Online citations, reference lists, and bibliographies.
← Back to Search

The Genome Of Black Cottonwood, Populus Trichocarpa (Torr. & Gray)

G. Tuskan, S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, U. Hellsten, N. Putnam, S. Ralph, S. Rombauts, A. Salamov, J. Schein, L. Sterck, A. Aerts, R. Bhalerao, R. Bhalerao, D. Blaudez, W. Boerjan, A. Brun, A. Brunner, V. Busov, M. Campbell, J. Carlson, M. Chalot, J. Chapman, G-L Chen, D. Cooper, P. Coutinho, J. Couturier, S. Covert, Q. Cronk, R. Cunningham, J. Davis, S. Degroeve, A. Déjardin, C. dePamphilis, J. Detter, B. Dirks, I. Dubchak, S. Duplessis, J. Ehlting, B. Ellis, K. Gendler, D. Goodstein, M. Gribskov, J. Grimwood, A. Groover, L. Gunter, B. Hamberger, B. Heinze, Y. Helariutta, B. Henrissat, D. Holligan, R. Holt, W. Huang, N. Islam-Faridi, S. Jones, M. Jones-Rhoades, R. Jørgensen, C. Joshi, J. Kangasjärvi, J. Karlsson, C. Kelleher, R. Kirkpatrick, M. Kirst, A. Kohler, U. Kalluri, F. Larimer, J. Leebens-Mack, J. Leplé, P. LoCascio, Y. Lou, S. Lucas, F. Martin, B. Montanini, C. Napoli, D. R. Nelson, C. Nelson, K. Nieminen, O. Nilsson, V. Pereda, G. Peter, R. Philippe, G. Pilate, A. Poliakov, J. Razumovskaya, P. Richardson, C. Rinaldi, K. Ritland, P. Rouzé, D. Ryaboy, J. Schmutz, J. Schrader, B. Segerman, H. Shin, A. Siddiqui, F. Sterky, A. Terry, C.-J. Tsai, E. Uberbacher, P. Unneberg, J. Vahala, K. Wall, S. Wessler, G. Yang, T. Yin, C. Douglas, M. Marra, G. Sandberg, Y. van de Peer, D. Rokhsar
Published 2006 · Biology, Medicine

Save to my Library
Download PDF
Analyze on Scholarcy Visualize in Litmaps
Reduce the time it takes to create your bibliography by a factor of 10 by using the world’s favourite reference manager
Time to take this seriously.
Get Citationsy
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.
This paper references
I. E. Somssich (1419)
Rapid Activation of Phenylpropanoid Metabolism in Elicitor-Treated Hybrid Poplar (Populus trichocarpa Torr. & Gray x Populus deltoides Marsh) Suspension-Cultured Cells.
M. M. de Sá (1992)
Purification, Characterization, and Cloning of Cinnamyl Alcohol Dehydrogenase in Loblolly Pine (Pinus taeda L.).
D. M. O'malley (1992)
L . A . Dode , Bulletin de la Societe d ' Historie Naturelle d ' Autun 18 , 161 ( 1905 ) . 23 . R . Regnier , Revue des Sociétés Savantes de Normandie ( 1956 ) . 24 . M . E . Collinson
T. M. Hinckley (1992)
Genetic variation and the natural history of quaking aspen
J. Mitton (1996)
The N gene of tobacco confers resistance to tobacco mosaic virus in transgenic tomato.
S. Whitham (1996)
Biology of populus and its implications for management and conservation
R. Stettler (1996)
Arabidopsis thaliana defense-related protein ELI3 is an aromatic alcohol:NADP+ oxidoreductase.
I. Somssich (1996)
CKI1, a Histidine Kinase Homolog Implicated in Cytokinin Signal Transduction
T. Kakimoto (1996)
Automated Gene Identification in Large-Scale Genomic Sequences
Y. Xu (1997)
R. Whetten (1998)
Short-rotation woody crop supply systems in the United States: what do we know and what do we need to know?
G. Tuskan (1998)
Clonal and seasonal differences in leaf osmotic potential and organic solutes of five hybrid poplar clones grown under field conditions.
G. Gebre (1998)
Xyloglucan fucosyltransferase, an enzyme involved in plant cell wall biosynthesis.
R. Perrin (1999)
The cellulose synthase superfamily.
T. Richmond (2000)
Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae).
M. Koch (2000)
Increased gibberellin biosynthesis in transgenic trees promotes growth, biomass production and xylem fiber length
Maria E Eriksson (2000)
The evolutionary fate and consequences of duplicate genes.
M. Lynch (2000)
Using GeneWise in the Drosophila annotation experiment.
E. Birney (2000)
Insights into SCF ubiquitin ligases from the structure of the Skp1–Skp2 complex
B. Schulman (2000)
Ab initio gene finding in Drosophila genomic DNA.
A. Salamov (2000)
Structure and Evolution of 4-Coumarate:Coenzyme A Ligase (4CL) Gene Families
Daniela Cukovica (2001)
The Last Step of Syringyl Monolignol Biosynthesis in Angiosperms Is Regulated by a Novel Gene Encoding Sinapyl Alcohol Dehydrogenase
L. Li (2001)
Computational Biology: selected papers from JOBIM'2000 number
T. Schiex (2001)
R . S . Nandety
S. Kiedrowski (2001)
Biosynthesis of flavonoids and effects of stress.
B. Winkel-Shirley (2002)
Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana
S. Aubourg (2002)
Molecular analysis of herbivore-induced condensed tannin synthesis: cloning and expression of dihydroflavonol reductase from trembling aspen (Populus tremuloides).
D. J. Peters (2002)
A preliminary investigation of the role of auxin and cytokinin in sylleptic branching of three hybrid poplar clones exhibiting contrasting degrees of sylleptic branching.
M. Cline (2002)
Resistance to Ralstonia solanacearum in Arabidopsis thaliana is conferred by the recessive RRS1-R gene, a member of a novel family of resistance genes
L. Deslandes (2002)
Environmental and auxin regulation of wood formation involves members of the Aux/IAA gene family in hybrid aspen.
R. Moyle (2002)
Arabidopsis Contains a Large Superfamily of Acyl-Activating Enzymes. Phylogenetic and Biochemical Analysis Reveals a New Class of Acyl-Coenzyme A Synthetases1
J. Shockey (2003)
Asymmetric expression of a poplar ACC oxidase controls ethylene production during gravitational induction of tension wood.
Sara Andersson-Gunnerås (2003)
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
J. Bowers (2003)
Proanthocyanidin Biosynthesis in Plants
G. J. Tanner (2003)
An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof.
M. A. Costa (2003)
Genome-Wide Characterization of the Lignification Toolbox in Arabidopsis1[w]
J. Raes (2003)
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome.
G. Blanc (2003)
Food and Agricultural Organization of the United Nations, State of the World's Forests
Genomics of cellulose biosynthesis in poplars.
C. Joshi (2004)
The 2R hypothesis and the human genome sequence
K. Hokamp (2004)
A High-Resolution Transcript Profile across the Wood-Forming Meristem of Poplar Identifies Potential Regulators of Cambial Stem Cell Identityw⃞
J. Schrader (2004)
Arabidopsis response regulator, ARR22, ectopic expression of which results in phenotypes similar to the wol cytokinin-receptor mutant.
T. Kiba (2004)
Patterns of Auxin Distribution during Gravitational Induction of Reaction Wood in Poplar and Pine1
Jenny M Hellgren (2004)
Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa
G. Tuskan (2004)
Genetic analysis of cinnamyl alcohol dehydrogenase in loblolly pine: single gene inheritance, molecular characterization and evolution
J. MacKay (2004)
Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map
T. Yin (2004)
Cytogenetic tools for Arabidopsis thaliana
M. Koornneef (2004)
Unravelling cell wall formation in the woody dicot stem
E. Mellerowicz (2004)
A Populus EST resource for plant functional genomics.
F. Sterky (2004)
Computational identification of plant microRNAs and their targets, including a stress-induced miRNA.
M. Jones-Rhoades (2004)
Auxin-responsive gene expression: genes, promoters and regulatory factors
G. Hagen (2004)
Molecular genetics of growth and development in Populus. I. Triploidy in hybrid poplars
H. Bradshaw (2004)
Differential expression patterns of two new primary cell wall-related cellulose synthase cDNAs, PtrCesA6 and PtrCesA7 from aspen trees.
Anita Samuga (2004)
EST data suggest that poplar is an ancient polyploid.
L. Sterck (2005)
Phenotypic variation in growth and biomass distribution for two advanced-generation pedigrees of hybrid poplar
S. Wullschleger (2005)
To B or Not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of the angiosperms.
L. Zahn (2005)
COBRA, an Arabidopsis Extracellular Glycosyl-Phosphatidyl Inositol-Anchored Protein, Specifically Controls Highly Anisotropic Expansion through Its Involvement in Cellulose Microfibril Orientationw⃞
F. Roudier (2005)
Plant conserved non-coding sequences and paralogue evolution.
S. Lockton (2005)
Novel patterns of gene expression in polyploid plants.
K. Adams (2005)
Evolving disease resistance genes.
B. Meyers (2005)
Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators
D. Weijers (2005)
The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes
Soraya Djerbi (2005)
Genome duplication and the origin of angiosperms.
Stefanie De Bodt (2005)
Rfam: annotating non-coding RNAs in complete genomes
S. Griffiths-Jones (2005)
Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation.
J. Ehlting (2005)
Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication.
B. Chapman (2006)
Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice[W]
T. Nakano (2006)
Cytokinin Signaling and Its Inhibitor AHP6 Regulate Cell Fate During Vascular Development
A. P. Mähönen (2006)
Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus.
Chung-Jui Tsai (2006)
Materials and methods are available as supporting material on Science Online
Office of Science for supporting the sequencing and assembly portion of this study

This paper is referenced by
Multiplex knockout of trichome-regulating MYBs in poplar affects light sensitivity and triterpene accumulation
W. P. Bewg (2021)
Plant sex chromosomes defy evolutionary models of expanding recombination suppression and genetic degeneration.
S. Renner (2021)
Enhancement of Zn tolerance and accumulation in plants mediated by the expression of Saccharomyces cerevisiae vacuolar transporter ZRC1
Giovanni DalCorso (2021)
Biomass formation and sugar release efficiency of Populus modified by altered expression of a NAC transcription factor
Raja S Payyavula (2021)
Adaptive introgression facilitate adaptation to high latitudes in European aspen (Populus tremula L.).
M. Rendón-Anaya (2021)
A Chromosome-level Assembly of A Wild Castor Genome Provides New Insights into the Adaptive Evolution in A Tropical Desert.
Jianjun Lu (2021)
Physiological and molecular basis of plants tolerance to linear halogenated hydrocarbons
M. Akram (2021)
Integrative genomics reveals paths to sex dimorphism in Salix purpurea L
Brennan Hyden (2021)
Identification of genetic markers and wood properties that predict wood biorefinery potential in aspen bioenergy feedstock (Populus tremula)
Sacha Escamez (2021)
Economical concerns of lignin in the energy sector
Archita Sharma (2021)
Polyamine oxidase (PAO)–mediated polyamine catabolism plays potential roles in peach (Prunus persica L.) fruit development and ripening
Wei Wang (2021)
A peroxisomal β-oxidative pathway contributes to the formation of C6-C1 aromatic volatiles in poplar.
Nathalie D Lackus (2021)
Genome-Wide Investigation of the NF-X1 Gene Family in Populus trichocarpa Expression Profiles during Development and Stress
Fang He (2021)
An improved and efficient method of Agrobacterium syringe infiltration for transient transformation and its application in the elucidation of gene function in poplar
Lin Zheng (2021)
Genome and Transcriptome Sequencing of Populus × sibirica Identified Sex-Associated Allele-Specific Expression of the CLC Gene
E. Pushkova (2021)
Genome-Wide Analysis of Coding and Non-coding RNA Reveals a Conserved miR164–NAC–mRNA Regulatory Pathway for Disease Defense in Populus
Sisi Chen (2021)
A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus
D. Conde (2021)
Physiological and Transcriptome Responses to Elevated CO2 Concentration in Populus
Tae-Lim Kim (2021)
Comparative transcriptome analysis of Salix cupularis under drought stress
Danping Xu (2021)
Analysis of Populus glycosyl hydrolase family I members and their potential role in the ABA treatment and drought stress response.
Zhan Bian (2021)
Gene duplication and rate variation in the evolution of non-photosynthetic pathways in plastids
Alissa M. Williams (2021)
Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica
N. Melnikova (2021)
Use of Genomic Resources to Assess Adaptive Divergence and Introgression in Oaks
Desanka Lazić (2021)
Complete chloroplast genome sequence and phylogenetic analysis of Populus deltoides Caihong
W. Zhuang (2021)
A Comprehensive Phylogenetic Analysis of the MAP4K Family in the Green Lineage
Lixia Pan (2021)
Genome-wide identification and characterization of the TPS gene family in wheat (Triticum aestivum L.) and expression analysis in response to aphid damage
Lei Zhao (2021)
Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees
Madhavi Latha Gandla (2021)
Genome sequence and evolution of Betula platyphylla
Su Chen (2021)
Contrasting genetic signal of recolonization after rainforest fragmentation in African trees with different dispersal abilities
R. Piñeiro (2021)
Integrating Transcriptome and Coexpression Network Analyses to Characterize Salicylic Acid- and Jasmonic Acid-Related Genes in Tolerant Poplars Infected with Rust
Qiaoli Chen (2021)
Ectomycorrhizal fungal communities differ among parental and hybrid Populus cross types within a natural riparian habitat
L. J. Lamit (2021)
Early Response to Dehydration Six-Like Transporter Family: Early Origin in Streptophytes and Evolution in Land Plants
Lucie Slawinski (2021)
See more
Semantic Scholar Logo Some data provided by SemanticScholar