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The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Gerald A. Tuskan 1, 2 Stephen Difazio 1, 3 Stefan Jansson 4 Jörg Bohlmann 5 Igor Grigoriev 6 Uffe Hellsten 6 Nicholas Putnam 6 Steven Ralph 5 Stephane Rombauts 7 Asaf Salamov 6 Jacquie Schein 8 Lieven Sterck 7 Andrea Aerts 6 Rishikesh Bhalerao 4 Rupali Bhalerao 4 Damien Blaudez 9 Wout Boerjan 7 Annick Brun-Jacob 9 Amy Brunner 10 Victor Busov 11 Malcolm Campbell 12 John Carlson 13 Michel Chalot 9 Jarod Chapman 6 Gwo-Liang Chen 14 D. Cooper 5 Pedro Coutinho 15 Jérémy Couturier 9 Sarah Covert 16 Quentin Cronk 17 R. Cunningham 1 John Davis 18 S. Degroeve 7 Annabelle Dejardin 19 Claude Depamphilis 13 John Detter 6 Bill Dirks 20 Inna Dubchak 6, 21 Sébastien Duplessis 9 Jürgen Ehlting 17 Brian Ellis 5 Karla Gendler 22 David Goodstein 6 Michael Gribskov 23 Jane Grimwood 24 Andrew Groover 25 Lee Gunter 1 Britta Hamberger 17 Berthold Heinze 26 Ykä Helariutta 4, 27, 28 Bernard Henrissat 15 Dawn Holligan 29 Robert Holt 8 Wayne Huang 6 Nurul Islam-Faridi 30, 31 Steven Jones 8 Matthew Jones-Rhoades 32 Richard Jorgensen 22 Chandrashekha Joshi 11 Jaakko Kangasjärvi 27 Jan Karlsson 4 Colin Kelleher 5 Robert Kirkpatrick 8 Matias Kirst 18 Annegret Kohler 9 Udaya Kalluri 1 Frank Larimer 14 Jim Leebens-Mack 29 Jean-Charles Leplé 19 Philip Locascio 14 Yunian Lou 6 Susan Lucas 6 Francis Martin 9 Barbara Montanini 9 Carolyn Napoli 22 David R Nelson 33 C. Dana Nelson 30 Kaisa Nieminen 27 Ove Nilsson 4 Veronica Pereda 9 Gary Peter 18 Ryan Philippe 5 Gilles Pilate 19 Alexandre Poliakov 21 Jane Razumovskaya 14 Paul Richardson 6 Cécile Rinaldi 34 Kermit Ritland 35 Pierre Rouzé 7 Dmitriy Ryaboy 21 Jeremy Schmutz 24 J. Schrader 36 Bo Segerman 4 Heesun Shin 8 Asim Siddiqui 8 Fredrik Sterky 37 Astrid Terry 6 Chung-Jui Tsai 11 Edward Uberbacher 14 Per Unneberg 37 Jorma Vahala 27 Kerr Wall 13 Susan Wessler 29 Guojun Yang 29 Tongming Yin 1 Carl Douglas 17 Marco Marra 8 Goran Sandberg 4 Yves van de Peer 7 Daniel S. Rokhsar 20
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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https://hal.inrae.fr/hal-02669155
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Gerald A. Tuskan, Stephen Difazio, Stefan Jansson, Jörg Bohlmann, Igor Grigoriev, et al.. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, American Association for the Advancement of Science, 2006, 313 (5793), pp.1596-1604. ⟨10.1126/science.1128691⟩. ⟨hal-02669155⟩

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