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Publications (8 of 8) Show all publications
Bernhardsson, C., Vidalis, A., Wang, X., Scofield, D., Schiffthaler, B., Baison, J., . . . Ingvarsson, P. K. (2019). An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies). G3: Genes, Genomes, Genetics, 9(5), 1623-1632
Open this publication in new window or tab >>An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)
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2019 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 9, no 5, p. 1623-1632Article in journal (Refereed) Published
Abstract [en]

Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (similar to 20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.

Place, publisher, year, edition, pages
Genetics Society of America, 2019
Keywords
genetic map, Norway spruce, Picea abies, sequence capture, genome assembly
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-159871 (URN)10.1534/g3.118.200840 (DOI)000467271400031 ()30898899 (PubMedID)
Projects
Bio4Energy
Funder
Knut and Alice Wallenberg Foundation
Available from: 2019-06-10 Created: 2019-06-10 Last updated: 2019-09-06Bibliographically approved
Wang, J., Ding, J., Tan, B., Robinson, K. M., Michelson, I. H., Johansson, A., . . . Ingvarsson, P. K. (2018). A major locus controls local adaptation and adaptive life history variation in a perennial plant. Genome Biology, 19, Article ID 72.
Open this publication in new window or tab >>A major locus controls local adaptation and adaptive life history variation in a perennial plant
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2018 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 19, article id 72Article in journal (Refereed) Published
Abstract [en]

Background: The initiation of growth cessation and dormancy represent critical life history trade offs between survival and growth and have important fitness effects in perennial plants Such adaptive life history traits often show strong local adaptation along environmental gradients but, despite then importance, the genetic architecture of these traits remains poorly understood.

Results: We integrate whole genome re sequencing with environmental and phenotypic data from common garden experiments to investigate the genomic basis of local adaptation across a latitudinal gradient in European aspen (Populus tremula). A single genomic region containing the PtFT2 gene mediates local adaptation in the timing of bud set and explains 65% of the observed genetic variation in bud set This locus is the likely target of a recent selective sweep that originated right before or during colonization of northern Scandinavia following the last glaciation Field and greenhouse experiments confirm that variation in PtFT2 gene expression affects the phenotypic variation in bud set that we observe in wild natural populations.

Conclusions: Our results reveal a major effect locus that determines the timing of bud set and that has facilitated rapid adaptation to shorter growing seasons and colder climates in European aspen. The discovery of a single locus explaining a substantial fraction of the variation in a key life-history trait is remarkable, given that such traits are generally considered to be highly polygenic. These findings provide a dramatic illustration of how loci of large effect for adaptive traits can arise and be maintained over large geographical scales in natural populations.

Place, publisher, year, edition, pages
BioMed Central, 2018
Keywords
Populus tremula, Local adaptation, Genomic basis, PtFT2, Adaptive traits, Selective sweep
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-150175 (URN)10.1186/s13059-018-1444-y (DOI)000434210500001 ()29866176 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

Originally included in thesis in manuscript form.

Available from: 2018-07-18 Created: 2018-07-18 Last updated: 2018-08-14Bibliographically approved
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
Cossu, R. M., Casola, C., Giacomello, S., Vidalis, A., Scofield, D. G. & Zuccolo, A. (2017). LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes. Genome Biology and Evolution, 9(12), 3449-3462
Open this publication in new window or tab >>LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes
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2017 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, no 12, p. 3449-3462Article in journal (Refereed) Published
Abstract [en]

The accumulat on and removal of transposable elements (TEs) is a major driver of genome size evolution in eukaryotes. In plants, long terminal repeat (LTR) retrotransposons (LTR-RTs) represent the majority of TEs and form most of the nuclear DNA in large genomes. Unequal recombination (UR) between LTRs leads to removal of intervening sequence and formation of solo-LTRs. UR is a major mechanism of LTR-RT removal in many angiosperms, but our understanding of LTR-RT-associated recombination within the large, LTR-RT-rich genomes of conifers is quite limited. We employ a novel read based methodology to estimate the relative rates of LTR-RT-associated UR within the genomes of four conifer and seven angiosperm species. We found the lowest rates of UR in the largest genomes studied, conifers and the angiosperm maize. Recombination may also resolve as gene conversion, which does not remove sequence, so we analyzed LTR-RT-associated gene conversion events (GCEs) in Norway spruce and six angiosperms. Opposite the trend for UR, we found the highest rates of GCEs in Norway spruce and maize. Unlike previous work in angiosperms, we found no evidence that rates of UR correlate with retroelement structural features in the conifers, suggesting that another process is suppressing UR in these species. Recent results from diverse eukaryotes indicate that heterochromatin affects the resolution of recombination, by favoring gene conversion over crossing-over, similar to our observation of opposed rates of UR and GCEs. Control of LTR-RT proliferation via formation of heterochromatin would be a likely step toward large genomes in eukaryotes carrying high LTR-RT content.

Place, publisher, year, edition, pages
Oxford University Press, 2017
Keywords
gymnosperm, Picea, Pinus, angiosperm, retroelement, gene conversion, recombination suppression, nome size
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-144974 (URN)10.1093/gbe/evx260 (DOI)000423460600017 ()29228262 (PubMedID)
Available from: 2018-02-21 Created: 2018-02-21 Last updated: 2018-06-09Bibliographically approved
Wang, J., Street, N., Scofield, D. & Ingvarsson, P. (2016). Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species. Genetics, 202(3), 1185-1200
Open this publication in new window or tab >>Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species
2016 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 202, no 3, p. 1185-1200Article in journal (Refereed) Published
Abstract [en]

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of PopulusPopulus tremulaP. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.

Place, publisher, year, edition, pages
Genetics Society of America, 2016
Keywords
Populus, whole-genome resequencing, nucleotide polymorphism, recombination, natural selection
National Category
Natural Sciences Evolutionary Biology Genetics
Research subject
Genetics
Identifiers
urn:nbn:se:umu:diva-117941 (URN)10.1534/genetics.115.183152 (DOI)000371596400026 ()
Available from: 2016-03-07 Created: 2016-03-07 Last updated: 2018-06-07Bibliographically approved
Wang, J., Street, N., Scofield, D. & Ingvarsson, P. (2016). Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens. Molecular biology and evolution, 33(7), 1754-1767
Open this publication in new window or tab >>Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens
2016 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 7, p. 1754-1767Article in journal (Refereed) Published
Abstract [en]

Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood. Populus tremula and P. tremuloides are two of the most widespread tree species in the Northern Hemisphere. Using whole-genome re-sequencing data of 24 P. tremula and 22 P. tremuloidesindividuals, we find that the two species diverged ~2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. Both species have experienced substantial population expansions following long-term declines after species divergence. We detect widespread and heterogeneous genomic differentiation between species, and in accordance with the expectation of allopatric speciation, coalescent simulations suggest that neutral evolutionary processes can account for most of the observed patterns of genetic differentiation. However, there is an excess of regions exhibiting extreme differentiation relative to those expected under demographic simulations, which is indicative of the action of natural selection. Overall genetic differentiation is negatively associated with recombination rate in both species, providing strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between species. Finally, we identify a number of candidate regions and genes that may have been subject to positive and/or balancing selection during the speciation process.

Keywords
Populus tremula, P. tremuloides, whole-genome re-sequencing, demographic histories, heterogeneous genomic differentiation, linked selection, recombination
National Category
Evolutionary Biology
Research subject
Genetics; evolutionary genetics
Identifiers
urn:nbn:se:umu:diva-118326 (URN)10.1093/molbev/msw051 (DOI)000378767100009 ()
Available from: 2016-03-16 Created: 2016-03-16 Last updated: 2018-06-07Bibliographically approved
Scofield, D. G., Smouse, P. E., Karubian, J. & Sork, V. L. (2012). Use of Alpha, Beta, and Gamma Diversity Measures to Characterize Seed Dispersal by Animals. American Naturalist, 180(6), 719-732
Open this publication in new window or tab >>Use of Alpha, Beta, and Gamma Diversity Measures to Characterize Seed Dispersal by Animals
2012 (English)In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 180, no 6, p. 719-732Article in journal (Refereed) Published
Abstract [en]

Seed dispersal shapes ecological and evolutionary dynamics of plant populations. Here, we extend classical diversity measures to study the impact of disperser behavior on seed dispersal. We begin by extending our previous diversity structure approach, which partitioned seed source diversity within and among dispersal sites, into the more general framework of traditional diversity measures. This statistical approach allows an assessment of the extent to which foraging behavior shapes alpha and gamma diversity, as well as the divergence in seed sources among dispersal sites, which we call delta. We also introduce tests to facilitate comparisons of diversity among dispersal sites and seed vectors and to compare overall diversity among sampled systems. We then apply these tools to investigate the diversity blend of parentage resulting from seed dispersal by two avian seed vectors with very different social and foraging behaviors: (1) acorn woodpeckers, transporting Quercus agrifolia acorns, and (2) long-wattled umbrellabirds, transporting Oenocarpus bataua palm nuts. Using these diversity and divergence measures, we test the hypothesis that different foraging behaviors generate distinctive diversity partitions for the two focal tree species. This approach provides a new tool for assessment of the impact of dispersal agents on the seed source structure of plant populations, which can be extended to include the impact of virtually any propagule vector for a range of systems.

Place, publisher, year, edition, pages
Chicago: University of Chicago Press, 2012
Keywords
alpha diversity, beta diversity, seed dispersal by animals, genetic diversity, foraging behavior, frugivory
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-62779 (URN)10.1086/668202 (DOI)000311090100005 ()
Available from: 2013-01-02 Created: 2012-12-18 Last updated: 2018-06-08Bibliographically approved
Smouse, P. E., Sork, V. L., Scofield, D. G. & Grivet, D. (2012). Using seedling and pericarp tissues to determine maternal parentage of dispersed valley oak recruits. Journal of Heredity, 103(2), 250-259
Open this publication in new window or tab >>Using seedling and pericarp tissues to determine maternal parentage of dispersed valley oak recruits
2012 (English)In: Journal of Heredity, ISSN 0022-1503, E-ISSN 1465-7333, Vol. 103, no 2, p. 250-259Article in journal (Refereed) Published
Abstract [en]

The spatial pattern of established seedlings yields valuable information about variation in fecundity, dispersal, and spatial structure of distributed recruits, but separating maternal and paternal contributions in monoecious species has been hampered by the "2 parent'' problem. It is now possible to determine the maternal parentage of established recruits with genetic assay of maternally derived tissues of the seed or fruit, but the DNA of weathered maternal tissues often yields unreliable genotypes, reducing the practical range of such assay. We develop a mixed assay of seedling and seed (pericarp) tissues and illustrate it with distributed recruits of California valley oak (Quercus lobata Nee). Detailed analysis indicates correct maternal assignment rates of canopy patch recruits of 56% (seedling assay only) versus 94% (mixed assay). For open patch recruits, maternal assignment rates were less than 50% (seedling assay only) versus 91% (mixed assay). The strategy of choice is to use seedling genotypes to identify a small set of credible parental candidates and then deploy 3-4 well-chosen pericarp/endocarp loci to reduce that list to a single obvious maternal candidate. The increase in the number of recruits available for subsequent analysis is pronounced, increasing precision and statistical power for subsequent inference.

Keywords
distributed recruits, maternal assay, microsatellites, Quercus
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-53873 (URN)10.1093/jhered/esr141 (DOI)000300723400010 ()
Available from: 2012-04-05 Created: 2012-04-04 Last updated: 2018-06-08Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-5235-6461

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