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 = Sveriges lantbruksuniversitet
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 [State College, PA]
14 ORNL - Oak Ridge National Laboratory [Oak Ridge]
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 UC Berkeley - University of California [Berkeley]
21 Genomics Division [LBNL Berkeley]
22 University of Arizona
23 Department of Biological Sciences [West Lafayette]
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 = University of Tübingen
37 KTH - KTH Royal Institute of Technology [Stockholm]
2 University of Tennessee
3 Department of Biology
4 SLU - Swedish University of Agricultural Sciences = Sveriges lantbruksuniversitet
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 [State College, PA]
14 ORNL - Oak Ridge National Laboratory [Oak Ridge]
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 UC Berkeley - University of California [Berkeley]
21 Genomics Division [LBNL Berkeley]
22 University of Arizona
23 Department of Biological Sciences [West Lafayette]
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 = University of Tübingen
37 KTH - KTH Royal Institute of Technology [Stockholm]
Igor Grigoriev
- Fonction : Auteur
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- ORCID : 0000-0002-3136-8903
- IdRef : 229928536
Lieven Sterck
- Fonction : Auteur
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- ORCID : 0000-0001-7116-4000
Damien Blaudez
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Annick Brun-Jacob
- Fonction : Auteur
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- ORCID : 0000-0002-0299-2766
Michel M. Chalot
- Fonction : Auteur
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- IdHAL : michel-chalot
- ORCID : 0000-0001-8614-0917
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Jérémy Couturier
- Fonction : Auteur
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- IdHAL : jeremy-couturier
- ORCID : 0000-0003-3127-2669
- IdRef : 120435713
Annabelle Dejardin
- Fonction : Auteur
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- IdHAL : annabelle-dejardin
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Sébastien Duplessis
- Fonction : Auteur
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- IdHAL : sebastien-duplessis
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- IdRef : 144092948
Bernard Henrissat
- Fonction : Auteur
- PersonId : 833340
Robert Holt
- Fonction : Auteur
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- ORCID : 0000-0002-6685-547X
Annegret Kohler
- Fonction : Auteur
- PersonId : 741288
- IdHAL : annegret-kohler
- ORCID : 0000-0002-9575-9567
- IdRef : 161080588
Jean-Charles Leplé
- Fonction : Auteur
- PersonId : 745829
- IdHAL : jean-charles-leple
- ORCID : 0000-0003-4125-0738
- IdRef : 225531011
Francis Martin
- Fonction : Auteur
- PersonId : 1203753
- ORCID : 0000-0002-4737-3715
- IdRef : 059918268
Gilles G. Pilate
- Fonction : Auteur
- PersonId : 737222
- IdHAL : gilles-pilate
- ORCID : 0000-0003-4802-8849
- IdRef : 057116849
Yves van de Peer
- Fonction : Auteur
- PersonId : 1361958
- ORCID : 0000-0003-4327-3730
- IdRef : 277522080
Résumé
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.