Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen.
Identifieur interne : 000E89 ( Main/Exploration ); précédent : 000E88; suivant : 000E90Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen.
Auteurs : Yao-Cheng Lin [Belgique, Taïwan] ; Jing Wang [Suède, Norvège] ; Nicolas Delhomme [Suède] ; Bastian Schiffthaler [Suède] ; Görel Sundström [Suède] ; Andrea Zuccolo [Italie] ; Björn Nystedt [Suède] ; Torgeir R. Hvidsten [Suède, Norvège] ; Amanda De La Torre [Suède, États-Unis] ; Rosa M. Cossu [Italie] ; Marc P. Hoeppner [Suède, Allemagne] ; Henrik Lantz [Suède] ; Douglas G. Scofield [Suède] ; Neda Zamani [Suède] ; Anna Johansson [Suède] ; Chanaka Mannapperuma [Suède] ; Kathryn M. Robinson [Suède] ; Niklas M Hler [Suède] ; Ilia J. Leitch [Royaume-Uni] ; Jaume Pellicer [Royaume-Uni] ; Eung-Jun Park [Corée du Sud] ; Marc Van Montagu [Belgique] ; Yves Van De Peer [Belgique, Afrique du Sud] ; Manfred Grabherr [Suède] ; Stefan Jansson [Suède] ; P R K. Ingvarsson [Suède] ; Nathaniel R. Street [Belgique]Source :
- Proceedings of the National Academy of Sciences of the United States of America [ 1091-6490 ] ; 2018.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), Analyse de séquence d'ADN (méthodes), Arbres (génétique), Déséquilibre de liaison (génétique), Génome végétal (MeSH), Génomique (MeSH), Génétique des populations (méthodes), Phylogenèse (MeSH), Populus (génétique), Sélection génétique (génétique), Variation génétique (MeSH), Évolution biologique (MeSH), Évolution moléculaire (MeSH).
- MESH :
English descriptors
- KwdEn :
- Biological Evolution (MeSH), DNA, Plant (genetics), Evolution, Molecular (MeSH), Genetic Variation (MeSH), Genetics, Population (methods), Genome, Plant (MeSH), Genomics (MeSH), Linkage Disequilibrium (genetics), Phylogeny (MeSH), Populus (genetics), Selection, Genetic (genetics), Sequence Analysis, DNA (methods), Trees (genetics).
- MESH :
- chemical , genetics : DNA, Plant.
- genetics : Linkage Disequilibrium, Populus, Selection, Genetic, Trees.
- methods : Genetics, Population, Sequence Analysis, DNA.
- Biological Evolution, Evolution, Molecular, Genetic Variation, Genome, Plant, Genomics, Phylogeny.
Abstract
The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus, we produced genome assemblies and population genetics resources of two aspen species, Populus tremula L. and Populus tremuloides Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with P. trichocarpa but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).
DOI: 10.1073/pnas.1801437115
PubMed: 30373829
PubMed Central: PMC6243237
Affiliations:
- Afrique du Sud, Allemagne, Belgique, Corée du Sud, Italie, Norvège, Royaume-Uni, Suède, Taïwan, États-Unis
- Arizona, East Middle Sweden, Province de Flandre-Orientale, Région flamande, Schleswig-Holstein, Svealand, Toscane
- Gand, Kiel, Pise, Uppsala
- Université d'Uppsala, Université de Gand
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Hoeppner</name><affiliation wicri:level="4"><nlm:affiliation>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, 24105 Kiel, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, 24105 Kiel</wicri:regionArea><placeName><region type="land" nuts="2">Schleswig-Holstein</region><settlement type="city">Kiel</settlement></placeName></affiliation></author><author><name sortKey="Lantz, Henrik" sort="Lantz, Henrik" uniqKey="Lantz H" first="Henrik" last="Lantz">Henrik Lantz</name><affiliation wicri:level="4"><nlm:affiliation>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>National Bioinformatics Infrastructure Sweden, Uppsala University, 751 23 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>National Bioinformatics Infrastructure Sweden, Uppsala University, 751 23 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation></author><author><name sortKey="Scofield, Douglas G" sort="Scofield, Douglas G" uniqKey="Scofield D" first="Douglas G" last="Scofield">Douglas G. Scofield</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:affiliation>Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, 751 05 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, 751 05 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, 751 05 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, 751 05 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation></author><author><name sortKey="Zamani, Neda" sort="Zamani, Neda" uniqKey="Zamani N" first="Neda" last="Zamani">Neda Zamani</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå</wicri:regionArea><wicri:noRegion>901 83 Umeå</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:affiliation>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation></author><author><name sortKey="Johansson, Anna" sort="Johansson, Anna" uniqKey="Johansson A" first="Anna" last="Johansson">Anna Johansson</name><affiliation wicri:level="4"><nlm:affiliation>Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, 751 24 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, 751 24 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation></author><author><name sortKey="Mannapperuma, Chanaka" sort="Mannapperuma, Chanaka" uniqKey="Mannapperuma C" first="Chanaka" last="Mannapperuma">Chanaka Mannapperuma</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå</wicri:regionArea><wicri:noRegion>901 87 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Robinson, Kathryn M" sort="Robinson, Kathryn M" uniqKey="Robinson K" first="Kathryn M" last="Robinson">Kathryn M. Robinson</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå</wicri:regionArea><wicri:noRegion>901 87 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="M Hler, Niklas" sort="M Hler, Niklas" uniqKey="M Hler N" first="Niklas" last="M Hler">Niklas M Hler</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå</wicri:regionArea><wicri:noRegion>901 87 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Leitch, Ilia J" sort="Leitch, Ilia J" uniqKey="Leitch I" first="Ilia J" last="Leitch">Ilia J. Leitch</name><affiliation wicri:level="1"><nlm:affiliation>Character Evolution Team, Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond TW9 3AB, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Character Evolution Team, Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond TW9 3AB</wicri:regionArea><wicri:noRegion>Richmond TW9 3AB</wicri:noRegion></affiliation></author><author><name sortKey="Pellicer, Jaume" sort="Pellicer, Jaume" uniqKey="Pellicer J" first="Jaume" last="Pellicer">Jaume Pellicer</name><affiliation wicri:level="1"><nlm:affiliation>Character Evolution Team, Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond TW9 3AB, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Character Evolution Team, Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond TW9 3AB</wicri:regionArea><wicri:noRegion>Richmond TW9 3AB</wicri:noRegion></affiliation></author><author><name sortKey="Park, Eung Jun" sort="Park, Eung Jun" uniqKey="Park E" first="Eung-Jun" last="Park">Eung-Jun Park</name><affiliation wicri:level="1"><nlm:affiliation>Forest Biotechnology Division, National Institute of Forest Science, Suwon 16631, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Forest Biotechnology Division, National Institute of Forest Science, Suwon 16631</wicri:regionArea><wicri:noRegion>Suwon 16631</wicri:noRegion></affiliation></author><author><name sortKey="Van Montagu, Marc" sort="Van Montagu, Marc" uniqKey="Van Montagu M" first="Marc" last="Van Montagu">Marc Van Montagu</name><affiliation wicri:level="4"><nlm:affiliation>VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; marc.vanmontagu@vib-ugent.be nathaniel.street@umu.se.</nlm:affiliation><country wicri:rule="url">Belgique</country><wicri:regionArea>VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation></author><author><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><affiliation wicri:level="4"><nlm:affiliation>VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0001, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0001</wicri:regionArea><wicri:noRegion>Pretoria 0001</wicri:noRegion></affiliation></author><author><name sortKey="Grabherr, Manfred" sort="Grabherr, Manfred" uniqKey="Grabherr M" first="Manfred" last="Grabherr">Manfred Grabherr</name><affiliation wicri:level="4"><nlm:affiliation>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation></author><author><name sortKey="Jansson, Stefan" sort="Jansson, Stefan" uniqKey="Jansson S" first="Stefan" last="Jansson">Stefan Jansson</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå</wicri:regionArea><wicri:noRegion>901 87 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Ingvarsson, P R K" sort="Ingvarsson, P R K" uniqKey="Ingvarsson P" first="P R K" last="Ingvarsson">P R K. Ingvarsson</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala</wicri:regionArea><wicri:noRegion>750 07 Uppsala</wicri:noRegion></affiliation></author><author><name sortKey="Street, Nathaniel R" sort="Street, Nathaniel R" uniqKey="Street N" first="Nathaniel R" last="Street">Nathaniel R. Street</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden; marc.vanmontagu@vib-ugent.be nathaniel.street@umu.se.</nlm:affiliation><country wicri:rule="url">Belgique</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå</wicri:regionArea><wicri:noRegion>901 87 Umeå</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:30373829</idno><idno type="pmid">30373829</idno><idno type="doi">10.1073/pnas.1801437115</idno><idno type="pmc">PMC6243237</idno><idno type="wicri:Area/Main/Corpus">000B97</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000B97</idno><idno type="wicri:Area/Main/Curation">000B97</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000B97</idno><idno type="wicri:Area/Main/Exploration">000B97</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Functional and evolutionary genomic inferences in <i>Populus</i> through genome and population sequencing of American and European aspen.</title><author><name sortKey="Lin, Yao Cheng" sort="Lin, Yao Cheng" uniqKey="Lin Y" first="Yao-Cheng" last="Lin">Yao-Cheng Lin</name><affiliation wicri:level="4"><nlm:affiliation>VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 74145, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 74145</wicri:regionArea><wicri:noRegion>Tainan 74145</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Agricultural Biotechnology Research Center, Academia Sinica, Tainan 74145, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Tainan 74145</wicri:regionArea><wicri:noRegion>Tainan 74145</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Jing" sort="Wang, Jing" uniqKey="Wang J" first="Jing" last="Wang">Jing Wang</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 5003 Ås, Norway.</nlm:affiliation><country xml:lang="fr">Norvège</country><wicri:regionArea>Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 5003 Ås</wicri:regionArea><wicri:noRegion>5003 Ås</wicri:noRegion></affiliation></author><author><name sortKey="Delhomme, Nicolas" sort="Delhomme, Nicolas" uniqKey="Delhomme N" first="Nicolas" last="Delhomme">Nicolas Delhomme</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå</wicri:regionArea><wicri:noRegion>901 83 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Schiffthaler, Bastian" sort="Schiffthaler, Bastian" uniqKey="Schiffthaler B" first="Bastian" last="Schiffthaler">Bastian Schiffthaler</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå</wicri:regionArea><wicri:noRegion>901 87 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Sundstrom, Gorel" sort="Sundstrom, Gorel" uniqKey="Sundstrom G" first="Görel" last="Sundström">Görel Sundström</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå</wicri:regionArea><wicri:noRegion>901 83 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Zuccolo, Andrea" sort="Zuccolo, Andrea" uniqKey="Zuccolo A" first="Andrea" last="Zuccolo">Andrea Zuccolo</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa</wicri:regionArea><placeName><settlement type="city">Pise</settlement><region nuts="2">Toscane</region></placeName></affiliation></author><author><name sortKey="Nystedt, Bjorn" sort="Nystedt, Bjorn" uniqKey="Nystedt B" first="Björn" last="Nystedt">Björn Nystedt</name><affiliation wicri:level="4"><nlm:affiliation>Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, 751 24 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, 751 24 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation></author><author><name sortKey="Hvidsten, Torgeir R" sort="Hvidsten, Torgeir R" uniqKey="Hvidsten T" first="Torgeir R" last="Hvidsten">Torgeir R. Hvidsten</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå</wicri:regionArea><wicri:noRegion>901 87 Umeå</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway.</nlm:affiliation><country xml:lang="fr">Norvège</country><wicri:regionArea>Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås</wicri:regionArea><wicri:noRegion>1432 Ås</wicri:noRegion></affiliation></author><author><name sortKey="De La Torre, Amanda" sort="De La Torre, Amanda" uniqKey="De La Torre A" first="Amanda" last="De La Torre">Amanda De La Torre</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:affiliation>School of Forestry, Northern Arizona University, Flagstaff, AZ 86011.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Arizona</region></placeName><wicri:cityArea>School of Forestry, Northern Arizona University, Flagstaff</wicri:cityArea></affiliation></author><author><name sortKey="Cossu, Rosa M" sort="Cossu, Rosa M" uniqKey="Cossu R" first="Rosa M" last="Cossu">Rosa M. Cossu</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa</wicri:regionArea><placeName><settlement type="city">Pise</settlement><region nuts="2">Toscane</region></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16163 Genova</wicri:regionArea><wicri:noRegion>16163 Genova</wicri:noRegion></affiliation></author><author><name sortKey="Hoeppner, Marc P" sort="Hoeppner, Marc P" uniqKey="Hoeppner M" first="Marc P" last="Hoeppner">Marc P. Hoeppner</name><affiliation wicri:level="4"><nlm:affiliation>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, 24105 Kiel, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, 24105 Kiel</wicri:regionArea><placeName><region type="land" nuts="2">Schleswig-Holstein</region><settlement type="city">Kiel</settlement></placeName></affiliation></author><author><name sortKey="Lantz, Henrik" sort="Lantz, Henrik" uniqKey="Lantz H" first="Henrik" last="Lantz">Henrik Lantz</name><affiliation wicri:level="4"><nlm:affiliation>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>National Bioinformatics Infrastructure Sweden, Uppsala University, 751 23 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>National Bioinformatics Infrastructure Sweden, Uppsala University, 751 23 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation></author><author><name sortKey="Scofield, Douglas G" sort="Scofield, Douglas G" uniqKey="Scofield D" first="Douglas G" last="Scofield">Douglas G. Scofield</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:affiliation>Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, 751 05 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, 751 05 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, 751 05 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, 751 05 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation></author><author><name sortKey="Zamani, Neda" sort="Zamani, Neda" uniqKey="Zamani N" first="Neda" last="Zamani">Neda Zamani</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå</wicri:regionArea><wicri:noRegion>901 83 Umeå</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:affiliation>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation></author><author><name sortKey="Johansson, Anna" sort="Johansson, Anna" uniqKey="Johansson A" first="Anna" last="Johansson">Anna Johansson</name><affiliation wicri:level="4"><nlm:affiliation>Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, 751 24 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, 751 24 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation></author><author><name sortKey="Mannapperuma, Chanaka" sort="Mannapperuma, Chanaka" uniqKey="Mannapperuma C" first="Chanaka" last="Mannapperuma">Chanaka Mannapperuma</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå</wicri:regionArea><wicri:noRegion>901 87 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Robinson, Kathryn M" sort="Robinson, Kathryn M" uniqKey="Robinson K" first="Kathryn M" last="Robinson">Kathryn M. Robinson</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå</wicri:regionArea><wicri:noRegion>901 87 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="M Hler, Niklas" sort="M Hler, Niklas" uniqKey="M Hler N" first="Niklas" last="M Hler">Niklas M Hler</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå</wicri:regionArea><wicri:noRegion>901 87 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Leitch, Ilia J" sort="Leitch, Ilia J" uniqKey="Leitch I" first="Ilia J" last="Leitch">Ilia J. Leitch</name><affiliation wicri:level="1"><nlm:affiliation>Character Evolution Team, Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond TW9 3AB, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Character Evolution Team, Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond TW9 3AB</wicri:regionArea><wicri:noRegion>Richmond TW9 3AB</wicri:noRegion></affiliation></author><author><name sortKey="Pellicer, Jaume" sort="Pellicer, Jaume" uniqKey="Pellicer J" first="Jaume" last="Pellicer">Jaume Pellicer</name><affiliation wicri:level="1"><nlm:affiliation>Character Evolution Team, Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond TW9 3AB, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Character Evolution Team, Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond TW9 3AB</wicri:regionArea><wicri:noRegion>Richmond TW9 3AB</wicri:noRegion></affiliation></author><author><name sortKey="Park, Eung Jun" sort="Park, Eung Jun" uniqKey="Park E" first="Eung-Jun" last="Park">Eung-Jun Park</name><affiliation wicri:level="1"><nlm:affiliation>Forest Biotechnology Division, National Institute of Forest Science, Suwon 16631, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Forest Biotechnology Division, National Institute of Forest Science, Suwon 16631</wicri:regionArea><wicri:noRegion>Suwon 16631</wicri:noRegion></affiliation></author><author><name sortKey="Van Montagu, Marc" sort="Van Montagu, Marc" uniqKey="Van Montagu M" first="Marc" last="Van Montagu">Marc Van Montagu</name><affiliation wicri:level="4"><nlm:affiliation>VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; marc.vanmontagu@vib-ugent.be nathaniel.street@umu.se.</nlm:affiliation><country wicri:rule="url">Belgique</country><wicri:regionArea>VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation></author><author><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><affiliation wicri:level="4"><nlm:affiliation>VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0001, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0001</wicri:regionArea><wicri:noRegion>Pretoria 0001</wicri:noRegion></affiliation></author><author><name sortKey="Grabherr, Manfred" sort="Grabherr, Manfred" uniqKey="Grabherr M" first="Manfred" last="Grabherr">Manfred Grabherr</name><affiliation wicri:level="4"><nlm:affiliation>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation></author><author><name sortKey="Jansson, Stefan" sort="Jansson, Stefan" uniqKey="Jansson S" first="Stefan" last="Jansson">Stefan Jansson</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå</wicri:regionArea><wicri:noRegion>901 87 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Ingvarsson, P R K" sort="Ingvarsson, P R K" uniqKey="Ingvarsson P" first="P R K" last="Ingvarsson">P R K. Ingvarsson</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala</wicri:regionArea><wicri:noRegion>750 07 Uppsala</wicri:noRegion></affiliation></author><author><name sortKey="Street, Nathaniel R" sort="Street, Nathaniel R" uniqKey="Street N" first="Nathaniel R" last="Street">Nathaniel R. Street</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden; marc.vanmontagu@vib-ugent.be nathaniel.street@umu.se.</nlm:affiliation><country wicri:rule="url">Belgique</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå</wicri:regionArea><wicri:noRegion>901 87 Umeå</wicri:noRegion></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="eISSN">1091-6490</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biological Evolution (MeSH)</term><term>DNA, Plant (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genetics, Population (methods)</term><term>Genome, Plant (MeSH)</term><term>Genomics (MeSH)</term><term>Linkage Disequilibrium (genetics)</term><term>Phylogeny (MeSH)</term><term>Populus (genetics)</term><term>Selection, Genetic (genetics)</term><term>Sequence Analysis, DNA (methods)</term><term>Trees (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (génétique)</term><term>Analyse de séquence d'ADN (méthodes)</term><term>Arbres (génétique)</term><term>Déséquilibre de liaison (génétique)</term><term>Génome végétal (MeSH)</term><term>Génomique (MeSH)</term><term>Génétique des populations (méthodes)</term><term>Phylogenèse (MeSH)</term><term>Populus (génétique)</term><term>Sélection génétique (génétique)</term><term>Variation génétique (MeSH)</term><term>Évolution biologique (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Linkage Disequilibrium</term><term>Populus</term><term>Selection, Genetic</term><term>Trees</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des plantes</term><term>Arbres</term><term>Déséquilibre de liaison</term><term>Populus</term><term>Sélection génétique</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genetics, Population</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Génétique des populations</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biological Evolution</term><term>Evolution, Molecular</term><term>Genetic Variation</term><term>Genome, Plant</term><term>Genomics</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Génome végétal</term><term>Génomique</term><term>Phylogenèse</term><term>Variation génétique</term><term>Évolution biologique</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The <i>Populus</i> genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily <i>Populus trichocarpa</i> (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in <i>Populus</i>, we produced genome assemblies and population genetics resources of two aspen species, <i>Populus tremula</i> L. and <i>Populus tremuloides</i> Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with <i>P. trichocarpa</i> but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30373829</PMID><DateCompleted><Year>2019</Year><Month>01</Month><Day>23</Day></DateCompleted><DateRevised><Year>2019</Year><Month>01</Month><Day>23</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1091-6490</ISSN><JournalIssue CitedMedium="Internet"><Volume>115</Volume><Issue>46</Issue><PubDate><Year>2018</Year><Month>11</Month><Day>13</Day></PubDate></JournalIssue><Title>Proceedings of the National Academy of Sciences of the United States of America</Title><ISOAbbreviation>Proc Natl Acad Sci U S A</ISOAbbreviation></Journal><ArticleTitle>Functional and evolutionary genomic inferences in <i>Populus</i> through genome and population sequencing of American and European aspen.</ArticleTitle><Pagination><MedlinePgn>E10970-E10978</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1073/pnas.1801437115</ELocationID><Abstract><AbstractText>The <i>Populus</i> genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily <i>Populus trichocarpa</i> (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in <i>Populus</i>, we produced genome assemblies and population genetics resources of two aspen species, <i>Populus tremula</i> L. and <i>Populus tremuloides</i> Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with <i>P. trichocarpa</i> but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).</AbstractText><CopyrightInformation>Copyright © 2018 the Author(s). Published by PNAS.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lin</LastName><ForeName>Yao-Cheng</ForeName><Initials>YC</Initials><AffiliationInfo><Affiliation>VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 74145, Taiwan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Agricultural Biotechnology Research Center, Academia Sinica, Tainan 74145, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Jing</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå, Sweden.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 5003 Ås, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Delhomme</LastName><ForeName>Nicolas</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schiffthaler</LastName><ForeName>Bastian</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sundström</LastName><ForeName>Görel</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zuccolo</LastName><ForeName>Andrea</ForeName><Initials>A</Initials><Identifier Source="ORCID">0000-0001-7574-0714</Identifier><AffiliationInfo><Affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nystedt</LastName><ForeName>Björn</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, 751 24 Uppsala, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hvidsten</LastName><ForeName>Torgeir R</ForeName><Initials>TR</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>de la Torre</LastName><ForeName>Amanda</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå, Sweden.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>School of Forestry, Northern Arizona University, Flagstaff, AZ 86011.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cossu</LastName><ForeName>Rosa M</ForeName><Initials>RM</Initials><AffiliationInfo><Affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hoeppner</LastName><ForeName>Marc P</ForeName><Initials>MP</Initials><AffiliationInfo><Affiliation>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, 24105 Kiel, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lantz</LastName><ForeName>Henrik</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>National Bioinformatics Infrastructure Sweden, Uppsala University, 751 23 Uppsala, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Scofield</LastName><ForeName>Douglas G</ForeName><Initials>DG</Initials><Identifier Source="ORCID">0000-0001-5235-6461</Identifier><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå, Sweden.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, 751 05 Uppsala, Sweden.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, 751 05 Uppsala, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zamani</LastName><ForeName>Neda</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Johansson</LastName><ForeName>Anna</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, 751 24 Uppsala, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mannapperuma</LastName><ForeName>Chanaka</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Robinson</LastName><ForeName>Kathryn M</ForeName><Initials>KM</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mähler</LastName><ForeName>Niklas</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Leitch</LastName><ForeName>Ilia J</ForeName><Initials>IJ</Initials><Identifier Source="ORCID">0000-0002-3837-8186</Identifier><AffiliationInfo><Affiliation>Character Evolution Team, Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond TW9 3AB, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pellicer</LastName><ForeName>Jaume</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Character Evolution Team, Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond TW9 3AB, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Park</LastName><ForeName>Eung-Jun</ForeName><Initials>EJ</Initials><AffiliationInfo><Affiliation>Forest Biotechnology Division, National Institute of Forest Science, Suwon 16631, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Van Montagu</LastName><ForeName>Marc</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; marc.vanmontagu@vib-ugent.be nathaniel.street@umu.se.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Van de Peer</LastName><ForeName>Yves</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0001, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grabherr</LastName><ForeName>Manfred</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jansson</LastName><ForeName>Stefan</ForeName><Initials>S</Initials><Identifier Source="ORCID">0000-0002-7906-6891</Identifier><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ingvarsson</LastName><ForeName>Pär K</ForeName><Initials>PK</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University 901 87, Umeå, Sweden.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Street</LastName><ForeName>Nathaniel R</ForeName><Initials>NR</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden; marc.vanmontagu@vib-ugent.be nathaniel.street@umu.se.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>10</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Proc Natl Acad Sci U S A</MedlineTA><NlmUniqueID>7505876</NlmUniqueID><ISSNLinking>0027-8424</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D005075" MajorTopicYN="N">Biological Evolution</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005828" MajorTopicYN="N">Genetics, Population</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015810" MajorTopicYN="N">Linkage Disequilibrium</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012641" MajorTopicYN="N">Selection, Genetic</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014197" MajorTopicYN="N">Trees</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Populus</Keyword><Keyword MajorTopicYN="Y">coexpression</Keyword><Keyword MajorTopicYN="Y">genome assembly</Keyword><Keyword MajorTopicYN="Y">natural selection</Keyword><Keyword MajorTopicYN="Y">population genetics</Keyword></KeywordList><CoiStatement>The authors declare no conflict of interest.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>10</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>1</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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Cossu</name><name sortKey="Cossu, Rosa M" sort="Cossu, Rosa M" uniqKey="Cossu R" first="Rosa M" last="Cossu">Rosa M. Cossu</name></country><country name="États-Unis"><region name="Arizona"><name sortKey="De La Torre, Amanda" sort="De La Torre, Amanda" uniqKey="De La Torre A" first="Amanda" last="De La Torre">Amanda De La Torre</name></region></country><country name="Allemagne"><region name="Schleswig-Holstein"><name sortKey="Hoeppner, Marc P" sort="Hoeppner, Marc P" uniqKey="Hoeppner M" first="Marc P" last="Hoeppner">Marc P. Hoeppner</name></region></country><country name="Royaume-Uni"><noRegion><name sortKey="Leitch, Ilia J" sort="Leitch, Ilia J" uniqKey="Leitch I" first="Ilia J" last="Leitch">Ilia J. Leitch</name></noRegion><name sortKey="Pellicer, Jaume" sort="Pellicer, Jaume" uniqKey="Pellicer J" first="Jaume" last="Pellicer">Jaume Pellicer</name></country><country name="Corée du Sud"><noRegion><name sortKey="Park, Eung Jun" sort="Park, Eung Jun" uniqKey="Park E" first="Eung-Jun" last="Park">Eung-Jun Park</name></noRegion></country><country name="Afrique du Sud"><noRegion><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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