The Genome of Black Cottonwood, <i>Populus trichocarpa</i> (Torr. & Gray)
Gerald A. TuskanDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAStephen DiFazioDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAStefan JanssonDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJöerg BohlmannDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAIgor V. GrigorievDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAUffe HellstenDepartment of Biology, West Virginia University, Morgantown, WV 26506, USANicholas H. PutnamDepartment of Biology, West Virginia University, Morgantown, WV 26506, USASteven RalphDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAStéphane RombautsDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAAsaf SalamovDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJacqueline E. ScheinDepartment of Biology, West Virginia University, Morgantown, WV 26506, USALieven SterckDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAAndrea AertsDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAR. R. BhaleraoDepartment of Biology, West Virginia University, Morgantown, WV 26506, USARishikesh P. BhaleraoDepartment of Biology, West Virginia University, Morgantown, WV 26506, USADamien BlaudezDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAWout BoerjanDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAAnnick BrunDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAAmy M. BrunnerDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAVictor BusovDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAMalcolm M. CampbellDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJohn E. CarlsonDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAMichel ChalotDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJarrod ChapmanDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAG.-L. ChenDepartment of Biology, West Virginia University, Morgantown, WV 26506, USADawn CooperDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAPedro M. CoutinhoDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJérémy CouturierDepartment of Biology, West Virginia University, Morgantown, WV 26506, USASarah F. CovertDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAQuentin CronkDepartment of Biology, West Virginia University, Morgantown, WV 26506, USARichard P. CunninghamDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJohn M. DavisDepartment of Biology, West Virginia University, Morgantown, WV 26506, USASven DegroeveDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAAnnabelle DéjardinDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAClaude W. dePamphilisDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJohn C. DetterDepartment of Biology, West Virginia University, Morgantown, WV 26506, USABill DirksDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAInna DubchakDepartment of Biology, West Virginia University, Morgantown, WV 26506, USASébastien DuplessisDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJürgen EhltingDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAB. E. EllisDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAKarla GendlerDepartment of Biology, West Virginia University, Morgantown, WV 26506, USADavid GoodsteinDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAMichael GribskovDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJane GrimwoodDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAAndrew GrooverDepartment of Biology, West Virginia University, Morgantown, WV 26506, USALee E. GunterDepartment of Biology, West Virginia University, Morgantown, WV 26506, USABjörn HambergerDepartment of Biology, West Virginia University, Morgantown, WV 26506, USABerthold HeinzeDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAYkä HelariuttaDepartment of Biology, West Virginia University, Morgantown, WV 26506, USABernard HenrissatDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAD. HolliganDepartment of Biology, West Virginia University, Morgantown, WV 26506, USARobert A. HoltDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAWenjiang HuangDepartment of Biology, West Virginia University, Morgantown, WV 26506, USANurul Islam‐FaridiDepartment of Biology, West Virginia University, Morgantown, WV 26506, USASteven J.M. JonesDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAMatthew W. Jones-RhoadesDepartment of Biology, West Virginia University, Morgantown, WV 26506, USARichard A. JorgensenDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAChandrashekhar P. JoshiDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJaakko KangasjärviDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJan KarlssonDepartment of Biology, West Virginia University, Morgantown, WV 26506, 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 KohlerDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAUdaya C. KalluriDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAFrank W. LarimerDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJim Leebens‐MackDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJean‐Charles LepléDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAPhilip LoCascioDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAYonggen LouDepartment of Biology, West Virginia University, Morgantown, WV 26506, USASusan LucasDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAFrancis MartinDepartment of Biology, West Virginia University, Morgantown, WV 26506, USABarbara MontaniniDepartment of Biology, West Virginia University, Morgantown, WV 26506, USACarolyn A. NapoliDepartment of Biology, West Virginia University, Morgantown, WV 26506, USADavid R. NelsonDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAC. Dana NelsonDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAKaisa NieminenDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAOve NilssonDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAV. PeredaDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAG. F. PeterDepartment of Biology, West Virginia University, Morgantown, WV 26506, USARyan N. PhilippeDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAGilles PilateDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAAlexandre PoliakovDepartment of Biology, West Virginia University, Morgantown, WV 26506, 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 RouzéDepartment of Biology, West Virginia University, Morgantown, WV 26506, USADmitriy RyaboyDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJeremy SchmutzDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAJarmo SchraderDepartment of Biology, West Virginia University, Morgantown, WV 26506, USABo SegermanDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAH. ShinDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAAsim SiddiquiDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAFredrik SterkyDepartment of Biology, West Virginia University, Morgantown, WV 26506, USAAstrid TerryDepartment of Biology, West Virginia University, Morgantown, WV 26506, 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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