Populus trichocarpa v1.1
Please note that this organism is for archival use only. Please see the current Poplar site on Phytozome for the latest data and information.

Status

The genome of Populus trichocarpa is estimated to be approximately 480 million base pairs contained in 19 chromosomes, and is being sequenced to approximately 7.5X depth.

The annotation v1.1 JamboreeModels includes a total of 45,555 gene models produced through the collaboration of JGI, ORNL and Ghent University (Belgium) annotation teams, and composed of known P. trichocarpa genes mapped to the genomic sequence, gene models built by homology to known plant proteins, and ab initio gene predictions. The models were consolidated and annotated using the JGI annotation pipeline. Genomic conservation with A.thaliana, Populus ESTs, alignments of EST assemblies and full-length cDNAs, and homology to curated plant proteins provide support for the predicted gene models and annotations.

Further analysis and community-wide manual curation of predicted genes continues. A snapshot of improved annotations will be published on this site and submitted to GenBank by the end of 2006.

Assembly

v1.0 (June 2004): This assembly of whole genome shotgun reads was constructed with the JGI assembler, JAZZ, using paired end sequencing reads at a coverage of 7.5X. After trimming for vector and quality, over 6 Million reads were assembled into 22,136 scaffolds totaling 473.1 Mbp. Roughly half of the genome is contained in 62 scaffolds all at least 2.1 Mb in length. 143 scaffolds were assigned to the genetic map, containing 295 Mb.

Collaborators

This project is a collaborative effort involving:

1New annotation and assembly.

References

  • The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
    G. A. Tuskan, S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, U. Hellsten, N. 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. Déjardin, 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, and D. Rokhsar (15 September 2006)
    Science 313 (5793), 1596. [DOI: 10.1126/science.1128691]

Links

Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.