ScholarLens Back to search
2006•ScienceOpen access

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

Gerald A. Tuskan, Stephen DiFazio, Stefan Jansson, Jöerg Bohlmann, Igor V. Grigoriev, Uffe Hellsten, Nicholas H. Putnam, Steven Ralph, Stéphane Rombauts, Asaf Salamov, Jacqueline E. Schein, Lieven Sterck, Andrea Aerts, R. R. Bhalerao, Rishikesh P. Bhalerao, Damien Blaudez, Wout Boerjan, Annick Brun, Amy M. Brunner, Victor Busov, Malcolm M. Campbell, John E. Carlson, Michel Chalot, Jarrod Chapman, G.-L. Chen, Dawn Cooper, Pedro M. Coutinho, Jérémy Couturier, Sarah F. Covert, Quentin Cronk, Richard P. Cunningham, John M. Davis, Sven Degroeve, Annabelle Déjardin, Claude W. dePamphilis, John C. Detter, Bill Dirks, Inna Dubchak, Sébastien Duplessis, Jürgen Ehlting, B. E. Ellis, Karla Gendler, David Goodstein, Michael Gribskov, Jane Grimwood, Andrew Groover, Lee E. Gunter, Björn Hamberger, Berthold Heinze, Ykä Helariutta, Bernard Henrissat, D. Holligan, Robert A. Holt, Wenjiang Huang, Nurul Islam‐Faridi, Steven J.M. Jones, Matthew W. Jones-Rhoades, Richard A. Jorgensen, Chandrashekhar P. Joshi, Jaakko Kangasjärvi, Jan Karlsson, Colin T. Kelleher, Robert B. Kirkpatrick, Matias Kirst, Annegret Kohler, Udaya C. Kalluri, Frank W. Larimer, Jim Leebens‐Mack, Jean‐Charles Leplé, Philip LoCascio, Yonggen Lou, Susan Lucas, Francis Martin, Barbara Montanini, Carolyn A. Napoli, David R. Nelson, C. Dana Nelson, Kaisa Nieminen, Ove Nilsson, V. Pereda, G. F. Peter, Ryan N. Philippe, Gilles Pilate, Alexandre Poliakov, Jane Razumovskaya, Paul Richardson, Cécile Rinaldi, Kermit Ritland, Pierre Rouzé, Dmitriy Ryaboy, Jeremy Schmutz, Jarmo Schrader, Bo Segerman, H. Shin, Asim Siddiqui, Fredrik Sterky, Astrid Terry, Chung‐Jui Tsai, Ed Uberbacher, Per Unneberg, Jorma Vahala, Kerr Wall, Susan R. Wessler, George Yang, T. M. Yin, Carl J. Douglas, Marco A. Marra, Göran Sandberg, Yves Van de Peer, Daniel S. Rokhsar

Open full text 4,491 citations

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.

Open-access reader

About this research paper

What this paper is about

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.

Why it matters

OpenAlex reports 4491 citations for this work. Citation counts describe recorded attention and do not establish research quality.

Key contribution

A contribution statement is not available in the OpenAlex record.

Method / approach

Method details are not available in the OpenAlex metadata.

Main findings

Findings are not separately available in the OpenAlex metadata.

Limitations

Limitations are not available in the OpenAlex metadata.

Applications

Application details are not available in the OpenAlex metadata.

Available 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.

Key concepts: Populus trichocarpa, Genome, Biology, Arabidopsis, Gene, Genetics, Functional divergence, Gene duplication

Related papers

Related paper 1Related paper 2Related paper 3
Back to paper searchBrowse research topicsOriginal source
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) — Research Paper | ScholarLens