Populus trichocarpa

Taxonomy:Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus

Introduction

The choice to sequence the poplar genome is not only driven by its great economical value but also because poplar is rapidly becoming the model organism for tree biotechnology. Poplar is a perennial plant and has an estimated genome size of ~520 Mbp divided into 19 chromosomes. That is four times larger then the genome of Arabidopsis, yet 40 to 50 times smaller than the genome of pine. The U.S. Department of Energy (DOE), and the Office of Biological and Environmental Research is sequencing the genome of the Populus trichocarpa (black cottonwood). As such, plant biologists will soon have access to a tremendous genetic resource.

The DOE Joint Genome Institute has provided a 3x draft sequence of the female poplar tree clone Nisqually-1 in late-2003 and will provide a second 3x draft in early to mid-2004. The genome is assembled using physical and genetic maps. A whole-genome shotgun approach was used to sequence the Populus genome. However, while the sequencing of the genome is being finished, many tasks need to be accomplished to ensure that the scientific community is able to take full advantage of this resource.

Our involvement

Our research group, who gained an excellent reputation on genome annotation over the past years, is an active partner in the IPGC where two American groups and us are in charge of producing a high quality annotation for this new genome. Producing a quality annotation for this new genome is one of the first tasks that need to be done. To accomplish this daunting task we use a software tool called EuGene, a genome annotation platform that has been developed in collaboration with the research group of T. Schiex for (re)annotating the Arabidopsis genome. For the moment we are retraining this software on Poplar data to get a poplar specific prediction platform capable of predicting genes in this new genome with high accuracy.

In collaboration with:

Publications

2006

Tuskan, G., * 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.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., 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., Luo, Y., Lucas, S., Martin, F., Montanini, B., Nelson, D.R., Nelson, C., Nieminen, K., Nilsson, O., 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., 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 ex Brayshaw). Science 313(5793):1596-604. *contributed equally

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Bioinformatics & Evolutionary Genomics
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