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The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

GA Tuskan, S DiFazio, S Jansson, J Bohlmann, I Grigoriev, U Hellsten, N Putnam, S Ralph, Stephane Rombauts UGent and A Salamov, et al. (2006) SCIENCE. 313(5793). p.1596-1604
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
ARABIDOPSIS-THALIANA, CINNAMYL ALCOHOL-DEHYDROGENASE, HYBRID POPLAR, GENE-EXPRESSION, TRANSCRIPTIONAL REGULATORS, PHENYLPROPANOID METABOLISM, GRAVITATIONAL INDUCTION, LIGNIN BIOSYNTHESIS, RESISTANCE GENES, QUAKING ASPEN
journal title
SCIENCE
Science
volume
313
issue
5793
pages
1596 - 1604
Web of Science type
Article
Web of Science id
000240498900035
JCR category
MULTIDISCIPLINARY SCIENCES
JCR impact factor
30.028 (2006)
JCR rank
1/50 (2006)
JCR quartile
1 (2006)
ISSN
0036-8075
DOI
10.1126/science.1128691
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
366692
handle
http://hdl.handle.net/1854/LU-366692
date created
2007-05-21 15:03:00
date last changed
2012-12-12 12:06:22
@article{366692,
  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.},
  author       = {Tuskan, GA and DiFazio, S and Jansson, S and Bohlmann, J and Grigoriev, I and Hellsten, U and Putnam, N and Ralph, S and Rombauts, Stephane and Salamov, A and Schein, J and Sterck, Lieven and Aerts, A and Bhalerao, RR and Bhalerao, RP and Blaudez, D and Boerjan, Wout and Brun, A and Brunner, A and Busov, V and Campbell, M and Carlson, J and Chalot, M and Chapman, J and Chen, G-L and Cooper, D and Coutinho, PM and Couturier, J and Covert, S and Cronk, Q and Cunningham, R and Davis, J and Degroeve, Sven and D{\'e}jardin, A and dePamphilis, C and Detter, J and Dirks, B and Dubchak, I and Duplessis, S and Ehlting, J and Ellis, B and Gendler, K and Goodstein, D and Gribskov, M and Grimwood, J and Groover, A and Gunter, L and Hamberger, B and Heinze, B and Helariutta, Y and Henrissat, B and Holligan, D and Holt, R and Huang, W and Islam-Faridi, N and Jones, S and Jones-Rhoades, M and Jorgensen, R and Joshi, C and Kangasj{\"a}rvi, J and Karlsson, J and Kelleher, C and Kirkpatrick, R and Kirst, M and Kohler, A and Kalluri, U and Larimer, F and Leebens-Mack, J and Lepl{\'e}, J-C and Locascio, P and Lou, Y and Lucas, S and Martin, F and Montanini, B and Napoli, C and Nelson, DR and Nelson, C and Nieminen, K and Nilsson, O and Pereda, V and Peter, G and Philippe, R and Pilate, G and Poliakov, A and Razumovskaya, J and Richardson, P and Rinaldi, C and Ritland, K and Rouz{\'e}, Pierre and Ryaboy, D and Schmutz, J and Schrader, J and Segerman, B and Shin, H and Siddiqui, A and Sterky, F and Terry, A and Tsai, C-J and Uberbacher, E and Unneberg, P and Vahala, J and Wall, K and Wessler, S and Yang, G and Yin, T and Douglas, C and Marra, M and Sandberg, G and Van de Peer, Yves and Rokhsar, D},
  issn         = {0036-8075},
  journal      = {SCIENCE},
  keyword      = {ARABIDOPSIS-THALIANA,CINNAMYL ALCOHOL-DEHYDROGENASE,HYBRID POPLAR,GENE-EXPRESSION,TRANSCRIPTIONAL REGULATORS,PHENYLPROPANOID METABOLISM,GRAVITATIONAL INDUCTION,LIGNIN BIOSYNTHESIS,RESISTANCE GENES,QUAKING ASPEN},
  language     = {eng},
  number       = {5793},
  pages        = {1596--1604},
  title        = {The genome of black cottonwood, Populus trichocarpa (Torr. \& Gray)},
  url          = {http://dx.doi.org/10.1126/science.1128691},
  volume       = {313},
  year         = {2006},
}

Chicago
Tuskan, GA, S DiFazio, S Jansson, J Bohlmann, I Grigoriev, U Hellsten, N Putnam, et al. 2006. “The Genome of Black Cottonwood, Populus Trichocarpa (Torr. & Gray).” Science 313 (5793): 1596–1604.
APA
Tuskan, G., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., et al. (2006). The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). SCIENCE, 313(5793), 1596–1604.
Vancouver
1.
Tuskan G, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). SCIENCE. 2006;313(5793):1596–604.
MLA
Tuskan, GA, S DiFazio, S Jansson, et al. “The Genome of Black Cottonwood, Populus Trichocarpa (Torr. & Gray).” SCIENCE 313.5793 (2006): 1596–1604. Print.