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The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
G. A. 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. R. Bhalerao ,
R. P. 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. M. Coutinho ,
J. Couturier ,
S. Covert ,
Q. Cronk ,
R. Cunningham ,
J. Davis ,
S. Degroeve ,
A. Dejardin ,
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. Jorgensen ,
C. Joshi ,
J. Kangasjarvi ,
J. Karlsson ,
C. Kelleher ,
R. Kirkpatrick ,
M. Kirst ,
A. Kohler ,
U. Kalluri ,
F. Larimer ,
J. Leebens-Mack ,
J.-C. Leple ,
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. Rouze ,
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
September 15 2006
September 15 2006
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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.