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Science 15 September 2006:
Vol. 313. no. 5793, pp. 1596 - 1604
DOI: 10.1126/science.1128691
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Research Articles

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

G. A. Tuskan,1,3* S. DiFazio,1,4{dagger} S. Jansson,5{dagger} J. Bohlmann,6{dagger} I. Grigoriev,9{dagger} U. Hellsten,9{dagger} N. Putnam,9{dagger} S. Ralph,6{dagger} S. Rombauts,10{dagger} A. Salamov,9{dagger} J. Schein,11{dagger} L. Sterck,10{dagger} 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,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{ddagger} M. Marra,11{ddagger} G. Sandberg,12{ddagger} Y. Van de Peer,10{ddagger} D. Rokhsar9,24{ddagger}

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.
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.

{dagger} These authors contributed equally to this work as second authors.

{ddagger} These authors contributed equally to this work as senior authors.

* To whom correspondence should be addressed. E-mail: gtk{at}ornl.gov

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S. A. Rensing, D. Lang, A. D. Zimmer, A. Terry, A. Salamov, H. Shapiro, T. Nishiyama, P.-F. Perroud, E. A. Lindquist, Y. Kamisugi, et al. (2008)
Science 319, 64-69
   Abstract »    Full Text »    PDF »
Isoprene Emission from Plants: Why and How.
T. D. Sharkey, A. E. Wiberley, and A. R. Donohue (2008)
Ann. Bot. 101, 5-18
   Abstract »    Full Text »    PDF »
CENL1 Expression in the Rib Meristem Affects Stem Elongation and the Transition to Dormancy in Populus.
R. Ruonala, P. L.H. Rinne, J. Kangasjarvi, and C. van der Schoot (2008)
PLANT CELL 20, 59-74
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Evolutionary Dynamics of Introns in Plastid-Derived Genes in Plants: Saturation Nearly Reached but Slow Intron Gain Continues.
M. K. Basu, I. B. Rogozin, O. Deusch, T. Dagan, W. Martin, and E. V. Koonin (2008)
Mol. Biol. Evol. 25, 111-119
   Abstract »    Full Text »    PDF »
Identification and Characterization of Nucleotide-Binding Site-Leucine-Rich Repeat Genes in the Model Plant Medicago truncatula.
C. Ameline-Torregrosa, B.-B. Wang, M. S. O'Bleness, S. Deshpande, H. Zhu, B. Roe, N. D. Young, and S. B. Cannon (2008)
Plant Physiology 146, 5-21
   Abstract »    Full Text »    PDF »
Extensive Allelic Variation in Gene Expression in Populus F1 Hybrids.
Y. Zhuang and K. L. Adams (2007)
Genetics 177, 1987-1996
   Abstract »    Full Text »    PDF »
Gene expression during the induction, maintenance, and release of dormancy in apical buds of poplar.
A. Rohde, T. Ruttink, V. Hostyn, L. Sterck, K. Van Driessche, and W. Boerjan (2007)
J. Exp. Bot. 58, 4047-4060
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Identification and Characterization of Lineage-Specific Genes within the Poaceae.
M. A. Campbell, W. Zhu, N. Jiang, H. Lin, S. Ouyang, K. L. Childs, B. J. Haas, J. P. Hamilton, and C. R. Buell (2007)
Plant Physiology 145, 1311-1322
   Abstract »    Full Text »    PDF »
Genomic Organization and Evolutionary Conservation of Plant D-Type Cyclins.
M. Menges, G. Pavesi, P. Morandini, L. Bogre, and J. A.H. Murray (2007)
Plant Physiology 145, 1558-1576
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Downregulation of Cinnamoyl-Coenzyme A Reductase in Poplar: Multiple-Level Phenotyping Reveals Effects on Cell Wall Polymer Metabolism and Structure.
J.-C. Leple, R. Dauwe, K. Morreel, V. Storme, C. Lapierre, B. Pollet, A. Naumann, K.-Y. Kang, H. Kim, K. Ruel, et al. (2007)
PLANT CELL 19, 3669-3691
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Differential Expansion and Expression of {alpha}- and beta-Tubulin Gene Families in Populus.
R. V. Oakley, Y.-S. Wang, W. Ramakrishna, S. A. Harding, and C.-J. Tsai (2007)
Plant Physiology 145, 961-973
   Abstract »    Full Text »    PDF »
Cytokinin Signaling Pathway.
B. Muller and J. Sheen (2007)
Sci. STKE 2007, cm4
   Abstract »    Full Text »    PDF »
From primary to secondary growth: origin and development of the vascular system.
M. Baucher, M. El Jaziri, and O. Vandeputte (2007)
J. Exp. Bot. 58, 3485-3501
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Identification and Mutational Analysis of Arabidopsis FLS2 Leucine-Rich Repeat Domain Residues That Contribute to Flagellin Perception.
F. M. Dunning, W. Sun, K. L. Jansen, L. Helft, and A. F. Bent (2007)
PLANT CELL 19, 3297-3313
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