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2. Sequence-tagged connector/DNA fingerprint framework for rice genome sequencing

Author

Wing, R. A., primary, Yu, Yeisoo, additional, Presting, G., additional, Frisch, D., additional, Wood, T., additional, Woo, Sung-Sick, additional, Budiman, M. Arief, additional, Mao, Long, additional, Kim, Hye Ran, additional, Rambo, T., additional, Fang, E., additional, Blackmon, B., additional, Goicoechea, J. L., additional, Higingbottom, S., additional, Sasinowski, M., additional, Tomkins, J., additional, Dean, R. A., additional, Soderlund, C., additional, McCombie, W. R., additional, Martienssen, R., additional, de la Bastide, M., additional, Wilson, R., additional, and Johnson, D., additional

Published
2008
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4. Initial sequencing and analysis of the human genome

Author

Lander, ES, Linton, LM, Birren, B, Nusbaum, C, Zody, MC, Baldwin, J, Devon, K, Dewar, K, Doyle, M, FitzHugh, W, Funke, R, Gage, D, Harris, K, Heaford, A, Howland, J, Kann, L, Lehoczky, J, LeVine, R, McEwan, P, McKernan, K, Meldrim, J, Mesirov, JP, Miranda, C, Morris, W, Naylor, J, Raymond, C, Rosetti, M, Santos, R, Sheridan, A, Sougnez, C, Stange-Thomann, N, Stojanovic, N, Subramanian, A, Wyman, D, Rogers, J, Sulston, J, Ainscough, R, Beck, S, Bentley, D, Burton, J, Clee, C, Carter, N, Coulson, A, Deadman, R, Deloukas, P, Dunham, A, Dunham, I, Durbin, R, French, L, Grafham, D, Gregory, S, Hubbard, T, Humphray, S, Hunt, A, Jones, M, Lloyd, C, McMurray, A, Matthews, L, Mercer, S, Milne, S, Mullikin, JC, Mungall, A, Plumb, R, Ross, M, Shownkeen, R, Sims, S, Waterston, RH, Wilson, RK, Hillier, LW, McPherson, JD, Marra, MA, Mardis, ER, Fulton, LA, Chinwalla, AT, Pepin, KH, Gish, WR, Chissoe, SL, Wendl, MC, Delehaunty, KD, Miner, TL, Delehaunty, A, Kramer, JB, Cook, LL, Fulton, RS, Johnson, DL, Minx, PJ, Clifton, SW, Hawkins, T, Branscomb, E, Predki, P, Richardson, P, Wenning, S, Slezak, T, Doggett, N, Cheng, JF, Olsen, A, Lucas, S, Elkin, C, Uberbacher, E, Frazier, M, Gibbs, RA, Muzny, DM, Scherer, SE, Bouck, JB, Sodergren, EJ, Worley, KC, Rives, CM, Gorrell, JH, Metzker, ML, Naylor, SL, Kucherlapati, RS, Nelson, DL, Weinstock, GM, Sakaki, Y, Fujiyama, A, Hattori, M, Yada, T, Toyoda, A, Itoh, T, Kawagoe, C, Watanabe, H, Totoki, Y, Taylor, T, Weissenbach, J, Heilig, R, Saurin, W, Artiguenave, F, Brottier, P, Bruls, T, Pelletier, E, Robert, C, Wincker, P, Smith, DR, Doucette-Stamm, L, Rubenfield, M, Weinstock, K, Lee, HM, Dubois, J, Rosenthal, A, Platzer, M, Nyakatura, G, Taudien, S, Rump, A, Yang, H, Yu, J, Wang, J, Huang, G, Gu, J, Hood, L, Rowen, L, Madan, A, Qin, S, Davis, RW, Federspiel, NA, Abola, AP, Proctor, MJ, Myers, RM, Schmutz, J, Dickson, M, Grimwood, J, Cox, DR, Olson, MV, Kaul, R, Shimizu, N, Kawasaki, K, Minoshima, S, Evans, GA, Athanasiou, M, Schultz, R, Roe, BA, Chen, F, Pan, H, Ramser, J, Lehrach, H, Reinhardt, R, McCombie, WR, de la Bastide, M, Dedhia, N, Blöcker, H, Hornischer, K, Nordsiek, G, Agarwala, R, Aravind, L, Bailey, JA, Bateman, A, Batzoglou, S, Birney, E, Bork, P, Brown, DG, Burge, CB, Cerutti, L, Chen, HC, Church, D, Clamp, M, Copley, RR, Doerks, T, Eddy, SR, Eichler, EE, Furey, TS, Galagan, J, Gilbert, JG, Harmon, C, Hayashizaki, Y, Haussler, D, Hermjakob, H, Hokamp, K, Jang, W, Johnson, LS, Jones, TA, Kasif, S, Kaspryzk, A, Kennedy, S, Kent, WJ, Kitts, P, Koonin, EV, Korf, I, Kulp, D, Lancet, D, Lowe, TM, McLysaght, A, Mikkelsen, T, Moran, JV, Mulder, N, Pollara, VJ, Ponting, CP, Schuler, G, Schultz, J, Slater, G, Smit, AF, Stupka, E, Szustakowski, J, Thierry-Mieg, D, Thierry-Mieg, J, Wagner, L, Wallis, J, Wheeler, R, Williams, A, Wolf, YI, Wolfe, KH, Yang, SP, Yeh, RF, Collins, F, Guyer, MS, Peterson, J, Felsenfeld, A, Wetterstrand, KA, Patrinos, A, Morgan, MJ, de Jong, P, Catanese, JJ, Osoegawa, K, Shizuya, H, Choi, S, Chen, YJ, and Szustakowki, J

Subjects
Genetics, Cancer genome sequencing, Chimpanzee genome project, Multidisciplinary, Cancer Genome Project, Gene density, DNA sequencing theory, Hybrid genome assembly, Computational biology, Biology, Genome, Personal genomics
Abstract

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Published
2016
Full Text
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5. Initial sequencing and analysis of the human genome

Author

Univ Michigan, Sch Med, Dept Human Genet, Ann Arbor, MI 48109 USA, Univ Michigan, Sch Med, Dept Internal Med, Ann Arbor, MI 48109 USA, Whitehead Inst Biomed Res, Ctr Genome Res, Cambridge, MA 02142 USA, Sanger Ctr, Hinxton CB10 1RQ, Cambs, England, Washington Univ, Genome Sequencing Ctr, St Louis, MO 63108 USA, US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA, Baylor Coll Med, Human Genome Sequencing Ctr, Dept Mol & Human Genet, Houston, TX 77030 USA, Univ Texas, Hlth Sci Ctr, Dept Cellular & Struct Biol, San Antonio, TX 78229 USA, Yeshiva Univ Albert Einstein Coll Med, Dept Mol Genet, Bronx, NY 10461 USA, Univ Texas, Sch Med, Dept Microbiol & Mol Genet, Houston, TX 77225 USA, RIKEN, Genom Sci Ctr, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan, Genoscope, F-91057 Evry, France, CNRS, UMR 8030, F-91057 Evry, France, Genome Therapeut Corp, GTC Sequencing Ctr, Waltham, MA 02453 USA, Inst Mol Biotechnol, Dept Genome Anal, D-07745 Jena, Germany, Chinese Acad Sci, Inst Genet, Ctr Human Genome, Beijing Genom Inst, Beijing 100101, Peoples R China, So China Natl Human Genome Res Ctr, Shanghai 201203, Peoples R China, No China Natl Human Genome Res Ctr, Beijing 100176, Peoples R China, Inst Syst Biol, Multimegabase Sequencing Ctr, Seattle, WA 98105 USA, Stanford Genome Technol Ctr, Palo Alto, CA 94304 USA, Stanford Univ, Dept Genet, Sch Med, Stanford, CA 94305 USA, Stanford Univ, Stanford Human Genome Ctrr, Sch Med, Stanford, CA 94305 USA, Univ Washington, Genome Ctr, Seattle, WA 98195 USA, Keio Univ, Sch Med, Dept Biol Mol, Shinjuku Ku, Tokyo 1608582, Japan, Univ Texas, SW Med Ctr, Dallas, TX 75235 USA, Univ Oklahoma, Adv Ctr Genome Technol, Dept Chem & Biochem, Norman, OK 73019 USA, Max Planck Inst Mol Genet, D-14195 Berlin, Germany, Cold Spring Harbor Lab, Lita Annenberg Hazen Genome Ctr, Cold Spring Harbor, NY 11724 USA, GBF, German Res Ctr Biotechnol, D-38124 Braunschweig, Germany, NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA, Case Western Reserve Univ, Sch Med, Dept Genet, Cleveland, OH 44106 USA, Univ Hosp Cleveland, Cleveland, OH 44106 USA, EMBL, European Bioinformat Inst, Cambridge CB10 1SD, England, Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany, MIT, Dept Biol, Cambridge, MA 02139 USA, Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA, Univ Calif Santa Cruz, Dept Comp Sci, Santa Cruz, CA 95064 USA, Affymetrix Inc, Berkeley, CA 94710 USA, RIKEN, Yokoham Inst, Genom Sci Ctr, Genom Explorat Res Grp, Tsurumi Ku, Kanagawa 2300045, Japan, Univ Calif Santa Cruz, Dept Comp Sci, Howard Hughes Med Inst, Santa Cruz, CA 95064 USA, Univ Dublin Trinity Coll, Dept Genet, Smurfit Inst, Dublin 2, Ireland, Compaq Comp Corp, Cambridge Res Lab, Cambridge, MA 02142 USA, MIT, Genome Ctr, Cambridge, MA 02142 USA, Univ Calif Santa Cruz, Dept Math, Santa Cruz, CA 95064 USA, Univ Calif Santa Cruz, Dept Biol, Santa Cruz, CA 95064 USA, Weizmann Inst Sci, Crown Human Genet Ctr, IL-71600 Rehovot, Israel, Weizmann Inst Sci, Dept Mol Genet, IL-71600 Rehovot, Israel, Univ Oxford, Dept Human Anat & Genet, MRC, Funct Genet Unit, Oxford OX1 3QX, England, Inst Syst Biol, Seattle, WA 98105 USA, NHGRI, NIH, Bethesda, MD 20892 USA, US Dept Energy, Off Sci, Germantown, MD 20874 USA, Wellcome Trust, London NW1 2BE, England, Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J.P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J.C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R.H., Wilson, R.K., Hillier, L.W., McPherson, John D., Marra, M.A., Mardis, E.R., Fulton, L.A., Chinwalla, A.T., Pepin, K.H., Gish, W.R., Chissoe, S.L., Wendl, M.C., Delehaunty, K.D., Miner, T.L., Delehaunty, A., Kramer, J.B., Cook, L.L., Fulton, R.S., Johnson, D.L., Minx, P.J., Clifton, S.W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J.F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E.C., Frazier, M., Gibbs, R.A., Muzny, D.M., Scherer, S.E., Bouck, J.B., Sodergren, E.J., Worley, K.C., Rives, C.M., Gorrell, J.H., Metzker, M.L., Naylor, S.L., Kucherlapati, R.S., Nelson, D.L., Weinstock, G.M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H.M., Yu, J., Wang, J., Huang, G.Y., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S.Z., Davis, R.W., Federspiel, N.A., Abola, A.P., Proctor, M.J., Myers, R.M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D.R., Olson, M.V., Kaul, R., Shimizu, N., Kawasaki, K., Minoshima, S., Evans, G.A., Athanasiou, M., Schultz, R., Roe, B.A., Chen, F., Pan, H.Q., Ramser, J., Lehrach, H., Reinhardt, R., McCombie, W.R., De la Bastide, M., Dedhia, N., Blocker, H., Hornischer, K., Nordsiek, G., Agarwala, R., Aravind, L., Bailey, J.A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D.G., Burge, C.B., Cerutti, L., Chen, H.C., Church, D., Clamp, M., Copley, R.R., Doerks, T., Eddy, S.R., Eichler, E.E., Furey, T.S., Galagan, J., Gilbert, Jgr, Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W.H., Johnson, L.S., Jones, T.A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W.J., Kitts, P., Koonin, E.V., Korf, I., Kulp, D., Lancet, D., Lowe, T.M., McLysaght, A., Mikkelsen, T., Moran, J.V., Mulder, N., Pollara, V.J., Ponting, C.P., Schuler, G., Schultz, J.R., Slater, G., Smit, A.F.A., Stupka, E., Szustakowki, J., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Wallis, J., Wheeler, R., Williams, A., Wolf, Y.I., Wolfe, K.H., Yang, S.P., Yeh, R.F., Collins, F., Guyer, M.S., Peterson, J., Felsenfeld, A., Wetterstrand, K.A., Patrinos, A., Morgan, M.J., Univ Michigan, Sch Med, Dept Human Genet, Ann Arbor, MI 48109 USA, Univ Michigan, Sch Med, Dept Internal Med, Ann Arbor, MI 48109 USA, Whitehead Inst Biomed Res, Ctr Genome Res, Cambridge, MA 02142 USA, Sanger Ctr, Hinxton CB10 1RQ, Cambs, England, Washington Univ, Genome Sequencing Ctr, St Louis, MO 63108 USA, US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA, Baylor Coll Med, Human Genome Sequencing Ctr, Dept Mol & Human Genet, Houston, TX 77030 USA, Univ Texas, Hlth Sci Ctr, Dept Cellular & Struct Biol, San Antonio, TX 78229 USA, Yeshiva Univ Albert Einstein Coll Med, Dept Mol Genet, Bronx, NY 10461 USA, Univ Texas, Sch Med, Dept Microbiol & Mol Genet, Houston, TX 77225 USA, RIKEN, Genom Sci Ctr, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan, Genoscope, F-91057 Evry, France, CNRS, UMR 8030, F-91057 Evry, France, Genome Therapeut Corp, GTC Sequencing Ctr, Waltham, MA 02453 USA, Inst Mol Biotechnol, Dept Genome Anal, D-07745 Jena, Germany, Chinese Acad Sci, Inst Genet, Ctr Human Genome, Beijing Genom Inst, Beijing 100101, Peoples R China, So China Natl Human Genome Res Ctr, Shanghai 201203, Peoples R China, No China Natl Human Genome Res Ctr, Beijing 100176, Peoples R China, Inst Syst Biol, Multimegabase Sequencing Ctr, Seattle, WA 98105 USA, Stanford Genome Technol Ctr, Palo Alto, CA 94304 USA, Stanford Univ, Dept Genet, Sch Med, Stanford, CA 94305 USA, Stanford Univ, Stanford Human Genome Ctrr, Sch Med, Stanford, CA 94305 USA, Univ Washington, Genome Ctr, Seattle, WA 98195 USA, Keio Univ, Sch Med, Dept Biol Mol, Shinjuku Ku, Tokyo 1608582, Japan, Univ Texas, SW Med Ctr, Dallas, TX 75235 USA, Univ Oklahoma, Adv Ctr Genome Technol, Dept Chem & Biochem, Norman, OK 73019 USA, Max Planck Inst Mol Genet, D-14195 Berlin, Germany, Cold Spring Harbor Lab, Lita Annenberg Hazen Genome Ctr, Cold Spring Harbor, NY 11724 USA, GBF, German Res Ctr Biotechnol, D-38124 Braunschweig, Germany, NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA, Case Western Reserve Univ, Sch Med, Dept Genet, Cleveland, OH 44106 USA, Univ Hosp Cleveland, Cleveland, OH 44106 USA, EMBL, European Bioinformat Inst, Cambridge CB10 1SD, England, Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany, MIT, Dept Biol, Cambridge, MA 02139 USA, Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA, Univ Calif Santa Cruz, Dept Comp Sci, Santa Cruz, CA 95064 USA, Affymetrix Inc, Berkeley, CA 94710 USA, RIKEN, Yokoham Inst, Genom Sci Ctr, Genom Explorat Res Grp, Tsurumi Ku, Kanagawa 2300045, Japan, Univ Calif Santa Cruz, Dept Comp Sci, Howard Hughes Med Inst, Santa Cruz, CA 95064 USA, Univ Dublin Trinity Coll, Dept Genet, Smurfit Inst, Dublin 2, Ireland, Compaq Comp Corp, Cambridge Res Lab, Cambridge, MA 02142 USA, MIT, Genome Ctr, Cambridge, MA 02142 USA, Univ Calif Santa Cruz, Dept Math, Santa Cruz, CA 95064 USA, Univ Calif Santa Cruz, Dept Biol, Santa Cruz, CA 95064 USA, Weizmann Inst Sci, Crown Human Genet Ctr, IL-71600 Rehovot, Israel, Weizmann Inst Sci, Dept Mol Genet, IL-71600 Rehovot, Israel, Univ Oxford, Dept Human Anat & Genet, MRC, Funct Genet Unit, Oxford OX1 3QX, England, Inst Syst Biol, Seattle, WA 98105 USA, NHGRI, NIH, Bethesda, MD 20892 USA, US Dept Energy, Off Sci, Germantown, MD 20874 USA, Wellcome Trust, London NW1 2BE, England, Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J.P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J.C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R.H., Wilson, R.K., Hillier, L.W., McPherson, John D., Marra, M.A., Mardis, E.R., Fulton, L.A., Chinwalla, A.T., Pepin, K.H., Gish, W.R., Chissoe, S.L., Wendl, M.C., Delehaunty, K.D., Miner, T.L., Delehaunty, A., Kramer, J.B., Cook, L.L., Fulton, R.S., Johnson, D.L., Minx, P.J., Clifton, S.W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J.F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E.C., Frazier, M., Gibbs, R.A., Muzny, D.M., Scherer, S.E., Bouck, J.B., Sodergren, E.J., Worley, K.C., Rives, C.M., Gorrell, J.H., Metzker, M.L., Naylor, S.L., Kucherlapati, R.S., Nelson, D.L., Weinstock, G.M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H.M., Yu, J., Wang, J., Huang, G.Y., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S.Z., Davis, R.W., Federspiel, N.A., Abola, A.P., Proctor, M.J., Myers, R.M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D.R., Olson, M.V., Kaul, R., Shimizu, N., Kawasaki, K., Minoshima, S., Evans, G.A., Athanasiou, M., Schultz, R., Roe, B.A., Chen, F., Pan, H.Q., Ramser, J., Lehrach, H., Reinhardt, R., McCombie, W.R., De la Bastide, M., Dedhia, N., Blocker, H., Hornischer, K., Nordsiek, G., Agarwala, R., Aravind, L., Bailey, J.A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D.G., Burge, C.B., Cerutti, L., Chen, H.C., Church, D., Clamp, M., Copley, R.R., Doerks, T., Eddy, S.R., Eichler, E.E., Furey, T.S., Galagan, J., Gilbert, Jgr, Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W.H., Johnson, L.S., Jones, T.A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W.J., Kitts, P., Koonin, E.V., Korf, I., Kulp, D., Lancet, D., Lowe, T.M., McLysaght, A., Mikkelsen, T., Moran, J.V., Mulder, N., Pollara, V.J., Ponting, C.P., Schuler, G., Schultz, J.R., Slater, G., Smit, A.F.A., Stupka, E., Szustakowki, J., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Wallis, J., Wheeler, R., Williams, A., Wolf, Y.I., Wolfe, K.H., Yang, S.P., Yeh, R.F., Collins, F., Guyer, M.S., Peterson, J., Felsenfeld, A., Wetterstrand, K.A., Patrinos, A., and Morgan, M.J.

Abstract

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Published
2009

6. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana

Author

UCL - SST/ISV - Institut des sciences de la vie, Mayer, K., Schüller, C., Wambutt, R., Murphy, G., Volckaert, G., Pohl, T., Düsterhöft, A., Stiekema, W., Entian, K.-D., Terryn, N., Harris, B., Ansorge, W., Brandt, P., Grivell, L., Rieger, M., Weichselgartner, M., de Simone, V., Obermaier, B., Mache, R., Müller, M., Kreis, M., Delseny, M., Puigdomenech, P., Watson, M., Schmidtheini, T., Reichert, B., Portatelle, D., Perez-Alonso, M., Boutry, Marc, Bancroft, I., Vos, P., Hoheisel, J., Zimmermann, W., Wedler, H., Ridley, P., Langham, S.-A., McCullagh, B., Bilham, L., Robben, J., Van der Schueren, J., Grymonprez, B., Chuang, Y.-J., Vandenbussche, F., Braeken, M., Weltjens, I., Voet, M., Bastiaens, I., Aert, R., Defoor, E., Weitzenegger, T., Bothe, G., Ramsperger, U., Hilbert, H., Braun, M., Holzer, E., Brandt, A., Peters, S., van Staveren, M., Dirkse, W., Mooijman, P., Lankhorst, R. Klein, Rose, M., Hauf, J., Kötter, P., Berneiser, S., Hempel, S., Feldpausch, M., Lamberth, S., Van den Daele, H., De Keyser, A., Buysshaert, C., Gielen, J., Villarroel, R., De Clercq, R., Van Montagu, M., Rogers, J., Cronin, A., Quail, M., Bray-Allen, S., Clark, L., Doggett, J., Hall, S., Kay, M., Lennard, N., McLay, K., Mayes, R., Pettett, A., Rajandream, M.-A., Lyne, M., Benes, V., Rechmann, S., Borkova, D., Blöcker, H., Scharfe, M., Grimm, M., Löhnert, T.-H., Dose, S., de Haan, M., Maarse, A., Schäfer, M., Müller-Auer, S., Gabel, C., Fuchs, M., Fartmann, B., Granderath, K., Dauner, D., Herzl, A., Neumann, S., Argiriou, A., Vitale, D., Liguori, R., Piravandi, E., Massenet, O., Quigley, F., Clabauld, G., Mündlein, A., Felber, R., Schnabl, S., Hiller, R., Schmidt, W., Lecharny, A., Aubourg, S., Chefdor, F., Cooke, R., Berger, C., Montfort, A., Casacuberta, E., Gibbons, T., Weber, N., Vandenbol, M., Bargues, M., Terol, J., Torres, A., Perez-Perez, A., Purnelle, B., Bent, E., Johnson, S., Tacon, D., Jesse, T., Heijnen, L., Schwarz, S., Scholler, P., Heber, S., Francs, P., Bielke, C., Frishman, D., Haase, D., Lemcke, K., Mewes, H. W., Stocker, S., Zaccaria, P., Wilson, R. K., de la Bastide, M., Habermann, K., Parnell, L., Dedhia, N., Gnoj, L., Schutz, K., Huang, E., Spiegel, L., Sehkon, M., Murray, J., Sheet, P., Cordes, M., Abu-Threideh, J., Stoneking, T., Kalicki, J., Graves, T., Harmon, G., Edwards, J., Latreille, P., Courtney, L., Cloud, J., Abbott, A., Scott, K., Johnson, D., Minx, P., Bentley, D., Fulton, B., Miller, N., Greco, T., Kemp, K., Kramer, J., Fulton, L., Mardis, E., Dante, M., Pepin, K., Hillier, L., Nelson, J., Spieth, J., Ryan, E., Andrews, S., Geisel, C., Layman, D., Du, H., Ali, J., Berghoff, A., Jones, K., Drone, K., Cotton, M., Joshu, C., Antonoiu, B., Zidanic, M., Strong, C., Sun, H., Lamar, B., Yordan, C., Ma, P., Zhong, J., Preston, R., Vil, D., Shekher, M., Matero, A., Shah, R., Swaby, I'K., O'Shaughnessy, A., Rodriguez, M., Hoffman, J., Till, S., Granat, S., Shohdy, N., Hasegawa, A., Hameed, A., Lodhi, M., Johnson, A., Chen, E., Marra, M., Martienssen, R., McCombie, W. R., UCL - SST/ISV - Institut des sciences de la vie, Mayer, K., Schüller, C., Wambutt, R., Murphy, G., Volckaert, G., Pohl, T., Düsterhöft, A., Stiekema, W., Entian, K.-D., Terryn, N., Harris, B., Ansorge, W., Brandt, P., Grivell, L., Rieger, M., Weichselgartner, M., de Simone, V., Obermaier, B., Mache, R., Müller, M., Kreis, M., Delseny, M., Puigdomenech, P., Watson, M., Schmidtheini, T., Reichert, B., Portatelle, D., Perez-Alonso, M., Boutry, Marc, Bancroft, I., Vos, P., Hoheisel, J., Zimmermann, W., Wedler, H., Ridley, P., Langham, S.-A., McCullagh, B., Bilham, L., Robben, J., Van der Schueren, J., Grymonprez, B., Chuang, Y.-J., Vandenbussche, F., Braeken, M., Weltjens, I., Voet, M., Bastiaens, I., Aert, R., Defoor, E., Weitzenegger, T., Bothe, G., Ramsperger, U., Hilbert, H., Braun, M., Holzer, E., Brandt, A., Peters, S., van Staveren, M., Dirkse, W., Mooijman, P., Lankhorst, R. Klein, Rose, M., Hauf, J., Kötter, P., Berneiser, S., Hempel, S., Feldpausch, M., Lamberth, S., Van den Daele, H., De Keyser, A., Buysshaert, C., Gielen, J., Villarroel, R., De Clercq, R., Van Montagu, M., Rogers, J., Cronin, A., Quail, M., Bray-Allen, S., Clark, L., Doggett, J., Hall, S., Kay, M., Lennard, N., McLay, K., Mayes, R., Pettett, A., Rajandream, M.-A., Lyne, M., Benes, V., Rechmann, S., Borkova, D., Blöcker, H., Scharfe, M., Grimm, M., Löhnert, T.-H., Dose, S., de Haan, M., Maarse, A., Schäfer, M., Müller-Auer, S., Gabel, C., Fuchs, M., Fartmann, B., Granderath, K., Dauner, D., Herzl, A., Neumann, S., Argiriou, A., Vitale, D., Liguori, R., Piravandi, E., Massenet, O., Quigley, F., Clabauld, G., Mündlein, A., Felber, R., Schnabl, S., Hiller, R., Schmidt, W., Lecharny, A., Aubourg, S., Chefdor, F., Cooke, R., Berger, C., Montfort, A., Casacuberta, E., Gibbons, T., Weber, N., Vandenbol, M., Bargues, M., Terol, J., Torres, A., Perez-Perez, A., Purnelle, B., Bent, E., Johnson, S., Tacon, D., Jesse, T., Heijnen, L., Schwarz, S., Scholler, P., Heber, S., Francs, P., Bielke, C., Frishman, D., Haase, D., Lemcke, K., Mewes, H. W., Stocker, S., Zaccaria, P., Wilson, R. K., de la Bastide, M., Habermann, K., Parnell, L., Dedhia, N., Gnoj, L., Schutz, K., Huang, E., Spiegel, L., Sehkon, M., Murray, J., Sheet, P., Cordes, M., Abu-Threideh, J., Stoneking, T., Kalicki, J., Graves, T., Harmon, G., Edwards, J., Latreille, P., Courtney, L., Cloud, J., Abbott, A., Scott, K., Johnson, D., Minx, P., Bentley, D., Fulton, B., Miller, N., Greco, T., Kemp, K., Kramer, J., Fulton, L., Mardis, E., Dante, M., Pepin, K., Hillier, L., Nelson, J., Spieth, J., Ryan, E., Andrews, S., Geisel, C., Layman, D., Du, H., Ali, J., Berghoff, A., Jones, K., Drone, K., Cotton, M., Joshu, C., Antonoiu, B., Zidanic, M., Strong, C., Sun, H., Lamar, B., Yordan, C., Ma, P., Zhong, J., Preston, R., Vil, D., Shekher, M., Matero, A., Shah, R., Swaby, I'K., O'Shaughnessy, A., Rodriguez, M., Hoffman, J., Till, S., Granat, S., Shohdy, N., Hasegawa, A., Hameed, A., Lodhi, M., Johnson, A., Chen, E., Marra, M., Martienssen, R., and McCombie, W. R.

Abstract

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

Published
1999

7. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana

Author

Mayer, K., primary, Schüller, C., additional, Wambutt, R., additional, Murphy, G., additional, Volckaert, G., additional, Pohl, T., additional, Düsterhöft, A., additional, Stiekema, W., additional, Entian, K.-D., additional, Terryn, N., additional, Harris, B., additional, Ansorge, W., additional, Brandt, P., additional, Grivell, L., additional, Rieger, M., additional, Weichselgartner, M., additional, de Simone, V., additional, Obermaier, B., additional, Mache, R., additional, Müller, M., additional, Kreis, M., additional, Delseny, M., additional, Puigdomenech, P., additional, Watson, M., additional, Schmidtheini, T., additional, Reichert, B., additional, Portatelle, D., additional, Perez-Alonso, M., additional, Boutry, M., additional, Bancroft, I., additional, Vos, P., additional, Hoheisel, J., additional, Zimmermann, W., additional, Wedler, H., additional, Ridley, P., additional, Langham, S.-A., additional, McCullagh, B., additional, Bilham, L., additional, Robben, J., additional, Van der Schueren, J., additional, Grymonprez, B., additional, Chuang, Y.-J., additional, Vandenbussche, F., additional, Braeken, M., additional, Weltjens, I., additional, Voet, M., additional, Bastiaens, I., additional, Aert, R., additional, Defoor, E., additional, Weitzenegger, T., additional, Bothe, G., additional, Ramsperger, U., additional, Hilbert, H., additional, Braun, M., additional, Holzer, E., additional, Brandt, A., additional, Peters, S., additional, van Staveren, M., additional, Dirkse, W., additional, Mooijman, P., additional, Lankhorst, R. Klein, additional, Rose, M., additional, Hauf, J., additional, Kötter, P., additional, Berneiser, S., additional, Hempel, S., additional, Feldpausch, M., additional, Lamberth, S., additional, Van den Daele, H., additional, De Keyser, A., additional, Buysshaert, C., additional, Gielen, J., additional, Villarroel, R., additional, De Clercq, R., additional, Van Montagu, M., additional, Rogers, J., additional, Cronin, A., additional, Quail, M., additional, Bray-Allen, S., additional, Clark, L., additional, Doggett, J., additional, Hall, S., additional, Kay, M., additional, Lennard, N., additional, McLay, K., additional, Mayes, R., additional, Pettett, A., additional, Rajandream, M.-A., additional, Lyne, M., additional, Benes, V., additional, Rechmann, S., additional, Borkova, D., additional, Blöcker, H., additional, Scharfe, M., additional, Grimm, M., additional, Löhnert, T.-H., additional, Dose, S., additional, de Haan, M., additional, Maarse, A., additional, Schäfer, M., additional, Müller-Auer, S., additional, Gabel, C., additional, Fuchs, M., additional, Fartmann, B., additional, Granderath, K., additional, Dauner, D., additional, Herzl, A., additional, Neumann, S., additional, Argiriou, A., additional, Vitale, D., additional, Liguori, R., additional, Piravandi, E., additional, Massenet, O., additional, Quigley, F., additional, Clabauld, G., additional, Mündlein, A., additional, Felber, R., additional, Schnabl, S., additional, Hiller, R., additional, Schmidt, W., additional, Lecharny, A., additional, Aubourg, S., additional, Chefdor, F., additional, Cooke, R., additional, Berger, C., additional, Montfort, A., additional, Casacuberta, E., additional, Gibbons, T., additional, Weber, N., additional, Vandenbol, M., additional, Bargues, M., additional, Terol, J., additional, Torres, A., additional, Perez-Perez, A., additional, Purnelle, B., additional, Bent, E., additional, Johnson, S., additional, Tacon, D., additional, Jesse, T., additional, Heijnen, L., additional, Schwarz, S., additional, Scholler, P., additional, Heber, S., additional, Francs, P., additional, Bielke, C., additional, Frishman, D., additional, Haase, D., additional, Lemcke, K., additional, Mewes, H. W., additional, Stocker, S., additional, Zaccaria, P., additional, Bevan, M., additional, Wilson, R. K., additional, de la Bastide, M., additional, Habermann, K., additional, Parnell, L., additional, Dedhia, N., additional, Gnoj, L., additional, Schutz, K., additional, Huang, E., additional, Spiegel, L., additional, Sehkon, M., additional, Murray, J., additional, Sheet, P., additional, Cordes, M., additional, Abu-Threideh, J., additional, Stoneking, T., additional, Kalicki, J., additional, Graves, T., additional, Harmon, G., additional, Edwards, J., additional, Latreille, P., additional, Courtney, L., additional, Cloud, J., additional, Abbott, A., additional, Scott, K., additional, Johnson, D., additional, Minx, P., additional, Bentley, D., additional, Fulton, B., additional, Miller, N., additional, Greco, T., additional, Kemp, K., additional, Kramer, J., additional, Fulton, L., additional, Mardis, E., additional, Dante, M., additional, Pepin, K., additional, Hillier, L., additional, Nelson, J., additional, Spieth, J., additional, Ryan, E., additional, Andrews, S., additional, Geisel, C., additional, Layman, D., additional, Du, H., additional, Ali, J., additional, Berghoff, A., additional, Jones, K., additional, Drone, K., additional, Cotton, M., additional, Joshu, C., additional, Antonoiu, B., additional, Zidanic, M., additional, Strong, C., additional, Sun, H., additional, Lamar, B., additional, Yordan, C., additional, Ma, P., additional, Zhong, J., additional, Preston, R., additional, Vil, D., additional, Shekher, M., additional, Matero, A., additional, Shah, R., additional, Swaby, I'K., additional, O'Shaughnessy, A., additional, Rodriguez, M., additional, Hoffman, J., additional, Till, S., additional, Granat, S., additional, Shohdy, N., additional, Hasegawa, A., additional, Hameed, A., additional, Lodhi, M., additional, Johnson, A., additional, Chen, E., additional, Marra, M., additional, Martienssen, R., additional, and McCombie, W. R., additional

Published
1999
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8. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.

Author

Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, and Matsumoto T

Abstract

Background: Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group)., Results: The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community., Conclusions: A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.

Published
2013
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9. Assembling genomic DNA sequences with PHRAP.

Author

de la Bastide M and McCombie WR

Subjects
Base Sequence, Molecular Sequence Data, Algorithms, Chromosome Mapping methods, DNA genetics, Sequence Alignment methods, Sequence Analysis, DNA methods, Software, User-Computer Interface
Abstract

The PHRAP assembly program provides rapid comparison, alignment, and assembly of large sets of DNA sequences. PHRAP compares sequences by searching for pairs of perfectly matching "words" or sequence regions that meet certain criteria. If a match is found, PHRAP then tries to extend the alignment into overlapping sections called contigs. PHRAP uses quality values produced by the PHRED basecaller to strike a balance between tolerance of discrepancies and prevention of stacking repeat sequences. The PHRAP assembly algorithm is generally used as part of the PHRED/PHRAP/Consed software suite for sequence analysis. This unit presents instructions for basic usage of the PHRAP assembler, including preparation of the input files (Support Protocols 1 and 2) and explanation of output files (Basic Protocols 1 and 2). Several command line options for changing the PHRAP assembly parameters are also discussed (Basic Protocol 3).

Published
2007
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10. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.

Author

Buell CR, Yuan Q, Ouyang S, Liu J, Zhu W, Wang A, Maiti R, Haas B, Wortman J, Pertea M, Jones KM, Kim M, Overton L, Tsitrin T, Fadrosh D, Bera J, Weaver B, Jin S, Johri S, Reardon M, Webb K, Hill J, Moffat K, Tallon L, Van Aken S, Lewis M, Utterback T, Feldblyum T, Zismann V, Iobst S, Hsiao J, de Vazeille AR, Salzberg SL, White O, Fraser C, Yu Y, Kim H, Rambo T, Currie J, Collura K, Kernodle-Thompson S, Wei F, Kudrna K, Ammiraju JS, Luo M, Goicoechea JL, Wing RA, Henry D, Oates R, Palmer M, Pries G, Saski C, Simmons J, Soderlund C, Nelson W, de la Bastide M, Spiegel L, Nascimento L, Huang E, Preston R, Zutavern T, Palmer L, O'Shaughnessy A, Dike S, McCombie WR, Minx P, Cordum H, Wilson R, Jin W, Lee HR, Jiang J, and Jackson S

Subjects
Arabidopsis genetics, Chromosome Mapping, Chromosomes, Artificial, Bacterial genetics, Genes, Plant, Minisatellite Repeats, Molecular Sequence Data, Oryza classification, Physical Chromosome Mapping, Poaceae classification, Proteome, Species Specificity, Zea mays classification, Zea mays genetics, Chromosomes, Plant genetics, Oryza genetics, Poaceae genetics
Abstract

Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb ( approximately 97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative function could be assigned to 3064 genes, with another 757 genes annotated as expressed, leaving 2094 that encode hypothetical proteins. Similarity searches against the proteome of Arabidopsis thaliana revealed putative homologs for 67% of the chromosome 3 proteins. Further searches of a nonredundant amino acid database, the Pfam domain database, plant Expressed Sequence Tags, and genomic assemblies from sorghum and maize revealed only 853 nontransposable element related proteins from chromosome 3 that lacked similarity to other known sequences. Interestingly, 426 of these have a paralog within the rice genome. A comparative physical map of the wild progenitor species, Oryza nivara, with japonica chromosome 3 revealed a high degree of sequence identity and synteny between these two species, which diverged approximately 10,000 years ago. Although no major rearrangements were detected, the deduced size of the O. nivara chromosome 3 was 21% smaller than that of japonica. Synteny between rice and other cereals using an integrated maize physical map and wheat genetic map was strikingly high, further supporting the use of rice and, in particular, chromosome 3, as a model for comparative studies among the cereals.

Published
2005
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11. Maize genome sequencing by methylation filtration.

Author

Palmer LE, Rabinowicz PD, O'Shaughnessy AL, Balija VS, Nascimento LU, Dike S, de la Bastide M, Martienssen RA, and McCombie WR

Subjects
Algorithms, Chromosomes, Artificial, Bacterial, Cloning, Molecular, Computational Biology, Conserved Sequence, Contig Mapping, CpG Islands, DNA Transposable Elements, DNA, Chloroplast genetics, DNA, Complementary, DNA, Mitochondrial genetics, DNA, Plant genetics, Databases, Nucleic Acid, Escherichia coli genetics, Exons, Expressed Sequence Tags, Genes, Plant, Genomic Library, Oryza genetics, Repetitive Sequences, Nucleic Acid, Retroelements, Reverse Transcriptase Polymerase Chain Reaction, DNA Methylation, Genome, Plant, Sequence Analysis, DNA methods, Zea mays genetics
Abstract

Gene enrichment strategies offer an alternative to sequencing large and repetitive genomes such as that of maize. We report the generation and analysis of nearly 100,000 undermethylated (or methylation filtration) maize sequences. Comparison with the rice genome reveals that methylation filtration results in a more comprehensive representation of maize genes than those that result from expressed sequence tags or transposon insertion sites sequences. About 7% of the repetitive DNA is unmethylated and thus selected in our libraries, but potentially active transposons and unmethylated organelle genomes can be identified. Reverse transcription polymerase chain reaction can be used to finish the maize transcriptome.

Published
2003
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12. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.

Author

Tabata S, Kaneko T, Nakamura Y, Kotani H, Kato T, Asamizu E, Miyajima N, Sasamoto S, Kimura T, Hosouchi T, Kawashima K, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Naruo K, Okumura S, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Sato S, de la Bastide M, Huang E, Spiegel L, Gnoj L, O'Shaughnessy A, Preston R, Habermann K, Murray J, Johnson D, Rohlfing T, Nelson J, Stoneking T, Pepin K, Spieth J, Sekhon M, Armstrong J, Becker M, Belter E, Cordum H, Cordes M, Courtney L, Courtney W, Dante M, Du H, Edwards J, Fryman J, Haakensen B, Lamar E, Latreille P, Leonard S, Meyer R, Mulvaney E, Ozersky P, Riley A, Strowmatt C, Wagner-McPherson C, Wollam A, Yoakum M, Bell M, Dedhia N, Parnell L, Shah R, Rodriguez M, See LH, Vil D, Baker J, Kirchoff K, Toth K, King L, Bahret A, Miller B, Marra M, Martienssen R, McCombie WR, Wilson RK, Murphy G, Bancroft I, Volckaert G, Wambutt R, Düsterhöft A, Stiekema W, Pohl T, Entian KD, Terryn N, Hartley N, Bent E, Johnson S, Langham SA, McCullagh B, Robben J, Grymonprez B, Zimmermann W, Ramsperger U, Wedler H, Balke K, Wedler E, Peters S, van Staveren M, Dirkse W, Mooijman P, Lankhorst RK, Weitzenegger T, Bothe G, Rose M, Hauf J, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Villarroel R, Gielen J, Ardiles W, Bents O, Lemcke K, Kolesov G, Mayer K, Rudd S, Schoof H, Schueller C, Zaccaria P, Mewes HW, Bevan M, and Fransz P

Subjects
Animals, Chromosome Mapping, DNA, Plant, Humans, Plant Proteins genetics, Sequence Analysis, DNA, Arabidopsis genetics, Genome, Plant
Abstract

The genome of the model plant Arabidopsis thaliana has been sequenced by an international collaboration, The Arabidopsis Genome Initiative. Here we report the complete sequence of chromosome 5. This chromosome is 26 megabases long; it is the second largest Arabidopsis chromosome and represents 21% of the sequenced regions of the genome. The sequence of chromosomes 2 and 4 have been reported previously and that of chromosomes 1 and 3, together with an analysis of the complete genome sequence, are reported in this issue. Analysis of the sequence of chromosome 5 yields further insights into centromere structure and the sequence determinants of heterochromatin condensation. The 5,874 genes encoded on chromosome 5 reveal several new functions in plants, and the patterns of gene organization provide insights into the mechanisms and extent of genome evolution in plants.

Published
2000
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