The Genome of Black Cottonwood, <i>Populus trichocarpa</i> (Torr. & Gray)
Gerald A. TuskanDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAStephen DiFazioEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAStefan JanssonDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJöerg BohlmannDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAIgor V. GrigorievLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAUffe HellstenUmeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, SwedenNicholas H. PutnamPlant Sciences Department, University of Tennessee, TN 37996, USASteven RalphPlant Sciences Department, University of Tennessee, TN 37996, USAStéphane RombautsDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAAsaf SalamovLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAJacqueline E. ScheinDepartment of Biology, West Virginia University, Morgantown, WV 26506, USALieven SterckPlant Sciences Department, University of Tennessee, TN 37996, USAAndrea AertsUmeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, SwedenR. R. BhaleraoLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USARishikesh P. BhaleraoDepartment of Biology, West Virginia University, Morgantown, WV 26506, USADamien BlaudezPlant Sciences Department, University of Tennessee, TN 37996, USAWout BoerjanPlant Sciences Department, University of Tennessee, TN 37996, USAAnnick BrunPlant Sciences Department, University of Tennessee, TN 37996, USAAmy M. BrunnerLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAVictor BusovEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAMalcolm M. CampbellLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAJohn E. CarlsonDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAMichel ChalotPlant Sciences Department, University of Tennessee, TN 37996, USAJarrod ChapmanDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAG.-L. ChenEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USADawn CooperEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAPedro M. CoutinhoEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAJérémy CouturierLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USASarah F. CovertLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAQuentin CronkPlant Sciences Department, University of Tennessee, TN 37996, USARichard P. CunninghamEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAJohn M. DavisLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USASven DegroeveEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAAnnabelle DéjardinEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAClaude W. dePamphilisPlant Sciences Department, University of Tennessee, TN 37996, USAJohn C. DetterPlant Sciences Department, University of Tennessee, TN 37996, USABill DirksEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAInna DubchakDepartment of Biology, West Virginia University, Morgantown, WV 26506, USASébastien DuplessisLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAJürgen EhltingPlant Sciences Department, University of Tennessee, TN 37996, USAB. E. EllisDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAKarla GendlerEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USADavid GoodsteinUmeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, SwedenMichael GribskovDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJane GrimwoodEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAAndrew GrooverPlant Sciences Department, University of Tennessee, TN 37996, USALee E. GunterPlant Sciences Department, University of Tennessee, TN 37996, USABjörn HambergerLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USABerthold HeinzeLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAYkä HelariuttaDepartment of Biology, West Virginia University, Morgantown, WV 26506, USABernard HenrissatDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAD. HolliganEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USARobert A. HoltPlant Sciences Department, University of Tennessee, TN 37996, USAWenjiang HuangPlant Sciences Department, University of Tennessee, TN 37996, USANurul Islam‐FaridiDepartment of Biology, West Virginia University, Morgantown, WV 26506, USASteven J.M. JonesPlant Sciences Department, University of Tennessee, TN 37996, USAMatthew W. Jones-RhoadesUmeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, SwedenRichard A. JorgensenLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAChandrashekhar P. JoshiLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAJaakko KangasjärviUmeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, SwedenJan KarlssonLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAColin T. KelleherDepartment of Biology, West Virginia University, Morgantown, WV 26506, USARobert B. KirkpatrickDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAMatias KirstDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAAnnegret KohlerPlant Sciences Department, University of Tennessee, TN 37996, USAUdaya C. KalluriLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAFrank W. LarimerPlant Sciences Department, University of Tennessee, TN 37996, USAJim Leebens‐MackEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAJean‐Charles LepléEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAPhilip LoCascioEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAYonggen LouPlant Sciences Department, University of Tennessee, TN 37996, USASusan LucasUmeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, SwedenFrancis MartinEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USABarbara MontaniniLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USACarolyn A. NapoliDepartment of Biology, West Virginia University, Morgantown, WV 26506, USADavid R. NelsonEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAC. Dana NelsonLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAKaisa NieminenUmeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, SwedenOve NilssonPlant Sciences Department, University of Tennessee, TN 37996, USAV. PeredaLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAG. F. PeterLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USARyan N. PhilippeLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAGilles PilateDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAAlexandre PoliakovLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAJane RazumovskayaDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAPaul RichardsonDepartment of Biology, West Virginia University, Morgantown, WV 26506, USACécile RinaldiDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAKermit RitlandDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAPierre RouzéEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USADmitriy RyaboyEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAJeremy SchmutzUmeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, SwedenJarmo SchraderDepartment of Biology, West Virginia University, Morgantown, WV 26506, USABo SegermanLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAH. ShinDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAAsim SiddiquiLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAFredrik SterkyLife Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAAstrid TerryPlant Sciences Department, University of Tennessee, TN 37996, USAChung‐Jui TsaiDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAEd UberbacherDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAPer UnnebergDepartment of Biology, West Virginia University, Morgantown, WV 26506, USA
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Annotatsiya
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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