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. Busov; M. 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

doi:10.1126/science.1128691

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

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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 language	English (US)
Pages (from-to)	1596-1604
Number of pages	9
Journal	Science
Volume	313
Issue number	5793
DOIs	https://doi.org/10.1126/science.1128691
State	Published - Sep 15 2006

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10.1126/science.1128691

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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., ... Rokhsar, D. (2006). The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 313(5793), 1596-1604. https://doi.org/10.1126/science.1128691

@article{7ccebd4ef0f9483aa8819ad01876e948,

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.",

author = "Tuskan, {G. A.} and S. DiFazio and S. Jansson and J. Bohlmann and I. Grigoriev and U. Hellsten and M. Putnam and S. Ralph and S. Rombauts and A. Salamov and J. Schein and L. Sterck and A. Aerts and Bhalerao, {R. R.} and Bhalerao, {R. P.} and D. Blaudez and W. Boerjan and A. Brun and A. Brunner and V. Busov and M. Campbell and J. Carlson and M. Chalot and J. Chapman and Chen, {G. L.} and D. Cooper and Coutinho, {P. M.} and J. Couturier and S. Covert and Q. Cronk and R. Cunningham and J. Davis and S. Degroeve and A. D{\'r}jardin and C. DePamphilis and J. Detter and B. Dirks and I. Dubchak and S. Duplessis and J. Ehlting and B. Ellis and K. Gendler and D. Goodstein and M. Gribskov and J. Grimwood and A. Groover and L. Gunter and B. Hamberger and B. Heinze and Y. Helariutta and B. Henrissat and D. Holligan and R. Holt and W. Huang and N. Islam-Faridi and S. Jones and M. Jones-Rhoades and R. Jorgensen and C. Joshi and J. Kangasj{\"a}rvi and J. Karlsson and C. Kelleher and R. Kirkpatrick and M. Kirst and A. Kohler and U. Kalluri and F. Larimer and J. Leebens-Mack and Lepl{\'e}, {J. C.} and P. Locascio and Y. Lou and S. Lucas and F. Martin and B. Montanini and C. Napoli and Nelson, {D. R.} and C. Nelson and K. Nieminen and O. Nilsson and V. Pereda and G. Peter and R. Philippe and G. Pilate and A. Poliakov and J. Razumovskaya and P. Richardson and C. Rinaldi and K. Ritland and P. Rouz{\'e} and D. Ryaboy and J. Schmutz and J. Schrader and B. Segerman and H. Shin and A. Siddiqui and F. Sterky and A. Terry and Tsai, {C. J.} and E. Uberbacher and P. Unneberg and J. Vahala and K. Wall and S. Wessler and G. Yang and T. Yin and C. Douglas and M. Marra and G. Sandberg and {Van De Peer}, Y. and D. Rokhsar",

year = "2006",

month = sep,

day = "15",

doi = "10.1126/science.1128691",

language = "English (US)",

volume = "313",

pages = "1596--1604",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "5793",

}

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

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.

UR - http://www.scopus.com/inward/record.url?scp=33748760611&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33748760611&partnerID=8YFLogxK

U2 - 10.1126/science.1128691

DO - 10.1126/science.1128691

M3 - Article

C2 - 16973872

AN - SCOPUS:33748760611

SN - 0036-8075

VL - 313

SP - 1596

EP - 1604

JO - Science

JF - Science

IS - 5793

ER -

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

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