The Genome of Black Cottonwood,
Populus trichocarpa
(Torr. & Gray)
Author:
Tuskan G. A.12345, DiFazio S.12345, Jansson S.12345, Bohlmann J.12345, Grigoriev I.12345, Hellsten U.12345, Putnam N.12345, Ralph S.12345, Rombauts S.12345, Salamov A.12345, Schein J.12345, Sterck L.12345, Aerts A.12345, Bhalerao R. R.12345, Bhalerao R. P.12345, Blaudez D.12345, Boerjan W.12345, Brun A.12345, Brunner A.12345, Busov V.12345, Campbell M.12345, Carlson J.12345, Chalot M.12345, Chapman J.12345, Chen G.-L.12345, Cooper D.12345, Coutinho P. M.12345, Couturier J.12345, Covert S.12345, Cronk Q.12345, Cunningham R.12345, Davis J.12345, Degroeve S.12345, Déjardin A.12345, dePamphilis C.12345, Detter J.12345, Dirks B.12345, Dubchak I.12345, Duplessis S.12345, Ehlting J.12345, Ellis B.12345, Gendler K.12345, Goodstein D.12345, Gribskov M.12345, Grimwood J.12345, Groover A.12345, Gunter L.12345, Hamberger B.12345, Heinze B.12345, Helariutta Y.12345, Henrissat B.12345, Holligan D.12345, Holt R.12345, Huang W.12345, Islam-Faridi N.12345, Jones S.12345, Jones-Rhoades M.12345, Jorgensen R.12345, Joshi C.12345, Kangasjärvi J.12345, Karlsson J.12345, Kelleher C.12345, Kirkpatrick R.12345, Kirst M.12345, Kohler A.12345, Kalluri U.12345, Larimer F.12345, Leebens-Mack J.12345, Leplé J.-C.12345, Locascio P.12345, Lou Y.12345, Lucas S.12345, Martin F.12345, Montanini B.12345, Napoli C.12345, Nelson D. R.12345, Nelson C.12345, Nieminen K.12345, Nilsson O.12345, Pereda V.12345, Peter G.12345, Philippe R.12345, Pilate G.12345, Poliakov A.12345, Razumovskaya J.12345, Richardson P.12345, Rinaldi C.12345, Ritland K.12345, Rouzé P.12345, Ryaboy D.12345, Schmutz J.12345, Schrader J.12345, Segerman B.12345, Shin H.12345, Siddiqui A.12345, Sterky F.12345, Terry A.12345, Tsai C.-J.12345, Uberbacher E.12345, Unneberg P.12345, Vahala J.12345, Wall K.12345, Wessler S.12345, Yang G.12345, Yin T.12345, Douglas C.12345, Marra M.12345, Sandberg G.12345, Van de Peer Y.12345, Rokhsar D.12345
Affiliation:
1. Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. 2. Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. 3. Plant Sciences Department, University of Tennessee, TN 37996, USA. 4. Department of Biology, West Virginia University, Morgantown, WV 26506, USA. 5. Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.
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.
Publisher
American Association for the Advancement of Science (AAAS)
Subject
Multidisciplinary
Reference83 articles.
1. State of the World's Forests 2003 2003 2. R. F. Stettler, H. D. Bradshaw Jr., in Biology of Populus and Its Implications for Management and Conservation, R. F. Stettler, H. D. Bradshaw Jr., P. E. Heilman, T. M. Hinckley, Eds. (NRC Research Press, Ottawa, 1996), pp. 1–7. 3. Poplar Genomics is Getting Popular: The Impact of the Poplar Genome Project on Tree Research 4. Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map 5. R. Meilan, C. Ma, in Agrobacterium Protocols, vol. 344 of Methods in Molecular Biology, K. Wang, Ed. (Humana Press, Totowa, NJ, 2006), pp. 143–151.
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