The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Tuskan, G. A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R. P., Bhalerao, R. P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G., Cooper, D., Coutinho, P. M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, 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., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J., 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., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C., 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. Science, 313(5793):1596–1604, September, 2006. Place: Washington Publisher: Amer Assoc Advancement Science WOS:000240498900035doi abstract bibtex 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.
@article{tuskan_genome_2006,
title = {The genome of black cottonwood, {Populus} trichocarpa ({Torr}. \& {Gray})},
volume = {313},
issn = {0036-8075},
doi = {10/c7hs34},
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.},
language = {English},
number = {5793},
journal = {Science},
author = {Tuskan, G. A. and DiFazio, S. and Jansson, S. and Bohlmann, J. and Grigoriev, I. and Hellsten, U. and Putnam, N. and Ralph, S. and Rombauts, S. and Salamov, A. and Schein, J. and Sterck, L. and Aerts, A. and Bhalerao, Rishikesh P. and Bhalerao, R. P. and Blaudez, D. and Boerjan, W. 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, P. M. and Couturier, J. and Covert, S. and Cronk, Q. and Cunningham, R. and Davis, J. and Degroeve, S. and Dejardin, 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 Kangasjarvi, 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 Leple, J.-C. and Locascio, P. and Lou, Y. and Lucas, S. and Martin, F. and Montanini, B. and Napoli, C. and Nelson, D. R. 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 Rouze, P. 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, Y. and Rokhsar, D.},
month = sep,
year = {2006},
note = {Place: Washington
Publisher: Amer Assoc Advancement Science
WOS:000240498900035},
keywords = {arabidopsis-thaliana, cinnamyl alcohol-dehydrogenase, gene-expression, gravitational induction, hybrid poplar, lignin biosynthesis, phenylpropanoid metabolism, quaking aspen, resistance genes, transcriptional regulators},
pages = {1596--1604},
}
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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. 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Washington Publisher: Amer Assoc Advancement Science WOS:000240498900035","keywords":"arabidopsis-thaliana, cinnamyl alcohol-dehydrogenase, gene-expression, gravitational induction, hybrid poplar, lignin biosynthesis, phenylpropanoid metabolism, quaking aspen, resistance genes, transcriptional regulators","pages":"1596–1604","bibtex":"@article{tuskan_genome_2006,\n\ttitle = {The genome of black cottonwood, {Populus} trichocarpa ({Torr}. \\& {Gray})},\n\tvolume = {313},\n\tissn = {0036-8075},\n\tdoi = {10/c7hs34},\n\tabstract = {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.},\n\tlanguage = {English},\n\tnumber = {5793},\n\tjournal = {Science},\n\tauthor = {Tuskan, G. A. and DiFazio, S. and Jansson, S. and Bohlmann, J. and Grigoriev, I. and Hellsten, U. and Putnam, N. and Ralph, S. and Rombauts, S. and Salamov, A. and Schein, J. and Sterck, L. and Aerts, A. and Bhalerao, Rishikesh P. and Bhalerao, R. P. and Blaudez, D. and Boerjan, W. 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, P. M. and Couturier, J. and Covert, S. and Cronk, Q. and Cunningham, R. and Davis, J. and Degroeve, S. and Dejardin, 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 Kangasjarvi, 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 Leple, J.-C. and Locascio, P. and Lou, Y. and Lucas, S. and Martin, F. and Montanini, B. and Napoli, C. and Nelson, D. R. 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 Rouze, P. 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, Y. and Rokhsar, D.},\n\tmonth = sep,\n\tyear = {2006},\n\tnote = {Place: Washington\nPublisher: Amer Assoc Advancement Science\nWOS:000240498900035},\n\tkeywords = {arabidopsis-thaliana, cinnamyl alcohol-dehydrogenase, gene-expression, gravitational induction, hybrid poplar, lignin biosynthesis, phenylpropanoid metabolism, quaking aspen, resistance genes, transcriptional regulators},\n\tpages = {1596--1604},\n}\n\n","author_short":["Tuskan, G. A.","DiFazio, S.","Jansson, S.","Bohlmann, J.","Grigoriev, I.","Hellsten, U.","Putnam, N.","Ralph, S.","Rombauts, S.","Salamov, A.","Schein, J.","Sterck, L.","Aerts, A.","Bhalerao, R. P.","Bhalerao, R. P.","Blaudez, D.","Boerjan, W.","Brun, A.","Brunner, A.","Busov, V.","Campbell, M.","Carlson, J.","Chalot, M.","Chapman, J.","Chen, G.","Cooper, D.","Coutinho, P. M.","Couturier, J.","Covert, S.","Cronk, Q.","Cunningham, R.","Davis, J.","Degroeve, S.","Dejardin, 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.","Kangasjarvi, J.","Karlsson, J.","Kelleher, C.","Kirkpatrick, R.","Kirst, M.","Kohler, A.","Kalluri, U.","Larimer, F.","Leebens-Mack, J.","Leple, J.","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.","Rouze, P.","Ryaboy, D.","Schmutz, J.","Schrader, J.","Segerman, B.","Shin, H.","Siddiqui, A.","Sterky, F.","Terry, A.","Tsai, C.","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."],"key":"tuskan_genome_2006","id":"tuskan_genome_2006","bibbaseid":"tuskan-difazio-jansson-bohlmann-grigoriev-hellsten-putnam-ralph-etal-thegenomeofblackcottonwoodpopulustrichocarpatorrgray-2006","role":"author","urls":{},"keyword":["arabidopsis-thaliana","cinnamyl alcohol-dehydrogenase","gene-expression","gravitational induction","hybrid poplar","lignin biosynthesis","phenylpropanoid metabolism","quaking aspen","resistance genes","transcriptional regulators"],"metadata":{"authorlinks":{}}},"bibtype":"article","biburl":"https://bibbase.org/zotero/upscpub","dataSources":["9cGcv2t8pRzC92kzs","fvfkWcShg3Mybjoog","Tu3jPdZyJF3j547xT"],"keywords":["arabidopsis-thaliana","cinnamyl alcohol-dehydrogenase","gene-expression","gravitational induction","hybrid poplar","lignin biosynthesis","phenylpropanoid metabolism","quaking aspen","resistance genes","transcriptional regulators"],"search_terms":["genome","black","cottonwood","populus","trichocarpa","torr","gray","tuskan","difazio","jansson","bohlmann","grigoriev","hellsten","putnam","ralph","rombauts","salamov","schein","sterck","aerts","bhalerao","bhalerao","blaudez","boerjan","brun","brunner","busov","campbell","carlson","chalot","chapman","chen","cooper","coutinho","couturier","covert","cronk","cunningham","davis","degroeve","dejardin","depamphilis ","detter","dirks","dubchak","duplessis","ehlting","ellis","gendler","goodstein","gribskov","grimwood","groover","gunter","hamberger","heinze","helariutta","henrissat","holligan","holt","huang","islam-faridi","jones","jones-rhoades","jorgensen","joshi","kangasjarvi","karlsson","kelleher","kirkpatrick","kirst","kohler","kalluri","larimer","leebens-mack","leple","locascio","lou","lucas","martin","montanini","napoli","nelson","nelson","nieminen","nilsson","pereda","peter","philippe","pilate","poliakov","razumovskaya","richardson","rinaldi","ritland","rouze","ryaboy","schmutz","schrader","segerman","shin","siddiqui","sterky","terry","tsai","uberbacher","unneberg","vahala","wall","wessler","yang","yin","douglas","marra","sandberg","van de peer","rokhsar"],"title":"The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)","year":2006}