复旦大学：《基因组学》课程教学资源（学习资料）杨树全基因组测序

全球首次完成杨树全基因组测序 由美国能源部启动并实施的杨树全基因组测序计划已圆满完成,并于2004年9月21日对 公众开放了全序列数据库。南京林业大学科研人员尹佟明副教授参与了此项研究。杨树基因 组的新闻发布及庆祝会定于12月6日在美国加州举行。该项研究可望使杨树这一重要树种 的品种改良时间大大缩短,用区区几十年跨越千年关。 硏究的完成,使杨树成为继拟南芥和水稻之后,第三个测定全序列的植物,并且是第 个测定全基因组序列的多年生木本植物。杨树因此被广泛接受为研究多年生植物基因组的模 式物种,这使该项工作具有重大的科学意义。杨树同时又是一种重要的工业用材树种,杨树 全基因组计划实施,将为生物能源的开发提供知识贮备,具有重要的实际应用价值。目前, 杨树的改良还处在一种半野生的初级改良阶段,在基因组研究的基础上,通过群体和数量遗 传学的手段在杨树属不同树种间开发有用等位基因,并通过遗传工程的手段进行基因重组, 可望在几十年的时间里完成一般作物几千年的改良历程 杨树全基因组全序列用“鸟枪法测定”,序列库中共含有7,649,993个序列片段,去 除叶绿体基因组的污染,测得的序列大约为8×基因组长度。目前对序列拼接的组装已完成 了483Mb,占杨树基因组物理全长的90%以上,基本上覆盖了杨树基因组常染色体的大部 分。基于基因芯片和单核苷酸多态性检测技术,对小的序列拼接及序列间隙的填充工作正在 进行中,预期这部分工作将于明年完成。南京林业大学尹佟明副教授自2001年以来一直参 与此项研究,对杨树基因组的注释工作将于今年12月初完成 国际杨树基因组计划协作组的总负责人杰瑞先生认为,从世界范围来看,杨树在中国的 林业生产中占有的比重是最大的,因此在杨树基因组信息的应用方面,中国在未来的研究中 可能会居于世界前列。杨树全基因组计划的完成对我国从事林业及生物技术的科学家而言 提供了前所未有的机遇和挑战 Science 15 September 2006 vo.313.no.5793,pp.1596-1604 DO:10.1126/ scIence.1128691 RESEARCH ARTICLES The Genome of Black Cottonwood, Populus trichocarpa (Torr. Gray) G A. Tuskan, t 3S. DiFazio, dt s Jansson, f J Bohlmann, of 1. Grigoriev, f u Hellsten, 9 N. Putnam, 9 S. Ralph, 6S. Rombauts, 0 A. Salamov, 9 J Schein, 11 L. Sterck,10 A Aerts,R.R Bhalerao, 'R. P. Bhalerao, 12 D. Blaudez, 13W. Boerjan, 10 A. Brun, 3A. Brunner, 4V. Busov, 15 M. Campbell, 16J. Carlson, 17 M. Chalot, 13J Chapman, 9G.L. Chen, 2D. Cooper, P. M Coutinho, 19J Couturier, 13S. Covert, 20 Q. Cronk, 'R. Cunningham, 1 J. Davis, 22S Degroeve, 10 A Dejardin, 23C dePamphilis, 18 J. Detter, B. Dirks, 24 L. Dubchak, 9, 25S. Duplessis, 13J. Ehlting, 7B. Ellis, K. Gendler, 26D. Goodstein 9 M. Gribskov, 27J. Grimwood, 28 A Groover 29 L. Gunter 1 B. Hamberger, 7 B Heinze,30Y. Helariutta, 12, 31, 33 B. Henrissat, 19 D. Holligan, 21R. Holt, 11 W. Huang, N. Islam-Faridi,34S. Jones, 11 M. Jones-Rhoades, 35R Jorgensen, 26C Joshi, 15 J Kangasjarvi, 32 J Karlsson, 5 C. Kelleher, R. Kirkpatrick, 11 M. Kirst, 22 A

全球首次完成杨树全基因组测序 由美国能源部启动并实施的杨树全基因组测序计划已圆满完成，并于 2004 年 9 月 21 日对 公众开放了全序列数据库。南京林业大学科研人员尹佟明副教授参与了此项研究。杨树基因 组的新闻发布及庆祝会定于 12 月 6 日在美国加州举行。该项研究可望使杨树这一重要树种 的品种改良时间大大缩短，用区区几十年跨越千年关。 研究的完成，使杨树成为继拟南芥和水稻之后，第三个测定全序列的植物，并且是第一 个测定全基因组序列的多年生木本植物。杨树因此被广泛接受为研究多年生植物基因组的模 式物种，这使该项工作具有重大的科学意义。杨树同时又是一种重要的工业用材树种，杨树 全基因组计划实施，将为生物能源的开发提供知识贮备，具有重要的实际应用价值。目前， 杨树的改良还处在一种半野生的初级改良阶段，在基因组研究的基础上，通过群体和数量遗 传学的手段在杨树属不同树种间开发有用等位基因，并通过遗传工程的手段进行基因重组， 可望在几十年的时间里完成一般作物几千年的改良历程。 杨树全基因组全序列用“鸟枪法测定”，序列库中共含有 7，649，993 个序列片段，去 除叶绿体基因组的污染，测得的序列大约为 8×基因组长度。目前对序列拼接的组装已完成 了 483Mb，占杨树基因组物理全长的 90%以上，基本上覆盖了杨树基因组常染色体的大部 分。基于基因芯片和单核苷酸多态性检测技术，对小的序列拼接及序列间隙的填充工作正在 进行中，预期这部分工作将于明年完成。南京林业大学尹佟明副教授自 2001 年以来一直参 与此项研究，对杨树基因组的注释工作将于今年 12 月初完成。 国际杨树基因组计划协作组的总负责人杰瑞先生认为，从世界范围来看，杨树在中国的 林业生产中占有的比重是最大的，因此在杨树基因组信息的应用方面，中国在未来的研究中 可能会居于世界前列。杨树全基因组计划的完成对我国从事林业及生物技术的科学家而言， 提供了前所未有的机遇和挑战。 Science 15 September 2006: Vol. 313. no. 5793, pp. 1596 - 1604 DOI: 10.1126/science.1128691 RESEARCH ARTICLES The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) G. A. Tuskan,1,3* S. DiFazio,1,4 S. Jansson,5 J. Bohlmann,6 I. Grigoriev,9 U. Hellsten,9 N. Putnam,9 S. Ralph,6 S. Rombauts,10 A. Salamov,9 J. Schein,11 L. Sterck,10 A. Aerts,9 R. R. Bhalerao,5 R. P. Bhalerao,12 D. Blaudez,13 W. Boerjan,10 A. Brun,13 A. Brunner,14 V. Busov,15 M. Campbell,16 J. Carlson,17 M. Chalot,13 J. Chapman,9 G.-L. Chen,2 D. Cooper, 6 P. M. Coutinho,19 J. Couturier,13 S. Covert,20 Q. Cronk,7 R. Cunningham,1 J. Davis,22 S. Degroeve,10 A. Déjardin,23 C. dePamphilis,18 J. Detter,9 B. Dirks,24 I. Dubchak,9,25 S. Duplessis,13 J. Ehlting,7 B. Ellis,6 K. Gendler,26 D. Goodstein,9 M. Gribskov,27 J. Grimwood,28 A. Groover,29 L. Gunter,1 B. Hamberger,7 B. Heinze,30 Y. Helariutta,12,31,33 B. Henrissat,19 D. Holligan,21 R. Holt,11 W. Huang,9 N. Islam-Faridi,34 S. Jones,11 M. Jones-Rhoades,35 R. Jorgensen,26 C. Joshi,15 J. Kangasjärvi,32 J. Karlsson,5 C. Kelleher,6 R. Kirkpatrick,11 M. Kirst,22 A

Kohler, 3U. Kalluri, 1 F Larimer, 2 J. Leebens-Mack, 21 J -C. Leple, 23 P Locascio, 2Y. Lou, S. Lucas, F. Martin, 13B. Montanini, 13C. Napoli, 25 D R. Nelson, 36 C. Nelson,37 K Nieminen,31O. Nilsson, 12 V. Pereda, 13G. Peter, 22R. Philippe, G. Pilate, 23A. Poliakov, 25J Razumovskaya, 2 P. Richardson, C. Rinaldi, 13K Ritland, P Rouze D. Ryaboy, 25 J Schmutz, 28 J. Schrader, 38B Segerman, 5 H Shin, 1 A Siddiqui, 11F. Sterky, 39 A. Terry, 9 C. J. Tsai, 15 E. Uberbacher, 2 P Unneberg, 39 J. Vahala, 32 K. Wal, 8 S Wessler, 1G. Yang, 1T. Yin, C. Douglas, F M. Marra, 1+ G. Sandberg, 1z+ Y. Van de peer. 10+ D. rokhsar, 24 Ve report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene However, the relative frequency of protein domains in the two genomes is similar Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport 1 Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA. 2 Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. 3 Plant Sciences Department, University of Tennessee, TN 37996, USA 4 Department of Biology, West Virginia University, Morgantown, W 26506, USA 5 Umea Plant Science Centre, Department of Plant Physiology, Umea University, SE-901 87. Umea. Sweden 6 Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada 7 Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada Department of Forest Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada 9U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA 10 Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, B-9052 Ghent, Belgium 11 Genome Sciences Centre. 100-570 West 7th Avenue. Vancouver. BC V5Z 4S6 Canada 12 Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umea, Sweden 3 Tree-Microbe Interactions Unit, Institut National de la Recherche Agronomique (INRA)-Universite Henri Poincare, INRA-Nancy, 54280 Champenoux, France 14 Department of Forestry, Virginia Polytechnic Institute and State University, Blacksburg VA 24061. USA

Kohler,13 U. Kalluri,1 F. Larimer,2 J. Leebens-Mack,21 J.-C. Leplé,23 P. Locascio,2 Y. Lou,9 S. Lucas,9 F. Martin,13 B. Montanini,13 C. Napoli,26 D. R. Nelson,36 C. Nelson,37 K. Nieminen,31 O. Nilsson,12 V. Pereda,13 G. Peter,22 R. Philippe,6 G. Pilate,23 A. Poliakov,25 J. Razumovskaya,2 P. Richardson,9 C. Rinaldi,13 K. Ritland,8 P. Rouzé,10 D. Ryaboy,25 J. Schmutz,28 J. Schrader,38 B. Segerman,5 H. Shin,11 A. Siddiqui,11 F. Sterky,39 A. Terry,9 C.-J. Tsai, 15 E. Uberbacher,2 P. Unneberg,39 J. Vahala,32 K. Wall,18 S. Wessler,21 G. Yang,21 T. Yin,1 C. Douglas,7 M. Marra,11 G. Sandberg,12 Y. Van de Peer,10 D. Rokhsar 9,24 We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified.Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport. 1 Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. 2 Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. 3 Plant Sciences Department, University of Tennessee, TN 37996, USA. 4 Department of Biology, West Virginia University, Morgantown, WV 26506, USA. 5 Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden. 6 Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. 7 Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. 8 Department of Forest Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. 9 U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA. 10 Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, B-9052 Ghent, Belgium. 11 Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada. 12 Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden. 13 Tree-Microbe Interactions Unit, Institut National de la Recherche Agronomique (INRA)–Université Henri Poincaré, INRA-Nancy, 54280 Champenoux, France. 14 Department of Forestry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA

15 Biotechnology Research Center, School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA 16 Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2 Canada 17 School of Forest Resources and Huck Institutes of the Life Sciences the Pennsylvania State University, University Park, PA 16802, USA. Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA 19 Architecture et Fonction des Macromolecules Biologiques, UMR6098, CNRS and Universities of Aix-Marseille I and l, case 932, 163 avenue de Luminy, 13288 Marseille France 20 Warnell School of Forest Resources, University of Georgia, Athens, GA 30602, USA 21 Department of Plant Biology, University of Georgia, Athens, GA 30602, USA 22 School of forest Resources and Conservation Genetics Institute. and Plant molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA. INRA-Orleans, Unit of Forest Improvement, Genetics and Physiology, 45166 Olivet 24 Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA. 25 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. 26 Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA. 27 Department of Biological Sciences, Purdue University, West Laf ayette, IN 47907, USA. 8 The Stanford Human Genome Center and the Department of Genetics, Stanford University School of Medicine, Palo Alto, CA 94305, USA. 29 Institute of Forest Genetics, United States Department of Agriculture, Forest Service, Davis. CA 95616 USA. 30 Federal Research Centre for Forests, Hauptstrasse 7, A-1140 Vienna, Austria 31 Plant Molecular Biology Laboratory, Institute of Biotechnology, University of Helsinki F1-00014 Helsinki Finland 32 Department of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki Finland 33 Department of Biology, 200014, University of Turku, F1-20014 Turku, Finland Southern Institute of Forest Genetics, United States Department of Agriculture, Forest Service and Department of Forest Science, Texas A&M University, College Station, TX 77843.UsA 35 Whitehead Institute for Biomedical Research and Department of biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA 36 Department of Molecular Sciences and Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, TN 38163, USA. 37 Southern Institute of Forest Genetics, United States Department of Agriculture, Forest Service. Saucier. MS 39574 USA. Developmental Genetics, University of Tubingen, D-72076 Tubingen, Germany 39 Department of Biotechnology, KTH, AlbaNova University Center, SE-106 91 Stockholm These authors contributed equally to this work as second authors

15 Biotechnology Research Center, School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA. 16 Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2 Canada. 17 School of Forest Resources and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA. 18 Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA. 19 Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS and Universities of Aix-Marseille I and II, case 932, 163 avenue de Luminy, 13288 Marseille, France. 20 Warnell School of Forest Resources, University of Georgia, Athens, GA 30602, USA. 21 Department of Plant Biology, University of Georgia, Athens, GA 30602, USA. 22 School of Forest Resources and Conservation, Genetics Institute, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA. 23 INRA-Orléans, Unit of Forest Improvement, Genetics and Physiology, 45166 Olivet Cedex, France. 24 Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA. 25 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. 26 Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA. 27 Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA. 28 The Stanford Human Genome Center and the Department of Genetics, Stanford University School of Medicine, Palo Alto, CA 94305, USA. 29 Institute of Forest Genetics, United States Department of Agriculture, Forest Service, Davis, CA 95616, USA. 30 Federal Research Centre for Forests, Hauptstrasse 7, A-1140 Vienna, Austria. 31 Plant Molecular Biology Laboratory, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland. 32 Department of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland. 33 Department of Biology, 200014, University of Turku, FI-20014 Turku, Finland. 34 Southern Institute of Forest Genetics, United States Department of Agriculture, Forest Service and Department of Forest Science, Texas A&M University, College Station, TX 77843, USA. 35 Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. 36 Department of Molecular Sciences and Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, TN 38163, USA. 37 Southern Institute of Forest Genetics, United States Department of Agriculture, Forest Service, Saucier, MS 39574, USA. 38 Developmental Genetics, University of Tübingen, D-72076 Tübingen, Germany. 39 Department of Biotechnology, KTH, AlbaNova University Center, SE-106 91 Stockholm, Sweden. These authors contributed equally to this work as second authors

These authors contributed equally to this work as senior authors. To whom correspondence should be addressed. E-mail: gtk(@ornl. gov

These authors contributed equally to this work as senior authors. * To whom correspondence should be addressed. E-mail: gtk@ornl.gov