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

G. A. Tuskan, S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, U. Hellsten, M. Putnam, S. Ralph, S. Rombauts, A. Salamov, J. Schein, L. Sterck, A. Aerts, R. R. Bhalerao, R. P. Bhalerao, D. Blaudez, W. Boerjan, A. Brun, A. Brunner, V. BusovM. Campbell, J. Carlson, M. Chalot, J. Chapman, G. L. Chen, D. Cooper, P. M. Coutinho, J. Couturier, S. Covert, Q. Cronk, R. Cunningham, J. Davis, S. Degroeve, A. Dŕjardin, C. DePamphilis, J. Detter, B. Dirks, I. Dubchak, S. Duplessis, J. Ehlting, B. Ellis, K. Gendler, D. Goodstein, M. Gribskov, J. Grimwood, A. Groover, L. Gunter, B. Hamberger, B. Heinze, Y. Helariutta, B. Henrissat, D. Holligan, R. Holt, W. Huang, N. Islam-Faridi, S. Jones, M. Jones-Rhoades, R. Jorgensen, C. Joshi, J. Kangasjärvi, J. Karlsson, C. Kelleher, R. Kirkpatrick, M. Kirst, A. Kohler, U. Kalluri, F. Larimer, J. Leebens-Mack, J. C. Leplé, P. Locascio, Y. Lou, S. Lucas, F. Martin, B. Montanini, C. Napoli, D. R. Nelson, C. Nelson, K. Nieminen, O. Nilsson, V. Pereda, G. Peter, R. Philippe, G. Pilate, A. Poliakov, J. Razumovskaya, P. Richardson, C. Rinaldi, K. Ritland, P. Rouzé, D. Ryaboy, J. Schmutz, J. Schrader, B. Segerman, H. Shin, A. Siddiqui, F. Sterky, A. Terry, C. J. Tsai, E. Uberbacher, P. Unneberg, J. Vahala, K. Wall, S. Wessler, G. Yang, T. Yin, C. Douglas, M. Marra, G. Sandberg, Y. Van De Peer, D. Rokhsar

Research output: Contribution to journalArticle

2570 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1596-1604
Number of pages9
JournalScience
Volume313
Issue number5793
DOIs
StatePublished - Sep 15 2006

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Populus
Genome
Arabidopsis
Genes
Disease Resistance
Gene Duplication
Meristem
Chromosome Mapping
Firearms
Proteins
Nucleotides

All Science Journal Classification (ASJC) codes

  • General

Cite this

Tuskan, G. A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., ... Rokhsar, D. (2006). The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 313(5793), 1596-1604. https://doi.org/10.1126/science.1128691

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). / Tuskan, G. A.; DiFazio, S.; Jansson, S.; Bohlmann, J.; Grigoriev, I.; Hellsten, U.; Putnam, M.; Ralph, S.; Rombauts, S.; Salamov, A.; Schein, J.; Sterck, L.; Aerts, A.; Bhalerao, R. R.; Bhalerao, R. P.; Blaudez, D.; Boerjan, W.; Brun, A.; Brunner, A.; Busov, V.; Campbell, M.; Carlson, J.; Chalot, M.; Chapman, J.; Chen, G. L.; Cooper, D.; Coutinho, P. M.; Couturier, J.; Covert, S.; Cronk, Q.; Cunningham, R.; Davis, J.; Degroeve, S.; Dŕjardin, A.; DePamphilis, C.; Detter, J.; Dirks, B.; Dubchak, I.; Duplessis, S.; Ehlting, J.; Ellis, B.; Gendler, K.; Goodstein, D.; Gribskov, M.; Grimwood, J.; Groover, A.; Gunter, L.; Hamberger, B.; Heinze, B.; Helariutta, Y.; Henrissat, B.; Holligan, D.; Holt, R.; Huang, W.; Islam-Faridi, N.; Jones, S.; Jones-Rhoades, M.; Jorgensen, R.; Joshi, C.; Kangasjärvi, J.; Karlsson, J.; Kelleher, C.; Kirkpatrick, R.; Kirst, M.; Kohler, A.; Kalluri, U.; Larimer, F.; Leebens-Mack, J.; Leplé, J. C.; Locascio, P.; Lou, Y.; Lucas, S.; Martin, F.; Montanini, B.; Napoli, C.; Nelson, D. R.; Nelson, C.; Nieminen, K.; Nilsson, O.; Pereda, V.; Peter, G.; Philippe, R.; Pilate, G.; Poliakov, A.; Razumovskaya, J.; Richardson, P.; Rinaldi, C.; Ritland, K.; Rouzé, P.; Ryaboy, D.; Schmutz, J.; Schrader, J.; Segerman, B.; Shin, H.; Siddiqui, A.; Sterky, F.; Terry, A.; Tsai, C. J.; Uberbacher, E.; Unneberg, P.; Vahala, J.; Wall, K.; Wessler, S.; Yang, G.; Yin, T.; Douglas, C.; Marra, M.; Sandberg, G.; Van De Peer, Y.; Rokhsar, D.

In: Science, Vol. 313, No. 5793, 15.09.2006, p. 1596-1604.

Research output: Contribution to journalArticle

Tuskan, GA, DiFazio, S, Jansson, S, Bohlmann, J, Grigoriev, I, Hellsten, U, Putnam, M, Ralph, S, Rombauts, S, Salamov, A, Schein, J, Sterck, L, Aerts, A, Bhalerao, RR, Bhalerao, RP, Blaudez, D, Boerjan, W, Brun, A, Brunner, A, Busov, V, Campbell, M, Carlson, J, Chalot, M, Chapman, J, Chen, GL, Cooper, D, Coutinho, PM, Couturier, J, Covert, S, Cronk, Q, Cunningham, R, Davis, J, Degroeve, S, Dŕjardin, A, DePamphilis, C, Detter, J, Dirks, B, Dubchak, I, Duplessis, S, Ehlting, J, Ellis, B, Gendler, K, Goodstein, D, Gribskov, M, Grimwood, J, Groover, A, Gunter, L, Hamberger, B, Heinze, B, Helariutta, Y, Henrissat, B, Holligan, D, Holt, R, Huang, W, Islam-Faridi, N, Jones, S, Jones-Rhoades, M, Jorgensen, R, Joshi, C, Kangasjärvi, J, Karlsson, J, Kelleher, C, Kirkpatrick, R, Kirst, M, Kohler, A, Kalluri, U, Larimer, F, Leebens-Mack, J, Leplé, JC, Locascio, P, Lou, Y, Lucas, S, Martin, F, Montanini, B, Napoli, C, Nelson, DR, Nelson, C, Nieminen, K, Nilsson, O, Pereda, V, Peter, G, Philippe, R, Pilate, G, Poliakov, A, Razumovskaya, J, Richardson, P, Rinaldi, C, Ritland, K, Rouzé, P, Ryaboy, D, Schmutz, J, Schrader, J, Segerman, B, Shin, H, Siddiqui, A, Sterky, F, Terry, A, Tsai, CJ, Uberbacher, E, Unneberg, P, Vahala, J, Wall, K, Wessler, S, Yang, G, Yin, T, Douglas, C, Marra, M, Sandberg, G, Van De Peer, Y & Rokhsar, D 2006, 'The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)', Science, vol. 313, no. 5793, pp. 1596-1604. https://doi.org/10.1126/science.1128691
Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006 Sep 15;313(5793):1596-1604. https://doi.org/10.1126/science.1128691
Tuskan, G. A. ; DiFazio, S. ; Jansson, S. ; Bohlmann, J. ; Grigoriev, I. ; Hellsten, U. ; Putnam, M. ; Ralph, S. ; Rombauts, S. ; Salamov, A. ; Schein, J. ; Sterck, L. ; Aerts, A. ; Bhalerao, R. R. ; Bhalerao, R. P. ; Blaudez, D. ; Boerjan, W. ; Brun, A. ; Brunner, A. ; Busov, V. ; Campbell, M. ; Carlson, J. ; Chalot, M. ; Chapman, J. ; Chen, G. L. ; Cooper, D. ; Coutinho, P. M. ; Couturier, J. ; Covert, S. ; Cronk, Q. ; Cunningham, R. ; Davis, J. ; Degroeve, S. ; Dŕjardin, A. ; DePamphilis, C. ; Detter, J. ; Dirks, B. ; Dubchak, I. ; Duplessis, S. ; Ehlting, J. ; Ellis, B. ; Gendler, K. ; Goodstein, D. ; Gribskov, M. ; Grimwood, J. ; Groover, A. ; Gunter, L. ; Hamberger, B. ; Heinze, B. ; Helariutta, Y. ; Henrissat, B. ; Holligan, D. ; Holt, R. ; Huang, W. ; Islam-Faridi, N. ; Jones, S. ; Jones-Rhoades, M. ; Jorgensen, R. ; Joshi, C. ; Kangasjärvi, J. ; Karlsson, J. ; Kelleher, C. ; Kirkpatrick, R. ; Kirst, M. ; Kohler, A. ; Kalluri, U. ; Larimer, F. ; Leebens-Mack, J. ; Leplé, J. C. ; Locascio, P. ; Lou, Y. ; Lucas, S. ; Martin, F. ; Montanini, B. ; Napoli, C. ; Nelson, D. R. ; Nelson, C. ; Nieminen, K. ; Nilsson, O. ; Pereda, V. ; Peter, G. ; Philippe, R. ; Pilate, G. ; Poliakov, A. ; Razumovskaya, J. ; Richardson, P. ; Rinaldi, C. ; Ritland, K. ; Rouzé, P. ; Ryaboy, D. ; Schmutz, J. ; Schrader, J. ; Segerman, B. ; Shin, H. ; Siddiqui, A. ; Sterky, F. ; Terry, A. ; Tsai, C. J. ; Uberbacher, E. ; Unneberg, P. ; Vahala, J. ; Wall, K. ; Wessler, S. ; Yang, G. ; Yin, T. ; Douglas, C. ; Marra, M. ; Sandberg, G. ; Van De Peer, Y. ; Rokhsar, D. / The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). In: Science. 2006 ; Vol. 313, No. 5793. pp. 1596-1604.
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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.",
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TY - JOUR

T1 - The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

AU - Tuskan, G. A.

AU - DiFazio, S.

AU - Jansson, S.

AU - Bohlmann, J.

AU - Grigoriev, I.

AU - Hellsten, U.

AU - Putnam, M.

AU - Ralph, S.

AU - Rombauts, S.

AU - Salamov, A.

AU - Schein, J.

AU - Sterck, L.

AU - Aerts, A.

AU - Bhalerao, R. R.

AU - Bhalerao, R. P.

AU - Blaudez, D.

AU - Boerjan, W.

AU - Brun, A.

AU - Brunner, A.

AU - Busov, V.

AU - Campbell, M.

AU - Carlson, J.

AU - Chalot, M.

AU - Chapman, J.

AU - Chen, G. L.

AU - Cooper, D.

AU - Coutinho, P. M.

AU - Couturier, J.

AU - Covert, S.

AU - Cronk, Q.

AU - Cunningham, R.

AU - Davis, J.

AU - Degroeve, S.

AU - Dŕjardin, A.

AU - DePamphilis, C.

AU - Detter, J.

AU - Dirks, B.

AU - Dubchak, I.

AU - Duplessis, S.

AU - Ehlting, J.

AU - Ellis, B.

AU - Gendler, K.

AU - Goodstein, D.

AU - Gribskov, M.

AU - Grimwood, J.

AU - Groover, A.

AU - Gunter, L.

AU - Hamberger, B.

AU - Heinze, B.

AU - Helariutta, Y.

AU - Henrissat, B.

AU - Holligan, D.

AU - Holt, R.

AU - Huang, W.

AU - Islam-Faridi, N.

AU - Jones, S.

AU - Jones-Rhoades, M.

AU - Jorgensen, R.

AU - Joshi, C.

AU - Kangasjärvi, J.

AU - Karlsson, J.

AU - Kelleher, C.

AU - Kirkpatrick, R.

AU - Kirst, M.

AU - Kohler, A.

AU - Kalluri, U.

AU - Larimer, F.

AU - Leebens-Mack, J.

AU - Leplé, J. C.

AU - Locascio, P.

AU - Lou, Y.

AU - Lucas, S.

AU - Martin, F.

AU - Montanini, B.

AU - Napoli, C.

AU - Nelson, D. R.

AU - Nelson, C.

AU - Nieminen, K.

AU - Nilsson, O.

AU - Pereda, V.

AU - Peter, G.

AU - Philippe, R.

AU - Pilate, G.

AU - Poliakov, A.

AU - Razumovskaya, J.

AU - Richardson, P.

AU - Rinaldi, C.

AU - Ritland, K.

AU - Rouzé, P.

AU - Ryaboy, D.

AU - Schmutz, J.

AU - Schrader, J.

AU - Segerman, B.

AU - Shin, H.

AU - Siddiqui, A.

AU - Sterky, F.

AU - Terry, A.

AU - Tsai, C. J.

AU - Uberbacher, E.

AU - Unneberg, P.

AU - Vahala, J.

AU - Wall, K.

AU - Wessler, S.

AU - Yang, G.

AU - Yin, T.

AU - Douglas, C.

AU - Marra, M.

AU - Sandberg, G.

AU - Van De Peer, Y.

AU - Rokhsar, D.

PY - 2006/9/15

Y1 - 2006/9/15

N2 - 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.

AB - 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.

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U2 - 10.1126/science.1128691

DO - 10.1126/science.1128691

M3 - Article

C2 - 16973872

AN - SCOPUS:33748760611

VL - 313

SP - 1596

EP - 1604

JO - Science

JF - Science

SN - 0036-8075

IS - 5793

ER -