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

We report the draft genome of the black cottonwood tree, Populus trichocarpa

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. 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. Jorgensen; C. Joshi; J. Kangasjärvi; J. Karlsson; C. Kelleher; R. Kirkpatrick; M. Kirst; A. Kohler; U. Kalluri; F. Larimer; J. Leebens-Mack; J.-C. 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


Scholarcy highlights

  • A phylogenetic analysis using the known and predicted auxin response factor protein sequences showed that Populus and Arabidopsis ARF gene families have expanded independently since they diverged from their common ancestor
  • The total number of members in gene families encoding cytokinin homeostasis related isopentenyl transferases and cytokinin oxidases is roughly similar between Populus and Arabidopsis, there appears to be lineage-specific expansion of IPT subfamilies
  • Our initial analyses provide a flavor of the opportunities for comparative plant genomics made possible by the generation of the Populus genome sequence
  • The differences in gene content between Populus and Arabidopsis have provided some tantalizing insights into the possible molecular bases of their strongly contrasting life histories, though it is important to note that factors unrelated to gene content may be of equal or greater importance
  • With the sequence of Populus, researchers can go beyond what could be learned from Arabidopsis alone to explore hypotheses to linking genome sequence features to wood development, nutrient and water movement, crown development, and disease resistance in perennial plants
  • Both of these gene families have been implicated in the negative regulation of cytokinin signaling , which is consistent with the idea of increased complexity in regulation of cytokinin signal transduction in Populus and Arabidopsis genomes contain almost identical number of genes for the three enzymes of ethylene biosynthesis, whereas the number of genes for proteins involved in ethylene perception and signaling is higher in Populus

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