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Whole Genome Sequencing: Methodology and Progress in Cereals

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References

  • Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., et al. The genome sequence of Drosophila melanogaster. Science 2000; 287:2185–2195

    Article  PubMed  Google Scholar 

  • Adams M.D., Kelley J.M., Gocayne J.D., Dubnick M., Polymeropoulos M.H., Xiao H., Merril C.R., Wu A., Olde B., Moreno R.F., et al. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 1991; 252: 1651–1656

    CAS  PubMed  Google Scholar 

  • Ahn S.N., Tanksley S.D. Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 1993, 90: 7980–7984

    CAS  PubMed  Google Scholar 

  • Anderson S., Bankier A.T., Barrell B.G., de Bruijn B.H., Coulson A.R., Drouin J., Eperon I.C., Nierlich D.P., Roe B.B., Sanger F., et al. Sequence and organization of the human mitochondrial genome. Nature 1981; 290: 457–465

    CAS  PubMed  Google Scholar 

  • Aparicio S., Chapman J., Stupka E., Putnam N., Chia J.M., Dehal P., Christoffels A., Rash S., Hoon S., Smit A., et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 2000; 297: 1301–1310

    Google Scholar 

  • Barry G.F.. The use of the Monsanto draft rice genome sequence in research. Plant Physiol 2001; 125: 1164–1165.

    Article  CAS  PubMed  Google Scholar 

  • Batzoglou S., Berger B., Mesirov J., Lander E.S. Sequencing a genome by walking with clone end sequences: a mathematical analysis. Genome Res 1999; 9: 1163–1174

    Article  CAS  PubMed  Google Scholar 

  • Batzoglou S., Jaffe D.B., Stanley K., Butler J., Gnerre S., Mauceli E., Berger B., Mesirov J.P., Lander E.S. ARACHNE: a whole-genome shotgun assembler. Genome Res 200212: 177–189

    Article  CAS  PubMed  Google Scholar 

  • Bennetzen J.L., Schrick K., Springer P.S., Brown W.E., SanMiguel P. Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome 1994; 37: 565–576

    CAS  PubMed  Google Scholar 

  • Burke D.T., Carle G.F., Olson M.V. Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 1987 236: 806–812

    CAS  PubMed  Google Scholar 

  • Causse M.A., Fulton T.M., Cho Y.G., Ahn S.N., Chungwongse J., Wu K., Xiao J., Yu Z., Ronald P.C., Harrington S.E., et al. Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 1994; 138: 1251–1274

    CAS  PubMed  Google Scholar 

  • Chen M., SanMiguel P., deOliveira A.C., Woo S.S., Zhang H., Wing R.A., Bennetzen J.L. Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc Natl Acad Sci USA 1997; 94: 3431–3435

    CAS  PubMed  Google Scholar 

  • Chen M., Presting G., Barbazuk W.B., Goicoechea J.L., Blackmon B., Fang G., Kim H., Frisch D., Yu Y., Sun S., et al. An integrated physical and genetic map of the rice genome. Plant Cell 2002; 14: 537–545

    PubMed  Google Scholar 

  • Cheng Z.K., Buell C.R., Wing R.A., Jiang J. Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chromosome Res 2002; 10: 379–387

    Article  CAS  PubMed  Google Scholar 

  • Christoffels A., van Gelder A., Greyling G., Miller R., Hide T., Hide W. STACK: Sequence Tag Alignment and Consensus Knowledgebase. Nucl Acids Res 2001; 29: 234–238

    Article  CAS  PubMed  Google Scholar 

  • Collins J., Hohn B. Cosmids: a type of plasmid gene-cloning vector that is packageable in vitro in bacteriophage lambda heads. Proc Natl Acad Sci USA 1978; 75: 4242–4246

    CAS  PubMed  Google Scholar 

  • Coulson A., Sulston J., Brenner S., Karn J. Towards a physical map of the genome of the nematode C. elegans. Proc Natl Acad Sci USA 1986; 83: 7821–7825

    CAS  Google Scholar 

  • Devos K.M., Chao S., Li Q.Y., Simonetti M.C., Gale M.D. Relationship between chromosome 9 of maize and wheat homeologous group 7 chromosomes. Genetics 1994; 138: 1287–1292

    CAS  PubMed  Google Scholar 

  • Devos K.M., Wang Z.M., Beales J., Sasaki Y., Gale M.D. Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa). Theor Appl Genet 1998; 96: 63–68

    Article  CAS  Google Scholar 

  • Ding Y., Johnson M.D., Chen W.Q., Wong D., Chen Y.J., Benson S.C., Lam J.Y., Kim Y.M., Shizuya H. Five-color-based high-information-content fingerprinting of bacterial artificial chromosome clones using type IIS restriction endonucleases. Genomics 2001; 74: 142–154

    Article  CAS  PubMed  Google Scholar 

  • Ewing B., Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998; 8: 186–194

    CAS  PubMed  Google Scholar 

  • Ewing B., Hillier L., Wendl M.C., Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998 8: 175–185

    CAS  PubMed  Google Scholar 

  • Feng Q., Zhang Y., Hao P., Wang S., Fu G., Huang Y., Li Y., Zhu J., Liu Y., Hu X., et al. Sequence and analysis of rice chromosome 4. Nature 2002; 420: 316–320

    Article  CAS  PubMed  Google Scholar 

  • Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F., Kerlavage A.R., Bult C.J., Tomb J.F., Dougherty B.A., Merrick J.M., et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995; 269: 496–512

    CAS  PubMed  Google Scholar 

  • Fransz P.F., Alonso-Blanco C., Liharska T.B., Peeters A.J., Zabel P., de Jong J.H.. High-resolution physical mapping in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres. Plant Jour 1996; 9: 421–430

    CAS  Google Scholar 

  • Fraser C.M., Gocayne J.D., White O., Adams M.D., Clayton R.A., Fleischmann R.D., Bult C.J., Kerlavage A.R., Sutton G., Kelley J.M. et al. The minimal gene complement of Mycoplasma genitalium. Science 1995; 270: 397–403

    CAS  PubMed  Google Scholar 

  • Gale M.D., Devos K.M. Comparative genetics in the grasses. Proc Natl Acad Sci USA 1998; 95: 1971–1974

    Article  CAS  PubMed  Google Scholar 

  • Gingeras T.R., Sciaky D., Gelinas R.E., Bing-Dong J., Yen C.E., Kelly M.M., Bullock P.A., Parsons B.L., O’Neill K.E., Roberts R.J.. Nucleotide sequences from the adenovirus-2 genome. Jour Biol Chem 1982; 257: 13475–13491

    CAS  Google Scholar 

  • Goff S.A., Ricke D., Lan T.H., Presting G., Wang R.L., Dunn M., Glazebrook J., Sessions A., Oeller P., Varma H., et al. A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 2002; 296: 92–100

    Article  CAS  PubMed  Google Scholar 

  • Goffeau A., Barrell B.G., Bussey H., Davis R.W., Dujon B., Feldmann H., Galibert F., Hoheisel J.D., Jacq C., Johnston M., et al. Life with 6000 genes. Science 1996; 274: 562–567

    Article  Google Scholar 

  • Gordon, D., Abajian C., Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998; 8: 195–202

    CAS  PubMed  Google Scholar 

  • Gordon D., Desmarais C., Green P. Automated finishing with autofinish. Genome Res 2001; 11: 614–625

    Article  CAS  PubMed  Google Scholar 

  • Green P. Against a whole-genome shotgun. Genome Res 1997; 7: 410–417

    CAS  PubMed  Google Scholar 

  • Green P. Documentation for phrap and cross_match (version 0.990319). 1999; http://bozeman.mbt.washington.edu/phrap.docs/phrap.html

  • Gregory S.G., Sekhon M., Schein J., Zhao S., Osoegawa K., Scott C.E., Evans R.S., Burridge P.W., Cox T.V., Fox C.A., et al. A physical map of the mouse genome. Nature 2002; 418: 743–750

    Article  CAS  PubMed  Google Scholar 

  • Guo H., Moose. S.P. Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell 2003; 15: 1143–1158

    CAS  PubMed  Google Scholar 

  • Harushima Y., Yano M., Shomura A., Sato M., Shimono T., Kuboki Y., Yamamoto T., Lin S.Y., Antonio B.A., Parco A. et al. A high density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 1998; 148: 479–494

    CAS  PubMed  Google Scholar 

  • Inada D.C., Bashir A., Lee C., Thomas B.C., Ko C., Goff S.A., Freeling M. Conserved noncoding sequences in the grasses. Genome Res 2003; 13: 2030–2041

    Article  CAS  PubMed  Google Scholar 

  • Ioannou P.A., Amemiya C.T., Garnes J., Kroisel P.M., Shizuya H., Chen C., Batzer M.A., de Jong P.J. A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nature Genet 1994; 6: 84–89

    CAS  PubMed  Google Scholar 

  • Jaffe, D.B., J. Butler, S. Gnerre, E. Mauceli, K. Lindblad-Toh, J.P. Mesirov, M.C. Zody, and E.S. Lander. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 2003; 13: 91–96

    Article  CAS  PubMed  Google Scholar 

  • Keller B., Feuillet C. Colinearity and gene density in grass genomes. Trends Plant Sci 2000; 5: 246–251

    Article  CAS  PubMed  Google Scholar 

  • Kikuchi S., Satoh K., Nagata T., Kawagashira N., Doi K., Kishimoto N., Yazaki J., Ishikawa M., Yamada H., Ooka H., et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 2003; 301:376–379

    Article  PubMed  Google Scholar 

  • Kurata, N., Moore, G., Nagamura, Y., Foote, T., Yano, M., Minobe, Y., and Gale, M. Conservation of genomic structure between rice and wheat. Bio/Technology 1994; 12: 276–278

    Article  CAS  Google Scholar 

  • Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., et al. Initial sequencing and analysis of the human genome. Nature 2001; 409:860–921

    Article  CAS  PubMed  Google Scholar 

  • Lander E.S., Waterman M.S. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 1988; 2: 231–239

    Article  CAS  PubMed  Google Scholar 

  • Leister D., Kurth J., Laurie D.A., Yano M., Sasaki T., Devos K., Graner A., Schulze-Lefert P. Rapid reorganization of resistance gene homologues in cereal genomes. Proc Nat Acad Sci USA 1998; 95: 370–375

    Article  CAS  PubMed  Google Scholar 

  • Luckey J.A., Drossman H., Kostichka A.J., Mead D.A., Cunha J. D.’, Norris T.B., Smith L.M.. 1990. High speed DNA sequencing by capillary electrophoresis. Nucl Acids Res 18: 4417–4421

    CAS  PubMed  Google Scholar 

  • Mahairas G.G., Wallace J.C., Smith K., Swartzell S., Holzman T., Keller A., Shaker R., Furlong J., Young J., Zhao S., et al. Sequence-tagged connectors: a sequence approach to mapping and scanning the human genome. Proc Natl Acad Sci USA 1999; 96: 9739–9744

    Article  CAS  PubMed  Google Scholar 

  • Mao L., Wood T.C., Yu Y., Budiman M.A., Tomkins J., Woo S., Sasinowski M., Presting G., Frisch D., Goff S., et al. Rice transposable elements: A survey of 73,000 sequence-tagged-connectors. Genome Res 2000; 7: 1072–1084

    Google Scholar 

  • Mardis E., McPherson J., Martienssen R., Wilson R.K., McCombie W.R. What is finished, and why does it matter. Genome Res 2002; 12: 669–671

    Article  CAS  PubMed  Google Scholar 

  • Marra M., Kucaba T., Sekhon M., Hillier L., Martienssen R., Chinwalla A., Crockett J., Fedele J., Grover H., Gund C., McCombie W.R., et al. 1999. A map for sequence analysis of the Arabidopsis thaliana genome. Nature Genet 22: 265–270

    Article  CAS  PubMed  Google Scholar 

  • McPherson J.D., Marra M., Hillier R.H., Waterston A., Chinwalla J., Wallis M., Sekhon K., Wylie E.R., Mardis R.K., Wilson R., et al. A physical map of the human genome. Nature 2001 409: 934–941

    Article  CAS  PubMed  Google Scholar 

  • Meyers B.C., Dickerman A.W., Michelmore R.W., Sivaramakrishnan S., Sobral B.W., Young N.D. Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant Jour 1999; 20: 317–332

    CAS  Google Scholar 

  • Monna L., Miyao A., Inoue T., Fukuoka S., Yamazaki M., Zhong H.S., Sasaki T., Minobe Y.. Determination of RAPD markers in rice and their conversion into sequence tagged sites (STSs) and STS-specific primers. DNA Res 1994; 1: 139–148

    Article  CAS  PubMed  Google Scholar 

  • Moore G., Devos K.M., Wang Z., Gale M.D. Grasses line up and form a circle. Curr Biol 1995; 5: 737–739

    CAS  PubMed  Google Scholar 

  • Mozo T., Dewar K., Dunn P., Ecker J.R., Fischer S., Kloska S., Lehrach H., Marra M., Martienssen R., Meier-Ewert S., Altmann T. A complete BAC-based physical map of the Arabidopsis thaliana genome. Nature Genet 1999 22: 271–275.

    CAS  PubMed  Google Scholar 

  • Mullikin J.C., Ning Z. The phusion assembler. Genome Res 2003; 13: 81–90

    Article  CAS  PubMed  Google Scholar 

  • Murray V. Improved double-stranded DNA sequencing using the linear polymerase chain reaction. Nucl Acids Res 1989; 17: 8889

    CAS  PubMed  Google Scholar 

  • Myers E.W., Sutton G.G., Delcher A.L., Dew I.M., Fasulo D.P., Flanigan M.J., Kravitz S.A., Mobarry C.M., Reinert K.H., Remington K.A., et al. A whole-genome assembly of Drosophila. Science 2000; 287: 2196–2204

    CAS  PubMed  Google Scholar 

  • Peterson D.G., Schulze S.R., Sciara E.B., Lee S.A., Bowers J.E., Nagel A., Jiang N., Tibbitts D.C., Wessler S.R., Paterson A.H. Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res 2002; 12: 795–807

    CAS  PubMed  Google Scholar 

  • Prober J.M., Trainor G.L., Dam R.J., Hobbs F.W., Robertson C.W., Zagursky R.J., Cocuzza A.J., Jensen M.A., Baumeister K. A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 1987; 238: 336–341

    CAS  PubMed  Google Scholar 

  • Quackenbush J., Cho J., Lee D., Liang F., Holt I., Karamycheva S., Parvizi B., Pertea G., Sultana R., White J. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucl Acids Res 2001; 29: 159–164

    Article  CAS  PubMed  Google Scholar 

  • Rabinowicz P.D., Schutz K., Dedhia N., Yordan C., Parnell L.D., Stein L., McCombie W.R., Martienssen R.A. Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nature Genet 1999; 23:305–308

    CAS  PubMed  Google Scholar 

  • Sakata K., Nagamura Y., Numa H., Antonio B.A., Nagasaki H., Idonuma A., Watanabe W., Shimizu Y., Horiuchi I., Matsumoto T., et al. RiceGAAS: an automated annotation system and database for rice genome sequence. Nucl Acids Res 2002; 30: 98–102

    Article  CAS  PubMed  Google Scholar 

  • Sanger F., Coulson A.R., Hong G.F., Hill D.F., Petersen G.B. Nucleotide sequence of bacteriophage lambda DNA. Jour Mol Biol 1982; 162: 729–773

    CAS  Google Scholar 

  • Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977; 74: 5463–5467

    CAS  PubMed  Google Scholar 

  • SanMiguel P., Gaut B.S., Tikhonov A., Nakajima Y., Bennetzen J.L. The paleontology of intergene retrotransposons of maize. Nature Genet 1998; 20: 43–45

    CAS  PubMed  Google Scholar 

  • Sasaki T., Burr B. International Rice Genome Sequencing Project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 2000; 3: 138–141

    Article  CAS  PubMed  Google Scholar 

  • Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y., Wu J., Niimura Y., Cheng Z., Nagamura Y., et al. The genome sequence and structure of rice chromosome 1. Nature 2002; 420: 312–316

    Article  CAS  PubMed  Google Scholar 

  • Shizuya H., Birren B., Kim U.J., Mancino V., Slepak T., Tachiiri Y., Simon M. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 1992; 89: 8794–8797

    CAS  PubMed  Google Scholar 

  • Siegel A.F., Trask B., Roach J.C., Mahairas G.G., Hood L., van den Engh G. Analysis of sequence-tagged-connector strategies for DNA sequencing. Genome Res 1999; 9: 297–307

    CAS  PubMed  Google Scholar 

  • Smith L.M., Sanders J.Z., Kaiser R.J., Hughes P., Dodd C., Connell C.R., Heiner C., Kent S.B., Hood L.E.. Fluorescence detection in automated DNA sequence analysis. Nature 1986; 321: 674–679

    CAS  PubMed  Google Scholar 

  • Smith T.F., Waterman M.S. Identification of common molecular subsequences. Jour Mol Biol 198; 1147: 195–197

    Google Scholar 

  • Soderlund C.S., Dunham H.A., French L. Contigs built with fingerprints, markers, and FPC V4.7. Genome Res 2000; 10: 1772–1787

    Article  CAS  PubMed  Google Scholar 

  • Strausberg R.L., Feingold E.A., Klausner R.D., Collins F.S. The mammalian gene collection. Science 1999; 286: 455–457

    Article  CAS  PubMed  Google Scholar 

  • Swerdlow H., Wu S.L., Harke H., Dovichi N.J.. Capillary gel electrophoresis for DNA sequencing. Laser-induced fluorescence detection with the sheath flow cuvette. Jour Chromatogr 1990; 516: 61–67

    CAS  Google Scholar 

  • TAGI, The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000; 408: 796–815

    Google Scholar 

  • The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 1998; 282: 2012–2018

    Google Scholar 

  • The Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, and PE Biosystems Arabidopsis Sequencing Consortium. 2000. The complete sequence of a heterochromatic island from a higher eukaryote. Cell 2000; 100: 377–386

    Google Scholar 

  • The Rice Chromosome 10 Sequencing Consortium: Yu Y., Rambo T., Currie J., Saski C., Kim H.R., Collura K., Thompson S., Simmons J., Yang T.-J., Nah G. et al. In-depth view of structure, activity, and evolution of rice chromosome 10. Science 2003; 300: 1566–1569

    CAS  Google Scholar 

  • Temnykh S., DeClerck G., Lukashova A., Lipovich L., Cartinhour S., McCouch S. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 2001; 11: 1441–1452

    Article  CAS  PubMed  Google Scholar 

  • Tikhonov A.P., SanMiguel P.J., Nakajima Y., Gorenstein N.M., Bennetzen J.L., Avramova Z. Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc Natl Acad Sci USA 1999; 96: 7409–7414

    Article  CAS  PubMed  Google Scholar 

  • Van Deynze A.E., Nelson J.C., Yglesias E.S., Harrington S.E., Braga D.P., McCouch S.R., Sorrells M.E. Comparative mapping in grasses. Wheat relationships. Mol Gen Genet 1995; 248: 744–754

    Article  PubMed  Google Scholar 

  • Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., et al. The sequence of the human genome. Science 2001; 291:1304–1351

    Article  CAS  PubMed  Google Scholar 

  • Venter J.C., Adams M.D., Sutton G.G., Kerlavage A.R., Smith H.O., Hunkapiller M. Shotgun sequencing of the human genome. Science 1998; 280: 1540–1542

    Article  CAS  PubMed  Google Scholar 

  • Venter J.C., Smith H.O., Hood L. A new strategy for genome sequencing. Nature 1996; 381: 364–366

    Article  CAS  PubMed  Google Scholar 

  • Wang J., Wong G.K., Ni P., Han Y., Huang X., Zhang J., Ye C., Zhang Y., Hu J., Zhang K., et al. RePS: a sequence assembler that masks exact repeats identified from the shotgun data. Genome Res 2002; 12: 824–831

    Article  CAS  PubMed  Google Scholar 

  • Waterston R.H., Lindblad-Toh K., Birney E., Rogers J., Abril J.F., Agarwal P., Agarwala R., Ainscough R., Alexandersson M., An P., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002; 420: 520–562

    CAS  PubMed  Google Scholar 

  • Ware D.H., Jaiswal P., Ni J., Yap I.V., Pan X., Clark K.Y., Teytelman L., Schmidt S.C., Zhao W., Chang K., et al. Gramene, a tool for grass genomics. Plant Physiol 2002; 130: 1606–1613

    Article  CAS  PubMed  Google Scholar 

  • Weber J.L., Myers E.W. Human whole-genome shotgun sequencing. Genome Res 1997; 7: 401–409

    CAS  PubMed  Google Scholar 

  • Woo S.S., Jiang J., Gill B.S., Paterson A.H., Wing R.A. Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucl Acids Res 1994; 22: 4922–4931

    CAS  PubMed  Google Scholar 

  • Yang T.J., Yu Y., Nah G., Atkins M., Lee S., Frisch D.A., Wing R.A. Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing. Theor Appl Genet 2003; 107: 652–60

    Article  CAS  PubMed  Google Scholar 

  • Yoshimura A., Ideta O., Iwata N. Linkage map of phenotype and RFLP markers in rice. Plant Mol Biol 1997; 35: 49–60

    Article  CAS  PubMed  Google Scholar 

  • Yu J., Hu S., Wang J., Wang G., Li S.G., Wong K.S.G., Liu B., Deng Y., Dai L., Zhou Y., Zhang X., et al. A draft sequence of the rice genome (Oryza sativa L. sspl. indica). Science 2002; 296:79–92

    CAS  PubMed  Google Scholar 

  • Yuan Q.P., Liang F., Hsiao J., Zismann V., Benito M.I., Quackenbush J., Wing R., Buell R. Anchoring of rice BAC clones to the rice genetic map in silico. Nucl Acids Res 2000; 28: 3636–3641

    Article  CAS  PubMed  Google Scholar 

  • Yuan, Y., SanMiguel P.J., Bennetzen J.L.. 2003. High-Cot sequence analysis of the maize genome. Plant Jour 34: 249–255.

    CAS  Google Scholar 

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Yu, Y., Wing, R.A. (2004). Whole Genome Sequencing: Methodology and Progress in Cereals. In: Gupta, P.K., Varshney, R.K. (eds) Cereal Genomics. Springer, Dordrecht. https://doi.org/10.1007/1-4020-2359-6_13

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