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The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

G. A. Tuskan, S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, U. Hellsten, N. Putnam, S. Ralph, S. Rombauts, A. Salamov, J. Schein, L. Sterck, A. Aerts, R. R. Bhalerao, R. P. Bhalerao, D. Blaudez, W. Boerjan, A. Brun, A. Brunner, V. Busov, M. Campbell, J. Carlson, M. Chalot, J. Chapman, G.-L. Chen, D. Cooper, P. M. Coutinho, J. Couturier, S. Covert, Q. Cronk, R. Cunningham, J. Davis, S. Degroeve, A. Déjardin, C. dePamphilis, J. Detter, B. Dirks, I. Dubchak, S. Duplessis, J. Ehlting, B. Ellis, K. Gendler, D. Goodstein, M. Gribskov, J. Grimwood, A. Groover, L. Gunter, B. Hamberger, B. Heinze, Y. Helariutta, B. Henrissat, D. Holligan, R. Holt, W. Huang, N. Islam-Faridi, S. Jones, M. Jones-Rhoades, R. Jorgensen, C. Joshi, J. Kangasjärvi, J. Karlsson, C. Kelleher, R. Kirkpatrick, M. Kirst, A. Kohler, U. Kalluri, F. Larimer, J. Leebens-Mack, J.-C. Leplé, P. Locascio, Y. Lou, S. Lucas, F. Martin, B. Montanini, C. Napoli, D. R. Nelson, C. Nelson, K. Nieminen, O. Nilsson, V. Pereda, G. Peter, R. Philippe, G. Pilate, A. Poliakov, J. Razumovskaya, P. Richardson, C. Rinaldi, K. Ritland, P. Rouzé, D. Ryaboy, J. Schmutz, J. Schrader, B. Segerman, H. Shin, A. Siddiqui, F. Sterky, A. Terry, C.-J. Tsai, E. Uberbacher, P. Unneberg, J. Vahala, K. Wall, S. Wessler, G. Yang, T. Yin, C. Douglas, M. Marra, G. Sandberg, Y. Van de Peer, and D. Rokhsar
Science • 15 Sep 2006 • Vol 313, Issue 5793 • pp. 1596-1604 • DOI: 10.1126/science.1128691
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Abstract

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.
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We thank the U.S. Department of Energy, Office of Science for supporting the sequencing and assembly portion of this study; Genome Canada and the Province of British Columbia for providing support for the BAC end, BAC genotyping, and full-length cDNA portions of this study; the Umeå University and the Royal Technological Institute (KTH) in Stockholm for supporting the EST assembly and annotation portion of this study; the membership of the International Populus Genome Consortium for supplying genetic and genomics resources used in the assembly and annotation of the genome; the NSF Plant Genome Program for supporting the development of Web-based tools; T. H. D. Bradshaw and R. Stettler for input and reviews on draft copies of the manuscript; J. M. Tuskan for guidance and input during the analysis and writing of the manuscript; and the anonymous reviewers who provided critical input and recommendations on the manuscript. GenBank Accession Number: AARH00000000.

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Published In

Science
Volume 313 | Issue 5793
15 September 2006

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American Association for the Advancement of Science.

Submission history

Received: 13 April 2006
Accepted: 9 August 2006
Published in print: 15 September 2006

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Authors

Affiliations

G. A. Tuskan*
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
Plant Sciences Department, University of Tennessee, TN 37996, USA.
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S. DiFazio†
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
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S. Jansson†
Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.
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J. Bohlmann†
Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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I. Grigoriev†
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
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U. Hellsten†
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
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N. Putnam†
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
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S. Ralph†
Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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S. Rombauts†
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, B-9052 Ghent, Belgium.
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A. Salamov†
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
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J. Schein†
Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada.
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L. Sterck†
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, B-9052 Ghent, Belgium.
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A. Aerts
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
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R. R. Bhalerao
Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.
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R. P. Bhalerao
Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
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D. Blaudez
Tree-Microbe Interactions Unit, Institut National de la Recherche Agronomique (INRA)–Université Henri Poincaré, INRA-Nancy, 54280 Champenoux, France.
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W. Boerjan
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, B-9052 Ghent, Belgium.
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A. Brun
Tree-Microbe Interactions Unit, Institut National de la Recherche Agronomique (INRA)–Université Henri Poincaré, INRA-Nancy, 54280 Champenoux, France.
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A. Brunner
Department of Forestry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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V. Busov
Biotechnology Research Center, School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
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M. Campbell
Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2 Canada.
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J. Carlson
School of Forest Resources and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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M. Chalot
Tree-Microbe Interactions Unit, Institut National de la Recherche Agronomique (INRA)–Université Henri Poincaré, INRA-Nancy, 54280 Champenoux, France.
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J. Chapman
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
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G.-L. Chen
Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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D. Cooper
Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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P. M. Coutinho
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.
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J. Couturier
Tree-Microbe Interactions Unit, Institut National de la Recherche Agronomique (INRA)–Université Henri Poincaré, INRA-Nancy, 54280 Champenoux, France.
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S. Covert
Warnell School of Forest Resources, University of Georgia, Athens, GA 30602, USA.
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Q. Cronk
Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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R. Cunningham
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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J. Davis
School of Forest Resources and Conservation, Genetics Institute, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
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S. Degroeve
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, B-9052 Ghent, Belgium.
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A. Déjardin
INRA-Orléans, Unit of Forest Improvement, Genetics and Physiology, 45166 Olivet Cedex, France.
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C. dePamphilis
Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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J. Detter
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
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B. Dirks
Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA.
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I. Dubchak
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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S. Duplessis
Tree-Microbe Interactions Unit, Institut National de la Recherche Agronomique (INRA)–Université Henri Poincaré, INRA-Nancy, 54280 Champenoux, France.
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J. Ehlting
Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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B. Ellis
Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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K. Gendler
Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
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D. Goodstein
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
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M. Gribskov
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
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J. Grimwood
The Stanford Human Genome Center and the Department of Genetics, Stanford University School of Medicine, Palo Alto, CA 94305, USA.
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A. Groover
Institute of Forest Genetics, United States Department of Agriculture, Forest Service, Davis, CA 95616, USA.
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L. Gunter
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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B. Hamberger
Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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B. Heinze
Federal Research Centre for Forests, Hauptstrasse 7, A-1140 Vienna, Austria.
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Y. Helariutta
Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
Plant Molecular Biology Laboratory, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland.
Department of Biology, 200014, University of Turku, FI-20014 Turku, Finland.
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B. Henrissat
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.
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D. Holligan
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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R. Holt
Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada.
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W. Huang
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
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N. Islam-Faridi
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.
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S. Jones
Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada.
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M. Jones-Rhoades
Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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R. Jorgensen
Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
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C. Joshi
Biotechnology Research Center, School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
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J. Kangasjärvi
Department of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland.
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J. Karlsson
Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.
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C. Kelleher
Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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R. Kirkpatrick
Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada.
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M. Kirst
School of Forest Resources and Conservation, Genetics Institute, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
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A. Kohler
Tree-Microbe Interactions Unit, Institut National de la Recherche Agronomique (INRA)–Université Henri Poincaré, INRA-Nancy, 54280 Champenoux, France.
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U. Kalluri
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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F. Larimer
Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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J. Leebens-Mack
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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J.-C. Leplé
INRA-Orléans, Unit of Forest Improvement, Genetics and Physiology, 45166 Olivet Cedex, France.
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P. Locascio
Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Y. Lou
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
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S. Lucas
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
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F. Martin
Tree-Microbe Interactions Unit, Institut National de la Recherche Agronomique (INRA)–Université Henri Poincaré, INRA-Nancy, 54280 Champenoux, France.
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B. Montanini
Tree-Microbe Interactions Unit, Institut National de la Recherche Agronomique (INRA)–Université Henri Poincaré, INRA-Nancy, 54280 Champenoux, France.
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C. Napoli
Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
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D. R. Nelson
Department of Molecular Sciences and Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, TN 38163, USA.
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C. Nelson
Southern Institute of Forest Genetics, United States Department of Agriculture, Forest Service, Saucier, MS 39574, USA.
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K. Nieminen
Plant Molecular Biology Laboratory, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland.
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O. Nilsson
Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
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V. Pereda
Tree-Microbe Interactions Unit, Institut National de la Recherche Agronomique (INRA)–Université Henri Poincaré, INRA-Nancy, 54280 Champenoux, France.
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G. Peter
School of Forest Resources and Conservation, Genetics Institute, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
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R. Philippe
Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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G. Pilate
INRA-Orléans, Unit of Forest Improvement, Genetics and Physiology, 45166 Olivet Cedex, France.
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A. Poliakov
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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J. Razumovskaya
Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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P. Richardson
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
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C. Rinaldi
Tree-Microbe Interactions Unit, Institut National de la Recherche Agronomique (INRA)–Université Henri Poincaré, INRA-Nancy, 54280 Champenoux, France.
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K. Ritland
Department of Forest Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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P. Rouzé
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, B-9052 Ghent, Belgium.
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D. Ryaboy
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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J. Schmutz
The Stanford Human Genome Center and the Department of Genetics, Stanford University School of Medicine, Palo Alto, CA 94305, USA.
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J. Schrader
Developmental Genetics, University of Tübingen, D-72076 Tübingen, Germany.
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B. Segerman
Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.
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H. Shin
Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada.
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A. Siddiqui
Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada.
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F. Sterky
Department of Biotechnology, KTH, AlbaNova University Center, SE-106 91 Stockholm, Sweden.
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A. Terry
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
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C.-J. Tsai
Biotechnology Research Center, School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
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E. Uberbacher
Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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P. Unneberg
Department of Biotechnology, KTH, AlbaNova University Center, SE-106 91 Stockholm, Sweden.
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J. Vahala
Department of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland.
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K. Wall
Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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S. Wessler
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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G. Yang
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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T. Yin
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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C. Douglas‡
Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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M. Marra‡
Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada.
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G. Sandberg‡
Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
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Y. Van de Peer‡
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, B-9052 Ghent, Belgium.
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D. Rokhsar‡
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA.
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Notes

* To whom correspondence should be addressed. E-mail: [email protected]

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