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Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen

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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).
Keywords
BURROWS-WHEELER TRANSFORM, NATURAL-SELECTION, NUCLEOTIDE POLYMORPHISM, DELETERIOUS MUTATIONS, BLACK COTTONWOOD, GENE-EXPRESSION, READ, ALIGNMENT, TRICHOCARPA, DIVERGENCE, SIGNATURES, genome assembly, natural selection, coexpression, population genetics, Populus

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Chicago
Lin, Yao-Cheng, Jing Wang, Nicolas Delhomme, Bastian Schiffthaler, Gorel Sundstrom, Andrea Zuccolo, Bjorn Nystedt, et al. 2018. “Functional and Evolutionary Genomic Inferences in Populus Through Genome and Population Sequencing of American and European Aspen.” Proceedings of the National Academy of Sciences of the United States of America 115 (46): E10970–E10978.
APA
Lin, Y.-C., Wang, J., Delhomme, N., Schiffthaler, B., Sundstrom, G., Zuccolo, A., Nystedt, B., et al. (2018). Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 115(46), E10970–E10978.
Vancouver
1.
Lin Y-C, Wang J, Delhomme N, Schiffthaler B, Sundstrom G, Zuccolo A, et al. Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2018;115(46):E10970–E10978.
MLA
Lin, Yao-Cheng, Jing Wang, Nicolas Delhomme, et al. “Functional and Evolutionary Genomic Inferences in Populus Through Genome and Population Sequencing of American and European Aspen.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 115.46 (2018): E10970–E10978. Print.
@article{8583857,
  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).},
  author       = {Lin, Yao-Cheng and Wang, Jing and Delhomme, Nicolas and Schiffthaler, Bastian and Sundstrom, Gorel and Zuccolo, Andrea and Nystedt, Bjorn and Hvidsten, Torgeir R and de la Torre, Amanda and Cossu, Rosa M and Hoeppner, Marc P and Lantz, Henrik and Scofield, Douglas G and Zamani, Neda and Johansson, Anna and Mannapperuma, Chanaka and Robinson, Kathryn M and Mahler, Niklas and Leitch, Ilia J and Pellicer, Jaume and Park, Eung-Jun and Van Montagu, Marc and Van de Peer, Yves and Grabherr, Manfred and Jansson, Stefan and Ingvarsson, Par K and Street, Nathaniel R},
  issn         = {0027-8424},
  journal      = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
  language     = {eng},
  number       = {46},
  pages        = {E10970--E10978},
  title        = {Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen},
  url          = {http://dx.doi.org/10.1073/pnas.1801437115},
  volume       = {115},
  year         = {2018},
}

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