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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 M. 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 G. 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

1 Environmental Sciences Division [Oak Ridge]

2 University of Tennessee

3 Department of Biology

4 SLU - Swedish University of Agricultural Sciences

5 Michael Smith Laboratories

6 JGI - Joint Genome Institute

7 Department of plant systems biology

8 CMSGSC - Canada's Michael Smith Genome Sciences Centre

9 IAM - Interactions Arbres-Microorganismes

10 Virginia Polytechnic Institute and State University [Blacksburg]

11 MTU - Michigan Technological University

12 Department of Cell and Systems Biology

13 Penn State - Pennsylvania State University

14 Oak Ridge National Laboratory

15 Université de la Méditerranée - Aix-Marseille 2

16 Warnell School of Forest Resources

17 Department of Botany

18 UF - University of Florida [Gainesville]

19 AGPF - Unité de recherche Amélioration, Génétique et Physiologie Forestières

20 University of California [Berkeley]

21 Genomics Division [LBNL Berkeley]

22 University of Arizona

23 Department of Biological Sciences [Lafayette IN]

24 Stanford University

25 US Forest Service

26 Federal Research and Training Centre for Forests Natural Hazards and Landscape

27 Helsingin yliopisto = Helsingfors universitet = University of Helsinki

28 Department of Biology

29 Department of Plant Biology

30 United States Department of Agriculture

31 Texas A&M University System

32 MIT - Whitehead Institute for Biomedical Research and Department of Biology

33 Department of Molecular Sciences and Center of Excellence in Genomics and Bioinformatics

34 EEF - Ecologie et Ecophysiologie Forestières [devient SILVA en 2018]

35 Department of Forest Sciences [Vancouver]

36 Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen

37 KTH - Royal Institute of Technology in Stockholm

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.

Keywords : IDENTIFICATION DE GENES

Document type :

Journal articles

Domain :

Life Sciences [q-bio] / Cellular Biology

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https://hal.inrae.fr/hal-02669155
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Submitted on : Sunday, May 31, 2020 - 2:27:30 PM
Last modification on : Monday, May 9, 2022 - 11:58:08 AM