Functional and evolutionary genomic inferences in <i>Populus</i> through genome and population sequencing of American and European aspen. Lin, Y., Wang, J., Delhomme, N., Schiffthaler, B., Sundström, G., Zuccolo, A., Nystedt, B., Hvidsten, T. R., de la Torre, A., Cossu, R. M., Hoeppner, M. P., Lantz, H., Scofield, D. G., Zamani, N., Johansson, A., Mannapperuma, C., Robinson, K. M., Mähler, N., Leitch, I. J., Pellicer, J., Park, E., Van Montagu, M., Van de Peer, Y., Grabherr, M., Jansson, S., Ingvarsson, P. K., & Street, N. R. Proceedings of the National Academy of Sciences, 115(46):E10970–E10978, November, 2018.
Functional and evolutionary genomic inferences in <i>Populus</i> through genome and population sequencing of American and European aspen [link]Paper  doi  abstract   bibtex   3 downloads  
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 ).
@article{lin_functional_2018,
	title = {Functional and evolutionary genomic inferences in \textit{{Populus}} through genome and population sequencing of {American} and {European} aspen},
	volume = {115},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1801437115},
	doi = {10.1073/pnas.1801437115},
	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
              ).},
	language = {en},
	number = {46},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Lin, Yao-Cheng and Wang, Jing and Delhomme, Nicolas and Schiffthaler, Bastian and Sundström, Görel and Zuccolo, Andrea and Nystedt, Björn 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 Mähler, 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, Pär K. and Street, Nathaniel R.},
	month = nov,
	year = {2018},
	pages = {E10970--E10978},
}
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