The Norway spruce genome sequence and conifer genome evolution

Björn Nystedt, Nathaniel R. Street, Anna Wetterbom, Andrea Zuccolo, Yao-Cheng Lin, Douglas G. Scofield, Francesco Vezzi, Nicolas Delhomme, Stefania Giacomello, Andrey Alexeyenko, Riccardo Vicedomini, Kristoffer Sahlin, Ellen Sherwood, Malin Elfstrand, Lydia Gramzow, Kristina Holmberg, Jimmie Hällman, Olivier Keech, Lisa Klasson, Maxim Koriabine, Melis Kucukoglu, Max Käller, Johannes Luthman, Fredrik Lysholm, Totte Niittylä, Åke Olson, Nemanja Rilakovic, Carol Ritland, Josep A. Rosselló, Juliana Sena, Thomas Svensson, Carlos Talavera-López, Günter Theißen, Hannele Tuominen, Kevin Vanneste, Zhi-Qiang Wu, Bo Zhang, Philipp Zerbe, Lars Arvestad, Rishikesh Bhalerao, Joerg Bohlmann, Jean Bousquet, Rosario Garcia Gil, Torgeir R. Hvidsten, Pieter de Jong, John MacKay, Michele Morgante, Kermit Ritland, Björn Sundberg, Stacey Lee Thompson, Yves Van de Peer, Björn Andersson, Ove Nilsson (), Pär K. Ingvarsson (), Joakim Lundeberg () and Stefan Jansson ()
Additional contact information
Björn Nystedt: Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden.
Nathaniel R. Street: Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden.
Anna Wetterbom: Science for Life Laboratory, Karolinska Institutet, Box 1031, 171 77 Stockholm, Sweden.
Andrea Zuccolo: Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy.
Yao-Cheng Lin: Technologiepark 927, 9052 Gent, Belgium.
Douglas G. Scofield: Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden.
Francesco Vezzi: School of Computer Science and Communication, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.
Nicolas Delhomme: Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden.
Stefania Giacomello: Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy.
Andrey Alexeyenko: School of Biotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.
Riccardo Vicedomini: Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy.
Kristoffer Sahlin: School of Computer Science and Communication, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.
Ellen Sherwood: Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden.
Malin Elfstrand: Uppsala Biocenter, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala, Sweden.
Lydia Gramzow: Friedrich-Schiller-University Jena, Philosophenweg 12, 07743 Jena, Germany.
Kristina Holmberg: School of Biotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.
Jimmie Hällman: School of Biotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.
Olivier Keech: Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden.
Lisa Klasson: Molecular Evolution, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden.
Maxim Koriabine: BACPAC Resources, Children’s Hospital of Oakland Research Institute, Bruce Lyon Memorial Research Building
Melis Kucukoglu: Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.
Max Käller: School of Biotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.
Johannes Luthman: Science for Life Laboratory, Karolinska Institutet, Box 1031, 171 77 Stockholm, Sweden.
Fredrik Lysholm: Science for Life Laboratory, Karolinska Institutet, Box 1031, 171 77 Stockholm, Sweden.
Totte Niittylä: Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.
Åke Olson: Uppsala Biocenter, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala, Sweden.
Nemanja Rilakovic: School of Biotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.
Carol Ritland: University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada.
Josep A. Rosselló: Jardí Botànic, Universitat de Valencia, c/Quart 80, 46008 Valencia, Spain.
Juliana Sena: Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec G1V 0A6, Canada.
Thomas Svensson: Science for Life Laboratory, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden.
Carlos Talavera-López: Science for Life Laboratory, Karolinska Institutet, Box 1031, 171 77 Stockholm, Sweden.
Günter Theißen: Friedrich-Schiller-University Jena, Philosophenweg 12, 07743 Jena, Germany.
Hannele Tuominen: Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden.
Kevin Vanneste: Technologiepark 927, 9052 Gent, Belgium.
Zhi-Qiang Wu: Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden.
Bo Zhang: Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden.
Philipp Zerbe: Michael Smith Laboratories, University of British Columbia, 321-2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada.
Lars Arvestad: School of Computer Science and Communication, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.
Rishikesh Bhalerao: Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.
Joerg Bohlmann: University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada.
Jean Bousquet: Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec G1V 0A6, Canada.
Rosario Garcia Gil: Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.
Torgeir R. Hvidsten: Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden.
Pieter de Jong: BACPAC Resources, Children’s Hospital of Oakland Research Institute, Bruce Lyon Memorial Research Building
John MacKay: Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec G1V 0A6, Canada.
Michele Morgante: Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy.
Kermit Ritland: University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada.
Björn Sundberg: Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.
Stacey Lee Thompson: Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden.
Yves Van de Peer: Technologiepark 927, 9052 Gent, Belgium.
Björn Andersson: Science for Life Laboratory, Karolinska Institutet, Box 1031, 171 77 Stockholm, Sweden.
Ove Nilsson: Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.
Pär K. Ingvarsson: Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden.
Joakim Lundeberg: School of Biotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.
Stefan Jansson: Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden.

Nature, 2013, vol. 497, issue 7451, 579-584

Abstract: Abstract Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

Date: 2013
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DOI: 10.1038/nature12211

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