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De La Torre, Amanda
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Publications (7 of 7) Show all publications
Lin, Y.-C., Wang, J., Delhomme, N., Schiffthaler, B., Sundström, G., Zuccolo, A., . . . Street, N. R. (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
Open this publication in new window or tab >>Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 46, p. E10970-E10978Article in journal (Refereed) Published
Abstract [en]

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).

Place, publisher, year, edition, pages
NATL ACAD SCIENCES, 2018
Keywords
genome assembly, natural selection, coexpression, population genetics, Populus
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-154950 (URN)10.1073/pnas.1801437115 (DOI)000449934400020 ()30373829 (PubMedID)2-s2.0-85056516875 (Scopus ID)
Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2019-01-07Bibliographically approved
de La Torre, A. R., Li, Z., Van de Peer, Y. & Ingvarsson, P. K. (2017). Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants. Molecular biology and evolution, 34(6), 1363-1377
Open this publication in new window or tab >>Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants
2017 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 34, no 6, p. 1363-1377Article in journal (Refereed) Published
Abstract [en]

The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes.

Place, publisher, year, edition, pages
Oxford University Press, 2017
Keywords
gymnosperms, angiosperms, substitution rates, selection, mutation, life-history traits
National Category
Evolutionary Biology Genetics Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-135960 (URN)10.1093/molbev/msx069 (DOI)000402061700006 ()28333233 (PubMedID)
Available from: 2017-06-29 Created: 2017-06-29 Last updated: 2018-06-09Bibliographically approved
Li, Z., De La Torre, A. R., Sterck, L., Cánovas, F. M., Avila, C., Merino, I., . . . Van de Peer, Y. (2017). Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants. Genome Biology and Evolution, 9(5), 1130-1147
Open this publication in new window or tab >>Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants
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2017 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, no 5, p. 1130-1147Article in journal (Refereed) Published
Abstract [en]

Phylogenetic relationships among seed plant taxa, especially within the gymnosperms, remain contested. In contrast to angio-sperms, for which several genomic, transcriptomic and phylogenetic resources are available, there are few, if any, molecular markers that allow broad comparisons among gymnosperm species. With few gymnosperm genomes available, recently obtained transcriptomes in gymnosperms are a great addition to identifying single-copy gene families as molecular markers for phylogenomic analysis in seed plants. Taking advantage of an increasing number of available genomes and transcriptomes, we identified single-copy genes in a broad collection of seed plants and used these to infer phylogenetic relationships between major seed plant taxa. This study aims at extending the current phylogenetic toolkit for seed plants, assessing its ability for resolving seed plant phylogeny, and discussing potential factors affecting phylogenetic reconstruction. In total, we identified 3,072 single-copy genes in 31 gymnosperms and 2,156 single-copy genes in 34 angiosperms. All studied seed plants shared 1,469 single-copy genes, which are generally involved in functions like DNA metabolism, cell cycle, and photosynthesis. A selected set of 106 single-copy genes provided good resolution for the seed plant phylogeny except for gnetophytes. Although some of our analyses support a sister relationship between gnetophytes and other gymnosperms, phylogenetic trees from concatenated alignments without 3rd codon positions and amino acid alignments under the CAT + GTR model, support gnetophytes as a sister group to Pinaceae. Our phylogenomic analyses demonstrate that, in general, single-copy genes can uncover both recent and deep divergences of seed plant phylogeny.

Place, publisher, year, edition, pages
Oxford University Press, 2017
Keywords
single-copy genes, gymnosperms, angiosperms, seed plants, phylogenomics
National Category
Biological Systematics Botany
Identifiers
urn:nbn:se:umu:diva-140245 (URN)10.1093/gbe/evx070 (DOI)000406760400002 ()28460034 (PubMedID)
Available from: 2017-10-19 Created: 2017-10-19 Last updated: 2018-06-09Bibliographically approved
De La Torre, A., Ingvarsson, P. & Aitken, S. N. (2015). Genetic architecture and genomic patterns of gene flow between hybridizing species of Picea. Heredity, 115(2), 153-164
Open this publication in new window or tab >>Genetic architecture and genomic patterns of gene flow between hybridizing species of Picea
2015 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 115, no 2, p. 153-164Article in journal (Refereed) Published
Abstract [en]

Hybrid zones provide an opportunity to study the effects of selection and gene flow in natural settings. We employed nuclear microsatellites (single sequence repeat (SSR)) and candidate gene single-nucleotide polymorphism markers (SNPs) to characterize the genetic architecture and patterns of interspecific gene flow in the Picea glauca x P. engelmannii hybrid zone across a broad latitudinal (40-60 degrees) and elevational (350-3500 m) range in western North America. Our results revealed a wide and complex hybrid zone with broad ancestry levels and low interspecific heterozygosity, shaped by asymmetric advanced-generation introgression, and low reproductive barriers between parental species. The clinal variation based on geographic variables, lack of concordance in clines among loci and the width of the hybrid zone points towards the maintenance of species integrity through environmental selection. Congruency between geographic and genomic clines suggests that loci with narrow clines are under strong selection, favoring either one parental species (directional selection) or their hybrids (overdominance) as a result of strong associations with climatic variables such as precipitation as snow and mean annual temperature. Cline movement due to past demographic events (evidenced by allelic richness and heterozygosity shifts from the average cline center) may explain the asymmetry in introgression and predominance of P. engelmannii found in this study. These results provide insights into the genetic architecture and fine-scale patterns of admixture, and identify loci that may be involved in reproductive barriers between the species.

Place, publisher, year, edition, pages
Nature Publishing Group, 2015
National Category
Ecology Earth and Related Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-106775 (URN)10.1038/hdy.2015.19 (DOI)000358007200009 ()25806545 (PubMedID)
Available from: 2015-08-14 Created: 2015-08-07 Last updated: 2018-06-07Bibliographically approved
De La Torre, A. R., Wang, T., Jaquish, B. & Aitken, S. N. (2014). Adaptation and exogenous selection in a Picea glauca x Picea engelmannii hybrid zone: implications for forest management under climate change. New Phytologist, 201(2), 687-699
Open this publication in new window or tab >>Adaptation and exogenous selection in a Picea glauca x Picea engelmannii hybrid zone: implications for forest management under climate change
2014 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 201, no 2, p. 687-699Article in journal (Refereed) Published
Abstract [en]

The nature of selection responsible for the maintenance of the economically and ecologically important Picea glaucaxPicea engelmannii hybrid zone was investigated. Genomic, phenotypic and climatic data were used to test assumptions of hybrid zone maintenance and to model future scenarios under climate change. Genome-wide estimates of admixture based on a panel of 86 candidate gene single nucleotide polymorphisms were combined with long-term quantitative data on growth and survival (over 20yr), as well as one-time assessments of bud burst and bud set phenology, and cold hardiness traits. A total of 15498 individuals were phenotyped for growth and survival. Our results suggest that the P.glaucaxP.engelmannii hybrid zone is maintained by local adaptation to growing season length and snowpack (exogenous selection). Hybrids appeared to be fitter than pure species in intermediate environments, which fits expectations of the bounded hybrid superiority model of hybrid zone maintenance. Adaptive introgression from parental species has probably contributed to increased hybrid fitness in intermediate habitats. While P.engelmannii ancestry is higher than P.glauca ancestry in hybrid populations, on average, selective breeding in managed hybrid populations is shifting genomic composition towards P.glauca, potentially pre-adapting managed populations to warmer climates.

Place, publisher, year, edition, pages
Hoboken: Wiley-Blackwell, 2014
Keywords
adaptive introgression, bounded hybrid superiority, breeding, climate change, exogenous selection
National Category
Natural Sciences
Identifiers
urn:nbn:se:umu:diva-84772 (URN)10.1111/nph.12540 (DOI)000328511700031 ()
Available from: 2014-01-28 Created: 2014-01-20 Last updated: 2018-06-08Bibliographically approved
De La Torre, A. R., Roberts, D. R. & Aitken, S. N. (2014). Genome-wide admixture and ecological niche modelling reveal the maintenance of species boundaries despite long history of interspecific gene flow. Molecular Ecology, 23(8), 2046-2059
Open this publication in new window or tab >>Genome-wide admixture and ecological niche modelling reveal the maintenance of species boundaries despite long history of interspecific gene flow
2014 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 8, p. 2046-2059Article in journal (Refereed) Published
Abstract [en]

The maintenance of species boundaries despite interspecific gene flow has been a continuous source of interest in evolutionary biology. Many hybridizing species have porous genomes with regions impermeable to introgression, conferring reproductive barriers between species. We used ecological niche modelling to study the glacial and postglacial recolonization patterns between the widely hybridizing spruce species Picea glauca and P.engelmannii in western North America. Genome-wide estimates of admixture based on a panel of 311 candidate gene single nucleotide polymorphisms (SNP) from 290 genes were used to assess levels of admixture and introgression and to identify loci putatively involved in adaptive differences or reproductive barriers between species. Our palaeoclimatic modelling suggests that these two closely related species have a long history of hybridization and introgression, dating to at least 21000years ago, yet species integrity is maintained by a combination of strong environmental selection and reduced current interspecific gene flow. Twenty loci showed evidence of divergent selection, including six loci that were both F-st outliers and associated with climatic gradients, and fourteen loci that were either outliers or showed associations with climate. These included genes responsible for carbohydrate metabolism, signal transduction and transcription factors.

Keywords
ecological niche modelling, admixture, outlier loci, spruce
National Category
Biochemistry and Molecular Biology Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-88392 (URN)10.1111/mec.12710 (DOI)000333858200013 ()
Available from: 2014-05-20 Created: 2014-05-05 Last updated: 2018-06-07Bibliographically approved
de La Torre, A. R., Birol, I., Bousquet, J., Ingvarsson, P. K., Jansson, S., Jones, S. J. M., . . . Bohlmann, J. (2014). Insights into conifer giga-genomes. Plant Physiology, 166(4), 1724-1732
Open this publication in new window or tab >>Insights into conifer giga-genomes
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2014 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 166, no 4, p. 1724-1732Article in journal (Refereed) Published
Abstract [en]

Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world's forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20-30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes.

Place, publisher, year, edition, pages
American Society of Plant Biologists, 2014
National Category
Genetics Forest Science
Identifiers
urn:nbn:se:umu:diva-97893 (URN)10.1104/pp.114.248708 (DOI)000346016400009 ()
Available from: 2015-01-12 Created: 2015-01-08 Last updated: 2018-06-07Bibliographically approved
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