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

Journal Article · Sun Jan 01 00:00:00 EST 2006 · Science

DOI:https://doi.org/10.1126/science.1128691· OSTI ID:1003672

Tuskan, Gerald A ^[1]; DiFazio, Stephen P ^[1]; Jansson, Bo S ^[1]; Bohlmann, J. ^[2]; Grigoriev, I. ^[3]; Hellsten, U. ^[3]; Putman, N. ^[3]; Ralph, S. ^[2]; Rombauts, S. ^[4]; Salamov, A. ^[3]; Schein, J. ^[5]; Sterck, L. ^[4]; Aerts, A. ^[3]; Bhalerao, R. R. ^[6]; Bhalerao, Rishikesh P ^[1]; Blaudez, D. ^[7]; Boerjan, W. ^[4]; Brun, A. ^[7]; Brunner, A. ^[8]; Busov, V. ^[9] ; Campbell, M. ^[10]; Larimer, Frank W ^[1]; Detter, J C ^[3]; Richardson, P M ^[3]; Chen, Gwo-Liang ^[1]; Gunter, Lee E ^[1]; Kalluri, Udaya C ^[1]; LoCascio, Philip F ^[1]; Uberbacher, Edward C ^[1]; Yin, Tongming ^[1]

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1. ORNL
2. University of British Columbia, Vancouver
3. U.S. Department of Energy, Joint Genome Institute
4. Ghent University, Belgium
5. Genome Sciences Centre, Vancouver, BC, Canada
6. Umea Plant Science Centre, Dept. of Plant Physiology, Sweden
7. Institut National de la Recherche Agronomique, France
8. Virginia Polytechnic Institute and State University (Virginia Tech)
9. Michigan Technological University
10. University of Toronto

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.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 1003672
• Journal Information: Science, Vol. 313, Issue 5793; ISSN 0036--8075
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
ARABIDOPSIS
BIOSYNTHESIS
COTTONWOODS
DISEASE RESISTANCE
GENES
GENETIC MAPPING
MERISTEMS
METABOLITES
NUCLEOTIDES
PROTEINS
TRANSPORT