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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}
}
  • 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. Over 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event, with approximately 8,000 pairs of duplicated genes from that event surviving 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 slower in Populus relative to Arabidopsis. Populus has more protein-coding genes thanmore » Arabidopsis, ranging on average between 1.4-1.6 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 disease resistance, meristem development, metabolite transport and lignocellulosic wall biosynthesis.« less
  • Methyl jasmonate is a metabolite known to be produced by many plants and has roles in diverse biological processes. It is biosynthesized by the action of S-adenosyl-L-methionine:jasmonic acid carboxyl methyltransferase (JMT), which belongs to the SABATH family of methyltransferases. Herein is reported the isolation and biochemical characterization of a JMT gene from black cottonwood (Populus trichocarpa). The genome of P. trichocarpa contains 28 SABATH genes (PtSABATH1 to PtSABATH28). Recombinant PtSABATH3 expressed in Escherichia coli showed the highest level of activity with jasmonic acid (JA) among carboxylic acids tested. It was therefore renamed PtJMT1. PtJMT1 also displayed activity with benzoic acidmore » (BA), with which the activity was about 22% of that with JA. PtSABATH2 and PtSABATH4 were most similar to PtJMT1 among all PtSABATHs. However, neither of them had activity with JA. The apparent Km values of PtJMT1 using JA and BA as substrate were 175 lM and 341 lM, respectively. Mutation of Ser-153 and Asn-361, two residues in the active site of PtJMT1, to Tyr and Ser respectively, led to higher specific activity with BA than with JA. Homology-based structural modeling indicated that substrate alignment, in which Asn-361 is involved, plays a role in determining the substrate specificity of PtJMT1. In the leaves of young seedlings of black cottonwood, the expression of PtJMT1 was induced by plant defense signal molecules methyl jasmonate and salicylic acid and a fungal elicitor alamethicin, suggesting that PtJMT1 may have a role in plant defense against biotic stresses. Phylogenetic analysis suggests that PtJMT1 shares a common ancestor with the Arabidopsis JMT, and functional divergence of these two apparent JMT orthologs has occurred since the split of poplar and Arabidopsis lineages.« less
  • Auxin/Indole-3-Acetic Acid (Aux/IAA) and Auxin Response Factor (ARF) transcription factors are key regulators of auxin responses in plants. A total of 35 Aux/IAA and 39 ARF genes were identified in the Populus genome. Comparative phylogenetic analysis revealed that the subgroups PoptrARF2, 6, 9 and 16 and PoptrIAA3, 16, 27 and 29 have differentially expanded in Populus relative to Arabidopsis. Activator ARFs were found to be two fold-overrepresented in the Populus genome. PoptrIAA and PoptrARF gene families appear to have expanded due to high segmental and low tandem duplication events. Furthermore, expression studies showed that genes in the expanded PoptrIAA3 subgroupmore » display differential expression. The gene-family analysis reported here will be useful in conducting future functional genomics studies to understand how the molecular roles of these large gene families translate into a diversity of biologically meaningful auxin effects.« less