The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

@article{Tuskan2006TheGO,
  title={The Genome of Black Cottonwood, Populus trichocarpa (Torr. \& Gray)},
  author={Gerald A. Tuskan and Stephen P. DiFazio and Sandra Jansson and Joerg Bohlmann and Igor V. Grigoriev and Uffe Hellsten and Nik Putnam and Steven G. Ralph and Stephane Rombauts and Asaf A. Salamov and Jacquie E. Schein and Lieven Sterck and Andrea Aerts and Rupali R Bhalerao and Rishikesh P. Bhalerao and Damien Blaudez and Wout Boerjan and A. Brun and Adrian Brunner and Victor B Busov and Micaela Campbell and Jessica Carlson and Michel Chalot and Jarod Chapman and G.-L. Chen and Donald Cooper and Pedro M. Coutinho and Jean Couturier and Sarah F. Covert and Quentin C. B. Cronk and R. Cunningham and J. Davis and Sven Degroeve and Annabelle D{\'e}jardin and Claude W. dePamphilis and John C. Detter and Bill Dirks and Inna Dubchak and S{\'e}bastien Duplessis and Juergen Ehlting and Barbara Ellis and Karla Gendler and David M. Goodstein and Michael Gribskov and Jane Grimwood and Andrew T. Groover and Lee E. Gunter and Bjoern Hamberger and B. Heinze and Yrj{\"o} Helariutta and Bernard Henrissat and Dawn Holligan and Roger Holt and W H Huang and Nurul Islam-Faridi and S. J. M. Jones and Matthew W. Jones-Rhoades and Roger J{\o}rgensen and Cj Joshi and Jaakko Kangasj{\"a}rvi and J. Karlsson and Caren Kelleher and Russell Kirkpatrick and Matias Kirst and Annegret Kohler and Udaya C. Kalluri and Frank W. Larimer and James H. Leebens-Mack and Jean-Charles Lepl{\'e} and Philip F. LoCascio and Yigong Lou and Susan M. Lucas and Frank Martin and Barbara Montanini and Chiara Napoli and David R. Nelson and Cathy Nelson and Kaisa Nieminen and Ove Nilsson and V. Pereda and G. Peter and Romain Philippe and Gilles Pilate and Alexandre Poliakov and Jane Razumovskaya and P. Paul Richardson and Cécile Rinaldi and Kelvin Ritland and Pierre Rouz{\'e} and Dmitriy V. Ryaboy and Jeremy Schmutz and J. Schrader and Bo Segerman and H. Shin and A. Siddiqui and Fredrik H. Sterky and Astrid Y Terry and C-J. Tsai and Edward C. Uberbacher and Per Unneberg and Jorma Vahala and Kerr Wall and Susan R. Wessler and G. Yang and Tao Yin and C. Douglas and Madison Marra and G{\"o}sta Sandberg and Yves van de Peer and Daniel S. Rokhsar},
  journal={Science},
  year={2006},
  volume={313},
  pages={1596 - 1604}
}
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… 
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References

SHOWING 1-10 OF 71 REFERENCES
The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes
TLDR
A phylogenetic analysis suggests that the CesA genes previously associated with secondary cell wall synthesis originate from a single ancestor gene and group in three distinct subgroups and give rise to a number of new questions concerning the mechanism of cellulose synthesis in trees.
Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana
TLDR
Phylogenetic analyses highlight events in the divergence of the TPS paralogs and suggest orthologous genes and a model for the evolution of theTPS gene family.
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
TLDR
It is shown that a genome-wide duplication post-dates the divergence of Arabidopsis from most dicots, and that additional, more ancient duplication events affect more distant taxonomic comparisons.
Genome-Wide Characterization of the Lignification Toolbox in Arabidopsis1[w]
TLDR
Together, these data describe the full complement of monolignol biosynthesis genes in Arabidopsis, provide a unified nomenclature, and serve as a basis for further functional studies.
A Populus EST resource for plant functional genomics.
  • F. Sterky, R. Bhalerao, S. Jansson
  • Environmental Science, Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2004
TLDR
The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation.
Genetic analysis of cinnamyl alcohol dehydrogenase in loblolly pine: single gene inheritance, molecular characterization and evolution
TLDR
The presence of a single gene suggests that different regulatory mechanisms for a single Cad gene, rather than differential regulation of several genes, can account for its expression in response to different cues.
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome.
TLDR
It is concluded that the Arabidopsis lineage underwent at least two distinct episodes of duplication, one of which was a polyploidy that occurred much more recently than estimated previously and probably during the early emergence of the crucifer family.
Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map
TLDR
It is hypothesized that divergent selection has occurred on chromosomal scales among the parental species used to create this pedigree, and the evolutionary implications of this observation are explored.
EST data suggest that poplar is an ancient polyploid.
TLDR
From this analysis, it is clear that all poplar species have shared the same large-scale gene-duplication event, suggesting that this event must have occurred in the ancestor of poplar, or at least very early in the evolution of the Populus genus.
...
1
2
3
4
5
...