The Genome of Black Cottonwood, <i>Populus trichocarpa</i> (Torr. & Gray)
Gerald A. Tuskan(West Virginia University), Stephen DiFazio(West Virginia University), Stefan Jansson(West Virginia University), Jöerg Bohlmann(West Virginia University), Igor V. Grigoriev(West Virginia University), Uffe Hellsten(West Virginia University), Nicholas H. Putnam(West Virginia University), Steven Ralph(West Virginia University), Stéphane Rombauts(West Virginia University), Asaf Salamov(West Virginia University), Jacqueline E. Schein(West Virginia University), Lieven Sterck(West Virginia University), Andrea Aerts(West Virginia University), R. R. Bhalerao(West Virginia University), Rishikesh P. Bhalerao(West Virginia University), Damien Blaudez(West Virginia University), Wout Boerjan(West Virginia University), Annick Brun(West Virginia University), Amy M. Brunner(West Virginia University), Victor Busov(Michigan Technological University), Malcolm M. Campbell(West Virginia University), John E. Carlson(West Virginia University), Michel Chalot(West Virginia University), Jarrod Chapman(West Virginia University), G.-L. Chen(West Virginia University), Dawn Cooper(West Virginia University), Pedro M. Coutinho(West Virginia University), Jérémy Couturier(West Virginia University), Sarah F. Covert(West Virginia University), Quentin Cronk(West Virginia University), Richard P. Cunningham(West Virginia University), John M. Davis(West Virginia University), Sven Degroeve(West Virginia University), Annabelle Déjardin(West Virginia University), Claude W. dePamphilis(West Virginia University), John C. Detter(West Virginia University), Bill Dirks(West Virginia University), Inna Dubchak(West Virginia University), Sébastien Duplessis(West Virginia University), Jürgen Ehlting(West Virginia University), B. E. Ellis(West Virginia University), Karla Gendler(West Virginia University), David Goodstein(West Virginia University), Michael Gribskov(West Virginia University), Jane Grimwood(West Virginia University), Andrew Groover(West Virginia University), Lee E. Gunter(West Virginia University), Björn Hamberger(West Virginia University), Berthold Heinze(West Virginia University), Ykä Helariutta(West Virginia University), Bernard Henrissat(West Virginia University), D. Holligan(West Virginia University), Robert A. Holt(West Virginia University), Wenjiang Huang(West Virginia University), Nurul Islam‐Faridi(West Virginia University), Steven J.M. Jones(West Virginia University), Matthew W. Jones-Rhoades(West Virginia University), Richard A. Jorgensen(West Virginia University), Chandrashekhar P. Joshi(Michigan Technological University), Jaakko Kangasjärvi(West Virginia University), Jan Karlsson(West Virginia University), Colin T. Kelleher(West Virginia University), Robert B. Kirkpatrick(West Virginia University), Matias Kirst(West Virginia University), Annegret Kohler(West Virginia University), Udaya C. Kalluri(West Virginia University), Frank W. Larimer(West Virginia University), Jim Leebens‐Mack(West Virginia University), Jean‐Charles Leplé(West Virginia University), Philip LoCascio(West Virginia University), Yonggen Lou(West Virginia University), Susan Lucas(West Virginia University), Francis Martin(West Virginia University), Barbara Montanini(West Virginia University), Carolyn A. Napoli(West Virginia University), David R. Nelson(West Virginia University), C. Dana Nelson(West Virginia University), Kaisa Nieminen(West Virginia University), Ove Nilsson(West Virginia University), V. Pereda(West Virginia University), G. F. Peter(West Virginia University), Ryan N. Philippe(West Virginia University), Gilles Pilate(West Virginia University), Alexandre Poliakov(West Virginia University), Jane Razumovskaya(West Virginia University), Paul Richardson(West Virginia University), Cécile Rinaldi(West Virginia University), Kermit Ritland(West Virginia University), Pierre Rouzé(West Virginia University), Dmitriy Ryaboy(West Virginia University), Jeremy Schmutz(West Virginia University), Jarmo Schrader(West Virginia University), Bo Segerman(West Virginia University), H. Shin(West Virginia University), Asim Siddiqui(West Virginia University), Fredrik Sterky(West Virginia University), Astrid Terry(West Virginia University), Chung‐Jui Tsai(Michigan Technological University), Ed Uberbacher(West Virginia University), Per Unneberg(West Virginia University), Jorma Vahala(West Virginia University), Kerr Wall(West Virginia University), Susan R. Wessler(West Virginia University), George Yang(West Virginia University), T. M. Yin(West Virginia University), Carl J. Douglas(West Virginia University), Marco A. Marra(West Virginia University), Göran Sandberg(West Virginia University), Yves Van de Peer(West Virginia University), Daniel S. Rokhsar(West Virginia University)
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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.
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