.K.4
Brar, D.S.5
-
26
-
-
0034987158
-
RAPD RFLP and SSLP analyses of phylogenetic relationships between cultivated and wild species of rice
-
Bautista, N. S., Solis, R., Kamijima, O. and Ishii, T. RAPD, RFLP and SSLP analyses of phylogenetic relationships between cultivated and wild species of rice. Genes Genet. Syst. 76, 71-79 (2001).
-
(2001)
Genes Genet. Syst.
, vol.76
, pp. 71-79
-
-
Bautista, N.S.1
Solis, R.2
Kamijima, O.3
Ishii, T.4
-
27
-
-
77954143052
-
Genetic diversity and evolutionary relationships in genus Oryza revealed by using highly variable regions of chloroplast DNA
-
Kumagai, M., Wang, L. and Ueda, S. Genetic diversity and evolutionary relationships in genus Oryza revealed by using highly variable regions of chloroplast DNA. Gene 462, 44-51 (2010).
-
(2010)
Gene
, vol.462
, pp. 44-51
-
-
Kumagai, M.1
Wang, L.2
Ueda, S.3
-
28
-
-
84867875610
-
A map of rice genome variation reveals the origin of cultivated rice
-
Huang, X. et al. A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497-501 (2012).
-
(2012)
Nature
, vol.490
, pp. 497-501
-
-
Huang, X.1
-
29
-
-
79958097465
-
Genetic diversity and domestication history of African rice (Oryza glaberrima) as inferred from multiple gene sequences
-
Li, Z. M., Zheng, X. M. and Ge, S. Genetic diversity and domestication history of African rice (Oryza glaberrima) as inferred from multiple gene sequences. Theor. Appl. Genet. 123, 21-31 (2011).
-
(2011)
Theor. Appl. Genet.
, vol.123
, pp. 21-31
-
-
Li, Z.M.1
Zheng, X.M.2
Ge, S.3
-
30
-
-
84922395367
-
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication
-
Wang, M. H. et al. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat. Genet. 46, 982-988 (2014).
-
(2014)
Nat. Genet.
, vol.46
, pp. 982-988
-
-
Wang, M.H.1
-
31
-
-
84905759590
-
-
[The Origin of African Rice] Elsevier Science, Burlington
-
Nayar, N. M. [The Origin of African Rice] Origins and Phylogeny of Rices [117-168] (Elsevier Science, Burlington, 2014).
-
(2014)
Origins and Phylogeny of Rices
, pp. 117-168
-
-
Nayar, N.M.1
-
32
-
-
0012055934
-
Berceaux agricoles primaires sur le continent Africain
-
Porteres, R. Berceaux Agricoles Primaires Sur le Continent Africain. J. Afr. Hist. 3, 195-210 (1962).
-
(1962)
J. Afr. Hist.
, vol.3
, pp. 195-210
-
-
Porteres, R.1
-
33
-
-
84871201714
-
Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice
-
Waters, D. L. E., Nock, C. J., Ishikawa, R., Rice, N. and Henry, R. J. Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice. Eco. Evol. 2, 211-217 (2012).
-
(2012)
Eco. Evol.
, vol.2
, pp. 211-217
-
-
Waters, D.L.E.1
Nock, C.J.2
Ishikawa, R.3
Rice, N.4
Henry, R.J.5
-
34
-
-
84882824442
-
Crossability patterns within and among Oryza series Sativae species from Asia and Australia
-
Banaticla-Hilario, M. C. N., McNally, K. L., Berg, R. G. and Hamilton, N. R. S. Crossability patterns within and among Oryza series Sativae species from Asia and Australia. Genet. Resour. Crop Evol. 60, 1899-1914 (2013).
-
(2013)
Genet. Resour. Crop Evol.
, vol.60
, pp. 1899-1914
-
-
Banaticla-Hilario, M.C.N.1
McNally, K.L.2
Berg, R.G.3
Hamilton, N.R.S.4
-
35
-
-
0001907141
-
Phylogenetic consequences of cytoplasmic gene flow in plants
-
Rieseberg, L. H. and Soltis, D. E. Phylogenetic consequences of cytoplasmic gene flow in plants. Evol. Trend Plants 5, 65-84 (1991).
-
(1991)
Evol. Trend Plants
, vol.5
, pp. 65-84
-
-
Rieseberg, L.H.1
Soltis, D.E.2
-
36
-
-
45549084713
-
Analysis of 142 genes resolves the rapid diversification of the rice genus
-
Zou, X. H. et al. Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biol. 9, R49-R49 (2008).
-
(2008)
Genome Biol.
, vol.9
, pp. R49-R49
-
-
Zou, X.H.1
-
37
-
-
70649104604
-
Evidence of chloroplast capture in South American nothofagus (subgenus Nothofagus, Nothofagaceae)
-
Cristina Acosta, M. and Premoli, A. C. Evidence of chloroplast capture in South American Nothofagus (subgenus Nothofagus, Nothofagaceae). Mol. Phylogenet. Evol. 54, 235-242 (2010).
-
(2010)
Mol. Phylogenet. Evol.
, vol.54
, pp. 235-242
-
-
Cristina Acosta, M.1
Premoli, A.C.2
-
38
-
-
78649694222
-
Geographic and phylogenetic patterns in Silene section Melandrium (Caryophyllaceae) as inferred from chloroplast and nuclear DNA sequences
-
Rautenberg, A. et al. Geographic and phylogenetic patterns in Silene section Melandrium (Caryophyllaceae) as inferred from chloroplast and nuclear DNA sequences. Mol. Phylogenet. Evol. 57, 978-991(2010).
-
(2010)
Mol. Phylogenet. Evol.
, vol.57
, pp. 978-991
-
-
Rautenberg, A.1
-
39
-
-
84926648413
-
Evolution of the bamboos (Bambusoideae; Poaceae): A full plastome phylogenomic analysis
-
Wysocki, W. P., Clark, L. G., Attigala, L., Ruiz-Sanchez, E. and Duvall, M. R. Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis. BMC Evol. Biol. 15, 50 (2015).
-
(2015)
BMC Evol. Biol.
, vol.15
, pp. 50
-
-
Wysocki, W.P.1
Clark, L.G.2
Attigala, L.3
Ruiz-Sanchez, E.4
Duvall, M.R.5
-
40
-
-
84911981909
-
Chloroplast genome of novel rice germplasm identified in Northern Australia
-
Brozynska, M. et al. Chloroplast genome of novel rice germplasm identified in Northern Australia. Trop. Plant Biol. 7, 111-120 (2014).
-
(2014)
Trop. Plant Biol.
, vol.7
, pp. 111-120
-
-
Brozynska, M.1
-
41
-
-
84901046780
-
Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms
-
Sotowa, M. et al. Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms. Rice 6, 26 (2013).
-
(2013)
Rice
, vol.6
, pp. 26
-
-
Sotowa, M.1
-
42
-
-
0028893298
-
Germinal transpositions of the maize element Dissociation from T-DNA loci in tomato
-
Carroll, B. J. et al. Germinal transpositions of the maize element Dissociation from T-DNA loci in tomato. Genetics 139, 407-420 (1995).
-
(1995)
Genetics
, vol.139
, pp. 407-420
-
-
Carroll, B.J.1
-
43
-
-
56149096455
-
Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology
-
Cronn, R. et al. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res. 36, e122-e122 (2008).
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. e122-e122
-
-
Cronn, R.1
-
44
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh, K., Misawa, K., Kuma, K.-I. and Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059-3066 (2002).
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.-I.3
Miyata, T.4
-
45
-
-
84890330527
-
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0
-
Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30, 2725-2729 (2013).
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 2725-2729
-
-
Tamura, K.1
Stecher, G.2
Peterson, D.3
Filipski, A.4
Kumar, S.5
-
47
-
-
0031773680
-
MODELTEST: Testing the model of DNA substitution
-
Posada, D. and Crandall, K. A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818 (1998).
-
(1998)
Bioinformatics
, vol.14
, pp. 817-818
-
-
Posada, D.1
Crandall, K.A.2
-
48
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist, F. and Huelsenbeck, J. P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
49
-
-
84901305512
-
BEAST 2: A software platform for Bayesian evolutionary analysis
-
Bouckaert, R. et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 10, e1003537 (2014).
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003537
-
-
Bouckaert, R.1
-
50
-
-
0024712231
-
Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data
-
USA
-
Wolfe, K. H., Gouy, M., Yang, Y. W., Sharp, P. M. and Li, W. H. Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc. Natl. Acad. Sci. USA 86, 6201-6205 (1989).
-
(1989)
Proc. Natl. Acad. Sci.
, vol.86
, pp. 6201-6205
-
-
Wolfe, K.H.1
Gouy, M.2
Yang, Y.W.3
Sharp, P.M.4
Li, W.H.5
-
51
-
-
84871211911
-
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences
-
Liu, C. et al. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics 13, 715-715 (2012).
-
(2012)
BMC Genomics
, vol.13
, pp. 715-715
-
-
Liu, C.1
-
52
-
-
0012306021
-
Apollo: A sequence annotation editor
-
Lewis, S. E. et al. Apollo: a sequence annotation editor. Genome Biol. 3, 0082 (2002).
-
(2002)
Genome Biol.
, vol.3
, pp. 0082
-
-
Lewis, S.E.1
-
53
-
-
84883584463
-
OrganellarGenomeDRAW- A suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets
-
Lohse, M., Drechsel, O., Kahlau, S. and Bock, R. OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 41, W575-W581 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. W575-W581
-
-
Lohse, M.1
Drechsel, O.2
Kahlau, S.3
Bock, R.4
|