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Volumn 70, Issue 1, 2014, Pages 348-361

Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions

Author keywords

AA genome; Evolutionary history; Genome divergence; Oryza; Phylogenomics; Rapid recent speciation

Indexed keywords

MYA; ORYZA; ORYZA MERIDIONALIS; ORYZA PUNCTATA;

EID: 84887121031     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2013.10.008     Document Type: Article
Times cited : (35)

References (105)
  • 1
    • 0030954893 scopus 로고    scopus 로고
    • Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization
    • Aggarwal R., Brar D., Khush G. Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization. Mol. Gen. Genet. 1997, 254:1-12.
    • (1997) Mol. Gen. Genet. , vol.254 , pp. 1-12
    • Aggarwal, R.1    Brar, D.2    Khush, G.3
  • 2
    • 0032766702 scopus 로고    scopus 로고
    • Phylogenetic relationships among Oryza species revealed by AFLP markers
    • Aggarwal R., Brar D., Nandi S., Huang N., Khush G. Phylogenetic relationships among Oryza species revealed by AFLP markers. Theor. Appl. Genet. 1999, 98:1320-1328.
    • (1999) Theor. Appl. Genet. , vol.98 , pp. 1320-1328
    • Aggarwal, R.1    Brar, D.2    Nandi, S.3    Huang, N.4    Khush, G.5
  • 3
    • 30044435245 scopus 로고    scopus 로고
    • The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza
    • Ammiraju J.S., Luo M., Goicoechea J.L., Wang W., Kudrna D., Mueller C., Talag J., Kim H.R., Sisneros N.B., Blackmon B. The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res. 2006, 16:140-147.
    • (2006) Genome Res. , vol.16 , pp. 140-147
    • Ammiraju, J.S.1    Luo, M.2    Goicoechea, J.L.3    Wang, W.4    Kudrna, D.5    Mueller, C.6    Talag, J.7    Kim, H.R.8    Sisneros, N.B.9    Blackmon, B.10
  • 6
    • 0001001759 scopus 로고
    • Combination of data in phylogenetic analysis
    • Bandelt H. Combination of data in phylogenetic analysis. Plant Syst. Evol. 1995, 9(suppl):355-361.
    • (1995) Plant Syst. Evol. , vol.9 , Issue.SUPPL. , pp. 355-361
    • Bandelt, H.1
  • 8
    • 0000959922 scopus 로고
    • Phylogenetic relationships of annual and perennial wild rice: probing by direct DNA sequencing
    • Barbier P., Morishima H., Ishihama A. Phylogenetic relationships of annual and perennial wild rice: probing by direct DNA sequencing. Theor. Appl. Genet. 1991, 81:693-702.
    • (1991) Theor. Appl. Genet. , vol.81 , pp. 693-702
    • Barbier, P.1    Morishima, H.2    Ishihama, A.3
  • 9
    • 33847298027 scopus 로고    scopus 로고
    • Patterns in grass genome evolution
    • Bennetzen J.L. Patterns in grass genome evolution. Curr. Opin. Plant Biol. 2007, 10:176-181.
    • (2007) Curr. Opin. Plant Biol. , vol.10 , pp. 176-181
    • Bennetzen, J.L.1
  • 10
    • 20444491634 scopus 로고    scopus 로고
    • A review of long-branch attraction
    • Bergsten J. A review of long-branch attraction. Cladistics 2005, 21:163-193.
    • (2005) Cladistics , vol.21 , pp. 163-193
    • Bergsten, J.1
  • 12
    • 32944456727 scopus 로고    scopus 로고
    • Wide hybridization for rice improvements: alien gene transfer and molecular characterization of introgression
    • WARDA, Cote divoire, M.P. Jones, M. Dingkhun, D.E. Johnson, S.O. Fagade (Eds.)
    • Brar D., Khush G. Wide hybridization for rice improvements: alien gene transfer and molecular characterization of introgression. Interspecific Hybridization: Progress and Prospect 1997, 21-29. WARDA, Cote divoire. M.P. Jones, M. Dingkhun, D.E. Johnson, S.O. Fagade (Eds.).
    • (1997) Interspecific Hybridization: Progress and Prospect , pp. 21-29
    • Brar, D.1    Khush, G.2
  • 13
    • 34250389706 scopus 로고
    • 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 1976, 25:425-441.
    • (1976) Euphytica , vol.25 , pp. 425-441
    • Chang, T.T.1
  • 14
    • 0035130163 scopus 로고    scopus 로고
    • Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees
    • Chen F.C., Li W.H. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 2001, 68:444-456.
    • (2001) Am. J. Hum. Genet. , vol.68 , pp. 444-456
    • Chen, F.C.1    Li, W.H.2
  • 16
    • 0036814150 scopus 로고    scopus 로고
    • Evolutionary relationships among rice species with AA genome based on SINE insertion analysis
    • Cheng C., Tsuchimoto S., Ohtsubo H., Ohtsubo E. Evolutionary relationships among rice species with AA genome based on SINE insertion analysis. Genes. Genet. Syst. 2002, 77:323-334.
    • (2002) Genes. Genet. Syst. , vol.77 , pp. 323-334
    • Cheng, C.1    Tsuchimoto, S.2    Ohtsubo, H.3    Ohtsubo, E.4
  • 17
    • 33750909456 scopus 로고    scopus 로고
    • Chloroplast diversity and phylogeny in wild and cultivated rice (Oryza spp.)
    • Chuayjaeng S., Volkaert H. Chloroplast diversity and phylogeny in wild and cultivated rice (Oryza spp.). Kasetsart J. 2006, 40:306-313.
    • (2006) Kasetsart J. , vol.40 , pp. 306-313
    • Chuayjaeng, S.1    Volkaert, H.2
  • 18
    • 0141853996 scopus 로고    scopus 로고
    • Asymmetric sequence divergence of duplicate genes
    • Conant G.C., Wagner A. Asymmetric sequence divergence of duplicate genes. Genome Res. 2003, 13:2052-2058.
    • (2003) Genome Res. , vol.13 , pp. 2052-2058
    • Conant, G.C.1    Wagner, A.2
  • 21
    • 27844438226 scopus 로고    scopus 로고
    • Genome-scale evidence of the nematode-arthropod clade
    • Dopazo H., Dopazo J. Genome-scale evidence of the nematode-arthropod clade. Genome Biol. 2005, 6:R41.
    • (2005) Genome Biol. , vol.6
    • Dopazo, H.1    Dopazo, J.2
  • 22
    • 0002594984 scopus 로고
    • A rapid DNA isolation procedure for small quantities of fresh leaf tissue
    • Doyle J.J., Doyle J.L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 1987, 19:11-15.
    • (1987) Phytochem. Bull. , vol.19 , pp. 11-15
    • Doyle, J.J.1    Doyle, J.L.2
  • 23
    • 33847117718 scopus 로고    scopus 로고
    • Phylogenetic analysis of AA-genome Oryza species (Poaceae) based on chloroplast, mitochondrial, and nuclear DNA sequences
    • Duan S., Lu B., Li Z., Tong J., Kong J., Yao W., Li S., Zhu Y. Phylogenetic analysis of AA-genome Oryza species (Poaceae) based on chloroplast, mitochondrial, and nuclear DNA sequences. Biochem. Genet. 2007, 45:113-129.
    • (2007) Biochem. Genet. , vol.45 , pp. 113-129
    • Duan, S.1    Lu, B.2    Li, Z.3    Tong, J.4    Kong, J.5    Yao, W.6    Li, S.7    Zhu, Y.8
  • 25
    • 0035527390 scopus 로고    scopus 로고
    • Phylogeny of Saxifragales (angiosperms, eudicots): analysis of a rapid, ancient radiation
    • Fishbein M., Hibsch-Jetter C., Soltis D.E., Hufford L. Phylogeny of Saxifragales (angiosperms, eudicots): analysis of a rapid, ancient radiation. Syst. Biol. 2001, 50:817-847.
    • (2001) Syst. Biol. , vol.50 , pp. 817-847
    • Fishbein, M.1    Hibsch-Jetter, C.2    Soltis, D.E.3    Hufford, L.4
  • 26
    • 8844244033 scopus 로고    scopus 로고
    • Very low gene duplication rate in the yeast genome
    • Gao L., Innan H. Very low gene duplication rate in the yeast genome. Science 2004, 306:1367-1370.
    • (2004) Science , vol.306 , pp. 1367-1370
    • Gao, L.1    Innan, H.2
  • 27
    • 2442657861 scopus 로고    scopus 로고
    • Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences
    • Gao L., McCarthy E., Ganko E., McDonald J. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genom. 2004, 5:18.
    • (2004) BMC Genom. , vol.5 , pp. 18
    • Gao, L.1    McCarthy, E.2    Ganko, E.3    McDonald, J.4
  • 28
    • 0029812835 scopus 로고    scopus 로고
    • Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL
    • Gaut B.S., Morton B.R., McCaig B.C., Clegg M.T. Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl. Acad. Sci. USA 1996, 93:10274-10279.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 10274-10279
    • Gaut, B.S.1    Morton, B.R.2    McCaig, B.C.3    Clegg, M.T.4
  • 29
    • 0033452726 scopus 로고    scopus 로고
    • Phylogeny of rice genomes with emphasis on origins of allotetraploid species
    • Ge S., Sang T., Lu B.R., Hong D.Y. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc. Natl. Acad. Sci. USA 1999, 96:14400-14405.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 14400-14405
    • Ge, S.1    Sang, T.2    Lu, B.R.3    Hong, D.Y.4
  • 32
    • 0035855865 scopus 로고    scopus 로고
    • Arthropod phylogeny based on eight molecular loci and morphology
    • Giribet G., Edgecombe G.D., Wheeler W.C. Arthropod phylogeny based on eight molecular loci and morphology. Nature 2001, 413:157-160.
    • (2001) Nature , vol.413 , pp. 157-160
    • Giribet, G.1    Edgecombe, G.D.2    Wheeler, W.C.3
  • 34
    • 23144433822 scopus 로고    scopus 로고
    • PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference
    • Guindon S., Lethiec F., Duroux P., Gascuel O. PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference. Nucl. Acids Res. 2005, 33(suppl 2):W557-W559.
    • (2005) Nucl. Acids Res. , vol.33 , Issue.SUPPL. 2
    • Guindon, S.1    Lethiec, F.2    Duroux, P.3    Gascuel, O.4
  • 35
    • 23944471581 scopus 로고    scopus 로고
    • Molecular phylogeny of Oryzeae (Poaceae) based on DNA sequences from chloroplast, mitochondrial, and nuclear genomes
    • Guo Y.L., Ge S. Molecular phylogeny of Oryzeae (Poaceae) based on DNA sequences from chloroplast, mitochondrial, and nuclear genomes. Am. J. Bot. 2005, 92:1548-1558.
    • (2005) Am. J. Bot. , vol.92 , pp. 1548-1558
    • Guo, Y.L.1    Ge, S.2
  • 37
    • 21144444309 scopus 로고    scopus 로고
    • Consensus networks: a method for visualising incompatibilities in collections of trees
    • Springer-Verlag, New York, G. Benson, R. Page (Eds.)
    • Holland B., Moulton V. Consensus networks: a method for visualising incompatibilities in collections of trees. Algorithms in Bioinformatics 2003, 165-176. Springer-Verlag, New York. G. Benson, R. Page (Eds.).
    • (2003) Algorithms in Bioinformatics , pp. 165-176
    • Holland, B.1    Moulton, V.2
  • 38
    • 3042637206 scopus 로고    scopus 로고
    • Using consensus networks to visualize contradictory evidence for species phylogeny
    • Holland B.R., Huber K.T., Moulton V., Lockhart P.J. Using consensus networks to visualize contradictory evidence for species phylogeny. Mol. Biol. Evol. 2004, 21:1459-1461.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1459-1461
    • Holland, B.R.1    Huber, K.T.2    Moulton, V.3    Lockhart, P.J.4
  • 39
    • 55549123888 scopus 로고    scopus 로고
    • Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice
    • Huang X., Lu G., Zhao Q., Liu X., Han B. Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice. Plant Physiol. 2008, 148:25-40.
    • (2008) Plant Physiol. , vol.148 , pp. 25-40
    • Huang, X.1    Lu, G.2    Zhao, Q.3    Liu, X.4    Han, B.5
  • 40
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23:254-267.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2
  • 41
    • 0035855871 scopus 로고    scopus 로고
    • Mitochondrial protein phylogeny joins myriapods with chelicerates
    • Hwang U.W., Friedrich M., Tautz D., Park C.J., Kim W. Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature 2001, 413:154-157.
    • (2001) Nature , vol.413 , pp. 154-157
    • Hwang, U.W.1    Friedrich, M.2    Tautz, D.3    Park, C.J.4    Kim, W.5
  • 42
    • 84907150192 scopus 로고    scopus 로고
    • International Rice Genome Sequencing Project
    • The map-based sequence of the rice genome. Nature 436, 793-800.
    • International Rice Genome Sequencing Project, 2005. The map-based sequence of the rice genome. Nature 436, 793-800.
    • (2005)
  • 43
    • 0029997149 scopus 로고    scopus 로고
    • Phylogenetic relationships in A-genome species of rice as revealed by RAPD analysis
    • Ishii T., Nakano T., Maeda H., Kamijima O. Phylogenetic relationships in A-genome species of rice as revealed by RAPD analysis. Genes. Genet. Syst. 1996, 71:195-210.
    • (1996) Genes. Genet. Syst. , vol.71 , pp. 195-210
    • Ishii, T.1    Nakano, T.2    Maeda, H.3    Kamijima, O.4
  • 44
    • 0034886886 scopus 로고    scopus 로고
    • Nuclear-and chloroplast-microsatellite variation in A-genome species of rice
    • Ishii T., Xu Y., McCouch S. Nuclear-and chloroplast-microsatellite variation in A-genome species of rice. Genome 2001, 44:658-666.
    • (2001) Genome , vol.44 , pp. 658-666
    • Ishii, T.1    Xu, Y.2    McCouch, S.3
  • 45
    • 0033059511 scopus 로고    scopus 로고
    • 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., Higo K. P-SINE1-like intron of the CatA catalase homologs and phylogenetic relationships among AA-genome Oryza and related species. Theor. Appl. Genet. 1999, 98:853-861.
    • (1999) Theor. Appl. Genet. , vol.98 , pp. 853-861
    • Iwamoto, M.1    Nagashima, H.2    Nagamine, T.3    Higo, H.4    Higo, K.5
  • 46
    • 50249151865 scopus 로고    scopus 로고
    • Nuclear and cpDNA sequences combined provide strong inference of higher phylogenetic relationships in the phlox family (Polemoniaceae)
    • Johnson L.A., Chan L.M., Weese T.L., Busby L.D., McMurry S. Nuclear and cpDNA sequences combined provide strong inference of higher phylogenetic relationships in the phlox family (Polemoniaceae). Mol. Phylogenet. Evol. 2008, 48:997-1012.
    • (2008) Mol. Phylogenet. Evol. , vol.48 , pp. 997-1012
    • Johnson, L.A.1    Chan, L.M.2    Weese, T.L.3    Busby, L.D.4    McMurry, S.5
  • 47
    • 0031799253 scopus 로고    scopus 로고
    • Taxonomic status of Oryza glumaepatula Steud. I. Comparative morphological studies of New World diploids and Asian AA genome species
    • Juliano A.B., Naredo M.E.B., Jackson M. Taxonomic status of Oryza glumaepatula Steud. I. Comparative morphological studies of New World diploids and Asian AA genome species. Genet. Resour. Crop Evol. 1998, 45:197-203.
    • (1998) Genet. Resour. Crop Evol. , vol.45 , pp. 197-203
    • Juliano, A.B.1    Naredo, M.E.B.2    Jackson, M.3
  • 49
    • 33645816587 scopus 로고    scopus 로고
    • Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
    • Keane T., Creevey C., Pentony M., Naughton T., Mclnerney J. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Biol. Evol. 2006, 6:29.
    • (2006) BMC Biol. Evol. , vol.6 , pp. 29
    • Keane, T.1    Creevey, C.2    Pentony, M.3    Naughton, T.4    Mclnerney, J.5
  • 50
    • 25144453704 scopus 로고    scopus 로고
    • Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks
    • Kennedy M., Holland B.R., Gray R.D., Spencer H.G. Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks. Syst. Biol. 2005, 54:620-633.
    • (2005) Syst. Biol. , vol.54 , pp. 620-633
    • Kennedy, M.1    Holland, B.R.2    Gray, R.D.3    Spencer, H.G.4
  • 51
    • 0031239092 scopus 로고    scopus 로고
    • Origin, dispersal, cultivation and variation of rice
    • Khush G.S. Origin, dispersal, cultivation and variation of rice. Plant Mol. Biol. 1997, 35:25-34.
    • (1997) Plant Mol. Biol. , vol.35 , pp. 25-34
    • Khush, G.S.1
  • 52
    • 0036804525 scopus 로고    scopus 로고
    • Phylogeny of the oriental Drosophila melanogaster species group: a multilocus reconstruction
    • Kopp A., True J.R. Phylogeny of the oriental Drosophila melanogaster species group: a multilocus reconstruction. Syst. Biol. 2002, 51:786-805.
    • (2002) Syst. Biol. , vol.51 , pp. 786-805
    • Kopp, A.1    True, J.R.2
  • 53
    • 2442562566 scopus 로고    scopus 로고
    • Phylogeny of Panax using chloroplast trnC-trnD intergenic region and the utility of trnC-trnD in interspecific studies of plants
    • Lee C., Wen J. Phylogeny of Panax using chloroplast trnC-trnD intergenic region and the utility of trnC-trnD in interspecific studies of plants. Mol. Phylogenet. Evol. 2004, 31:894-903.
    • (2004) Mol. Phylogenet. Evol. , vol.31 , pp. 894-903
    • Lee, C.1    Wen, J.2
  • 54
    • 0007411173 scopus 로고    scopus 로고
    • Preliminary studies on taxonomy and biosystematics of the AA genome Oryza species (Poaceae)
    • CSIRO, Melbourne, S.W.L. Jacobs (Ed.)
    • Lu B.R., Naredo M.E.B., Juliano A.B., Jackson M.T. Preliminary studies on taxonomy and biosystematics of the AA genome Oryza species (Poaceae). Grasses: Systematics and Evolution 2000, 51-58. CSIRO, Melbourne. S.W.L. Jacobs (Ed.).
    • (2000) Grasses: Systematics and Evolution , pp. 51-58
    • Lu, B.R.1    Naredo, M.E.B.2    Juliano, A.B.3    Jackson, M.T.4
  • 56
    • 4344616881 scopus 로고    scopus 로고
    • Rapid recent growth and divergence of rice nuclear genomes
    • Ma J., Bennetzen J.L. Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl. Acad. Sci. USA 2004, 101:12404-12410.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 12404-12410
    • Ma, J.1    Bennetzen, J.L.2
  • 57
    • 0030311441 scopus 로고    scopus 로고
    • Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae)
    • Mason-Gamer R.J., Kellogg E.A. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst. Biol. 1996, 45:524-545.
    • (1996) Syst. Biol. , vol.45 , pp. 524-545
    • Mason-Gamer, R.J.1    Kellogg, E.A.2
  • 58
    • 0031796608 scopus 로고    scopus 로고
    • Granule-bound starch synthase: structure, function, and phylogenetic utility
    • Mason-Gamer R.J., Weil C.F., Kellogg E.A. Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol. Biol. Evol. 1998, 15:1658-1673.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 1658-1673
    • Mason-Gamer, R.J.1    Weil, C.F.2    Kellogg, E.A.3
  • 59
    • 0027073866 scopus 로고
    • Evolutionary studies in cultivated rice and its wild relatives
    • Morishima H., Sano Y., Oka H.I. Evolutionary studies in cultivated rice and its wild relatives. Oxford Surveys Evol. Biol. 1992, 8:135-184.
    • (1992) Oxford Surveys Evol. Biol. , vol.8 , pp. 135-184
    • Morishima, H.1    Sano, Y.2    Oka, H.I.3
  • 60
    • 77951586581 scopus 로고    scopus 로고
    • Using data-display networks for exploratory data analysis in phylogenetic studies
    • Morrison D.A. Using data-display networks for exploratory data analysis in phylogenetic studies. Mol. Biol. Evol. 2010, 27:1044-1057.
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 1044-1057
    • Morrison, D.A.1
  • 61
    • 22944482184 scopus 로고    scopus 로고
    • SeqState: primer design and sequence statistics for phylogenetic DNA datasets
    • Muller K. SeqState: primer design and sequence statistics for phylogenetic DNA datasets. Appl. Bioinform. 2005, 4:65-69.
    • (2005) Appl. Bioinform. , vol.4 , pp. 65-69
    • Muller, K.1
  • 62
    • 0031747451 scopus 로고    scopus 로고
    • Taxonomic status of Oryza glumaepatula Steud. II. Hybridization between New World diploids and AA genome species from Asia and Australia
    • Naredo M.E.B., Juliano A.B., Lu B.R., Jackson M.T. Taxonomic status of Oryza glumaepatula Steud. II. Hybridization between New World diploids and AA genome species from Asia and Australia. Genet. Resour. Crop Evol. 1998, 45:205-214.
    • (1998) Genet. Resour. Crop Evol. , vol.45 , pp. 205-214
    • Naredo, M.E.B.1    Juliano, A.B.2    Lu, B.R.3    Jackson, M.T.4
  • 63
    • 0001231343 scopus 로고
    • Origin and cytogenetics of rice
    • Nayar N. Origin and cytogenetics of rice. Adv. Genet. 1973, 17:153-292.
    • (1973) Adv. Genet. , vol.17 , pp. 153-292
    • Nayar, N.1
  • 64
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • Nei M., Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 1986, 3:418-426.
    • (1986) Mol. Biol. Evol. , vol.3 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 65
    • 39749188544 scopus 로고    scopus 로고
    • Rooting the eutherian tree: the power and pitfalls of phylogenomics
    • Nishihara H., Okada N., Hasegawa M. Rooting the eutherian tree: the power and pitfalls of phylogenomics. Genome Biol. 2007, 8:R199.
    • (2007) Genome Biol. , vol.8
    • Nishihara, H.1    Okada, N.2    Hasegawa, M.3
  • 67
    • 0042208126 scopus 로고    scopus 로고
    • Genetic variations of AA genome Oryza species measured by MITE-AFLP
    • Park K., Kim N., Cho Y., Kang K., Lee J., Kim N.S. Genetic variations of AA genome Oryza species measured by MITE-AFLP. Theor. Appl. Genet. 2003, 107:203-209.
    • (2003) Theor. Appl. Genet. , vol.107 , pp. 203-209
    • Park, K.1    Kim, N.2    Cho, Y.3    Kang, K.4    Lee, J.5    Kim, N.S.6
  • 68
    • 33745591114 scopus 로고    scopus 로고
    • Genetic evidence for complex speciation of humans and chimpanzees
    • Patterson N., Richter D.J., Gnerre S., Lander E.S., Reich D. Genetic evidence for complex speciation of humans and chimpanzees. Nature 2006, 441:1103-1108.
    • (2006) Nature , vol.441 , pp. 1103-1108
    • Patterson, N.1    Richter, D.J.2    Gnerre, S.3    Lander, E.S.4    Reich, D.5
  • 69
    • 33749392949 scopus 로고    scopus 로고
    • Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis , a wild relative of rice
    • Piegu B., Guyot R., Picault N., Roulin A., Saniyal A., Kim H., Collura K., Brar D.S., Jackson S., Wing R.A. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis , a wild relative of rice. Genome Res. 2006, 16:1262-1269.
    • (2006) Genome Res. , vol.16 , pp. 1262-1269
    • Piegu, B.1    Guyot, R.2    Picault, N.3    Roulin, A.4    Saniyal, A.5    Kim, H.6    Collura, K.7    Brar, D.S.8    Jackson, S.9    Wing, R.A.10
  • 70
    • 33746272317 scopus 로고    scopus 로고
    • HyPhy: hypothesis testing using phylogenies
    • Pond S.L.K., Muse S.V. HyPhy: hypothesis testing using phylogenies. Stat. Methods Mol. Evol. 2005, 21:125-181.
    • (2005) Stat. Methods Mol. Evol. , vol.21 , pp. 125-181
    • Pond, S.L.K.1    Muse, S.V.2
  • 71
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest: testing the model of DNA substitution
    • Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 73
    • 38849160068 scopus 로고    scopus 로고
    • Accurate gene-tree reconstruction by learning gene-and species-specific substitution rates across multiple complete genomes
    • Rasmussen M.D., Kellis M. Accurate gene-tree reconstruction by learning gene-and species-specific substitution rates across multiple complete genomes. Genome Res. 2007, 17:1932-1942.
    • (2007) Genome Res. , vol.17 , pp. 1932-1942
    • Rasmussen, M.D.1    Kellis, M.2
  • 74
    • 0346038786 scopus 로고    scopus 로고
    • A comparative study of genetic relationships among the AA-genome Oryza species using RAPD and SSR markers
    • Ren F., Lu B.R., Li S., Huang J., Zhu Y. A comparative study of genetic relationships among the AA-genome Oryza species using RAPD and SSR markers. Theor. Appl. Genet. 2003, 108:113-120.
    • (2003) Theor. Appl. Genet. , vol.108 , pp. 113-120
    • Ren, F.1    Lu, B.R.2    Li, S.3    Huang, J.4    Zhu, Y.5
  • 75
  • 76
    • 0042313795 scopus 로고    scopus 로고
    • Conflicting phylogenetic signals at the base of the metazoan tree
    • Rokas A., King N., Finnerty J., Carroll S.B. Conflicting phylogenetic signals at the base of the metazoan tree. Evol. Dev. 2003, 5:346-359.
    • (2003) Evol. Dev. , vol.5 , pp. 346-359
    • Rokas, A.1    King, N.2    Finnerty, J.3    Carroll, S.B.4
  • 77
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • Rokas A., Williams B.L., King N., Carroll S.B. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425:798-804.
    • (2003) Nature , vol.425 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 78
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 79
    • 68549085151 scopus 로고    scopus 로고
    • Genome-wide analysis of conservation and divergence of microsatellites in rice
    • Roorkiwal M., Grover A., Sharma P.C. Genome-wide analysis of conservation and divergence of microsatellites in rice. Mol. Genet. Genomics 2009, 282:205-215.
    • (2009) Mol. Genet. Genomics , vol.282 , pp. 205-215
    • Roorkiwal, M.1    Grover, A.2    Sharma, P.C.3
  • 80
    • 0036926048 scopus 로고    scopus 로고
    • Troubleshooting molecular phylogenetic analyses
    • Sanderson M.J., Shaffer H.B. Troubleshooting molecular phylogenetic analyses. Annu. Rev. Ecol. Syst. 2002, 33:49-72.
    • (2002) Annu. Rev. Ecol. Syst. , vol.33 , pp. 49-72
    • Sanderson, M.J.1    Shaffer, H.B.2
  • 81
    • 0000809084 scopus 로고
    • Molecular markers in rice systematics and the evaluation of genetic resources
    • Springer, New York, Y.P.S. Bajaj (Ed.)
    • Second G. Molecular markers in rice systematics and the evaluation of genetic resources. Biotechnology in Agriculture and Forestry 1991, 468-494. Springer, New York. Y.P.S. Bajaj (Ed.).
    • (1991) Biotechnology in Agriculture and Forestry , pp. 468-494
    • Second, G.1
  • 82
    • 0030733827 scopus 로고    scopus 로고
    • Congruence and consensus in the cotton tribe (Malvaceae)
    • Seelanan T., Schnabel A., Wendel J.F. Congruence and consensus in the cotton tribe (Malvaceae). Syst. Bot. 1997, 22:259-290.
    • (1997) Syst. Bot. , vol.22 , pp. 259-290
    • Seelanan, T.1    Schnabel, A.2    Wendel, J.F.3
  • 83
    • 0037002267 scopus 로고    scopus 로고
    • Rice as a model for comparative genomics of plants
    • Shimamoto K., Kyozuka J. Rice as a model for comparative genomics of plants. Annu. Rev. Plant Biol. 2002, 53:399-419.
    • (2002) Annu. Rev. Plant Biol. , vol.53 , pp. 399-419
    • Shimamoto, K.1    Kyozuka, J.2
  • 84
    • 0034350427 scopus 로고    scopus 로고
    • Gaps as characters in sequence-based phylogenetic analyses
    • Simmons M.P., Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 2000, 49:369-381.
    • (2000) Syst. Biol. , vol.49 , pp. 369-381
    • Simmons, M.P.1    Ochoterena, H.2
  • 85
    • 0013055350 scopus 로고
    • Incompatibility barriers operating in crosses of Oryza sativa with related species and genera
    • Plenum, New York, J.P. Gustafon (Ed.)
    • Sitch L.A. Incompatibility barriers operating in crosses of Oryza sativa with related species and genera. Gene Manipulation in Plant Improvement II 1990, 77-93. Plenum, New York. J.P. Gustafon (Ed.).
    • (1990) Gene Manipulation in Plant Improvement II , pp. 77-93
    • Sitch, L.A.1
  • 86
    • 0001957537 scopus 로고
    • Crossability of wild Oryza species and their potential use for improvement of cultivated rice
    • Sitch L., Dalmacio R., Romero G. Crossability of wild Oryza species and their potential use for improvement of cultivated rice. Rice Genet. Newsl. 1989, 6:56-60.
    • (1989) Rice Genet. Newsl. , vol.6 , pp. 56-60
    • Sitch, L.1    Dalmacio, R.2    Romero, G.3
  • 87
    • 0038781903 scopus 로고    scopus 로고
    • Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes
    • Subramanian S., Kumar S. Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res. 2003, 13:838-844.
    • (2003) Genome Res. , vol.13 , pp. 838-844
    • Subramanian, S.1    Kumar, S.2
  • 88
    • 84888201675 scopus 로고    scopus 로고
    • PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods), Version 4. Sinauer Associates, Sunderland (MA).
    • Swofford, D.L., 2003. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods), Version 4. Sinauer Associates, Sunderland (MA).
    • (2003)
    • Swofford, D.L.1
  • 89
    • 0027453388 scopus 로고
    • Simple methods for testing the molecular evolutionary clock hypothesis
    • Tajima F. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 1993, 135:599-607.
    • (1993) Genetics , vol.135 , pp. 599-607
    • Tajima, F.1
  • 90
    • 3242743113 scopus 로고    scopus 로고
    • The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of forty-four nuclear genes
    • Takezaki N., Figueroa F., Zaleska-Rutczynska Z., Takahata N., Klein J. The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of forty-four nuclear genes. Mol. Biol. Evol. 2004, 21:1512-1524.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1512-1524
    • Takezaki, N.1    Figueroa, F.2    Zaleska-Rutczynska, Z.3    Takahata, N.4    Klein, J.5
  • 91
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0
    • Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 92
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 1997, 25:4876-4882.
    • (1997) Nucl. Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 95
    • 0032805794 scopus 로고    scopus 로고
    • Polytomies and the power of phylogenetic inference
    • Walsh H., Kidd M., Moum T., Friesen V. Polytomies and the power of phylogenetic inference. Evolution 1999, 53:932-937.
    • (1999) Evolution , vol.53 , pp. 932-937
    • Walsh, H.1    Kidd, M.2    Moum, T.3    Friesen, V.4
  • 96
    • 34249840289 scopus 로고
    • Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs
    • Wang Z., Second G., Tanksley S. Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs. Theor. Appl. Genet. 1992, 83:565-581.
    • (1992) Theor. Appl. Genet. , vol.83 , pp. 565-581
    • Wang, Z.1    Second, G.2    Tanksley, S.3
  • 97
    • 0000162362 scopus 로고    scopus 로고
    • Phylogenetic incongruence: window into genome history and molecular evolution
    • Kluwer, Dordrecht, D.E. Soltis, P.S. Soltis, J.J. Doyle (Eds.)
    • Wendel J.F., Doyle J.J. Phylogenetic incongruence: window into genome history and molecular evolution. Molecular Systematics of Plants II DNA Sequencing 1998, 265-296. Kluwer, Dordrecht. D.E. Soltis, P.S. Soltis, J.J. Doyle (Eds.).
    • (1998) Molecular Systematics of Plants II DNA Sequencing , pp. 265-296
    • Wendel, J.F.1    Doyle, J.J.2
  • 100
    • 28944442228 scopus 로고    scopus 로고
    • How much data are needed to resolve a difficult phylogeny? Case study in Lamiales
    • Wortley A.H., Rudall P.J., Harris D.J., Scotland R.W. How much data are needed to resolve a difficult phylogeny? Case study in Lamiales. Syst. Biol. 2005, 54:697-709.
    • (2005) Syst. Biol. , vol.54 , pp. 697-709
    • Wortley, A.H.1    Rudall, P.J.2    Harris, D.J.3    Scotland, R.W.4
  • 101
    • 0034848170 scopus 로고    scopus 로고
    • DAMBE: software package for data analysis in molecular biology and evolution
    • Xia X., Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 2001, 92:371-373.
    • (2001) J. Hered. , vol.92 , pp. 371-373
    • Xia, X.1    Xie, Z.2
  • 103
    • 34250167927 scopus 로고    scopus 로고
    • New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification
    • Zhang S., Gu Y.Q., Singh J., Coleman-Derr D., Brar D.S., Jiang N., Lemaux P.G. New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification. Plant Mol. Biol. 2007, 64:589-600.
    • (2007) Plant Mol. Biol. , vol.64 , pp. 589-600
    • Zhang, S.1    Gu, Y.Q.2    Singh, J.3    Coleman-Derr, D.4    Brar, D.S.5    Jiang, N.6    Lemaux, P.G.7
  • 104
    • 21244501403 scopus 로고    scopus 로고
    • Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes
    • Zhu Q., Ge S. Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol. 2005, 167:249-265.
    • (2005) New Phytol. , vol.167 , pp. 249-265
    • Zhu, Q.1    Ge, S.2


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