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

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.

Authors:
 [1];  [1];  [1];  [2];  [3];  [3];  [3];  [2];  [4];  [3];  [5];  [4];  [3];  [6];  [1];  [7];  [4];  [7];  [8];  [9] more »;  [10];  [1];  [3];  [3];  [1];  [1];  [1];  [1];  [1];  [1] « less
  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
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1003672
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Science; Journal Volume: 313; Journal Issue: 5793
Country of Publication:
United States
Language:
English
Subject:
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

Citation Formats

Tuskan, Gerald A, DiFazio, Stephen P, Jansson, Bo S, Bohlmann, J., Grigoriev, I., Hellsten, U., Putman, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R. R., Bhalerao, Rishikesh P, Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Larimer, Frank W, Detter, J C, Richardson, P M, Chen, Gwo-Liang, Gunter, Lee E, Kalluri, Udaya C, LoCascio, Philip F, Uberbacher, Edward C, and Yin, Tongming. The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray). United States: N. p., 2006. Web. doi:10.1126/science.1128691.
Tuskan, Gerald A, DiFazio, Stephen P, Jansson, Bo S, Bohlmann, J., Grigoriev, I., Hellsten, U., Putman, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R. R., Bhalerao, Rishikesh P, Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Larimer, Frank W, Detter, J C, Richardson, P M, Chen, Gwo-Liang, Gunter, Lee E, Kalluri, Udaya C, LoCascio, Philip F, Uberbacher, Edward C, & Yin, Tongming. The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray). United States. doi:10.1126/science.1128691.
Tuskan, Gerald A, DiFazio, Stephen P, Jansson, Bo S, Bohlmann, J., Grigoriev, I., Hellsten, U., Putman, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R. R., Bhalerao, Rishikesh P, Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Larimer, Frank W, Detter, J C, Richardson, P M, Chen, Gwo-Liang, Gunter, Lee E, Kalluri, Udaya C, LoCascio, Philip F, Uberbacher, Edward C, and Yin, Tongming. Sun . "The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)". United States. doi:10.1126/science.1128691.
@article{osti_1003672,
title = {The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)},
author = {Tuskan, Gerald A and DiFazio, Stephen P and Jansson, Bo S and Bohlmann, J. and Grigoriev, I. and Hellsten, U. and Putman, N. and Ralph, S. and Rombauts, S. and Salamov, A. and Schein, J. and Sterck, L. and Aerts, A. and Bhalerao, R. R. and Bhalerao, Rishikesh P and Blaudez, D. and Boerjan, W. and Brun, A. and Brunner, A. and Busov, V. and Campbell, M. and Larimer, Frank W and Detter, J C and Richardson, P M and Chen, Gwo-Liang and Gunter, Lee E and Kalluri, Udaya C and LoCascio, Philip F and Uberbacher, Edward C and Yin, Tongming},
abstractNote = {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.},
doi = {10.1126/science.1128691},
journal = {Science},
number = 5793,
volume = 313,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}