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Hall, D., Zhao, W., Wennström, U., Andersson Gull, B. & Wang, X.-R. (2020). Parentage and relatedness reconstruction in Pinus sylvestris using genotyping-by-sequencing. Heredity
Open this publication in new window or tab >>Parentage and relatedness reconstruction in Pinus sylvestris using genotyping-by-sequencing
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2020 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540Article in journal (Refereed) Epub ahead of print
Abstract [en]

Estimating kinship is fundamental for studies of evolution, conservation, and breeding. Genotyping-by-sequencing (GBS) and other restriction based genotyping methods have become widely applied in these applications in non-model organisms. However, sequencing errors, depth, and reproducibility between library preps could potentially hinder accurate genetic inferences. In this study, we tested different sets of parameters in data filtering, different reference populations and eight estimation methods to obtain a robust procedure for relatedness estimation in Scots pine (Pinus sylvestris L.). We used a seed orchard as our study system, where candidate parents are known and pedigree reconstruction can be compared with theoretical expectations. We found that relatedness estimates were lower than expected for all categories of kinship estimated if the proportion of shared SNPs was low. However, estimates reached expected values if loci showing an excess of heterozygotes were removed and genotyping error rates were considered. The genetic variance-covariance matrix (G-matrix) estimation, however, performed poorly in kinship estimation. The reduced relatedness estimates are likely due to false heterozygosity calls. We analyzed the mating structure in the seed orchard and identified a selfing rate of 3% (including crosses between clone mates) and external pollen contamination of 33.6%. Little genetic structure was observed in the sampled Scots pine natural populations, and the degree of inbreeding in the orchard seed crop is comparable to natural stands. We illustrate that under our optimized data processing procedure, relatedness, and genetic composition, including level of pollen contamination within a seed orchard crop, can be established consistently by different estimators.

Place, publisher, year, edition, pages
Nature Publishing Group, 2020
National Category
Forest Science Genetics
Identifiers
urn:nbn:se:umu:diva-169061 (URN)10.1038/s41437-020-0302-3 (DOI)000517737800001 ()32123330 (PubMedID)
Available from: 2020-03-19 Created: 2020-03-19 Last updated: 2020-03-19
Sullivan, A. R., Eldfjell, Y., Schiffthaler, B., Delhomme, N., Asp, T., Hebelstrup, K. H., . . . Wang, X.-R. (2020). The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants. Genome Biology and Evolution, 12(1), 3586-3598
Open this publication in new window or tab >>The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants
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2020 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 12, no 1, p. 3586-3598Article in journal (Refereed) Published
Abstract [en]

Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.

Place, publisher, year, edition, pages
Oxford University Press, 2020
Keywords
mitogenome, repeats, recombination, rearrangement rates, structural variation
National Category
Earth and Related Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-168043 (URN)10.1093/gbe/evz263 (DOI)
Available from: 2020-02-14 Created: 2020-02-14 Last updated: 2020-02-14Bibliographically approved
Liu, Y.-J., Wang, X.-R. & Zeng, Q.-Y. (2019). De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China. Science China Life Sciences, 62(5), 609-618
Open this publication in new window or tab >>De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China
2019 (English)In: Science China Life Sciences, ISSN 1674-7305, E-ISSN 1869-1889, Vol. 62, no 5, p. 609-618Article in journal (Refereed) Published
Abstract [en]

The white poplar (Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa (black cottonwood) occurred similar to 5.0 Mya (3.0, 7.1). Fourfold synonymous third-codon transversion (4DTV) and synonymous substitution rate (ks) distributions supported the occurrence of the salicoid WGD event (similar to 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170 +/- 0.014, which was lower than that in Italy (0.271 +/- 0.051) and Hungary (0.264 +/- 0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P. alba populations examined.

Keywords
Populus alba, de novo assembly, genetic diversity, population expansion
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-159401 (URN)10.1007/s11427-018-9455-2 (DOI)000467172000001 ()30661181 (PubMedID)
Available from: 2019-06-10 Created: 2019-06-10 Last updated: 2019-06-10Bibliographically approved
Xu, C.-Q., Liu, H., Zhou, S.-S., Zhang, D.-X., Zhao, W., Wang, S., . . . Mao, J.-F. (2019). Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. GigaScience, 8(2), Article ID giy164.
Open this publication in new window or tab >>Genome sequence of Malania oleifera, a tree with great value for nervonic acid production
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2019 (English)In: GigaScience, ISSN 2047-217X, E-ISSN 2047-217X, Vol. 8, no 2, article id giy164Article in journal (Refereed) Published
Abstract [en]

Background Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. Findings We generated 51 Gb and 135Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted approximate to 82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. Conclusions Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.

Place, publisher, year, edition, pages
Oxford University Press, 2019
Keywords
de novo genome assembly, vulnerable plant, Malania, nervonic acid, transcriptomes
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-158120 (URN)10.1093/gigascience/giy164 (DOI)000462551600008 ()30689848 (PubMedID)
Available from: 2019-04-12 Created: 2019-04-12 Last updated: 2019-04-12Bibliographically approved
Jin, Y., Zhao, W., Nie, S., Liu, S.-S., El-Kassaby, Y. A., Wang, X.-R. & Mao, J.-F. (2019). Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for Platycladus orientalis (Cupressaceae). G3: Genes, Genomes, Genetics, 9(11), 3663-3672
Open this publication in new window or tab >>Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for Platycladus orientalis (Cupressaceae)
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2019 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 9, no 11, p. 3663-3672Article in journal (Refereed) Published
Abstract [en]

Platycladus orientalis is an ecologically important native conifer in Northern China and exotic species in many parts of the world; however, knowledge about the species' genetics and genome are very limited. The availability of well-developed battery of genetic markers, with large genome coverage, is a prerequisite for the species genetic dissection of adaptive attributes and efficient selective breeding. Here, we present a genome-wide genotyping method with double-digestion restriction site associated DNA sequencing (ddRAD-seq) that is effective in generating large number of Mendelian markers for genome mapping and other genetic applications. Using 139 megagametophytes collected from a single mother tree, we assembled 397,226 loci, of which 108,683 (27.4%) were polymorphic. After stringent filtering for 1:1 segregation ratio and missing rate of <20%, the remaining 23,926 loci (22% of the polymorphic loci) were ordered into 11 linkage groups (LGs) and distributed across 7,559 unique positions, with a total map length of 1,443 cM and an average spacing of 0.2 cM between adjacent unique positions. The 11 LGs correspond to the species' 11 haploid genome chromosome number. This genetic map is among few high-density maps available for conifers to date, and represents the first genetic map for P. orientalis. The information generated serves as a solid foundation not only for marker-assisted breeding efforts, but also for comparative conifer genomic studies.

Place, publisher, year, edition, pages
The Genetics Society of America, 2019
Keywords
RADseq, linkage map, marker distribution, segregation, genome organization
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-165769 (URN)10.1534/g3.119.400684 (DOI)000495646300017 ()31506321 (PubMedID)
Available from: 2019-12-05 Created: 2019-12-05 Last updated: 2019-12-05Bibliographically approved
Jia, K.-H., Zhao, W., Maier, P. A., Hu, X.-G., Jin, Y., Zhou, S.-S., . . . Mao, J.-F. (2019). Landscape genomics predicts climate change-related genetic offset for the widespread Platycladus orientalis (Cupressaceae). Evolutionary Applications
Open this publication in new window or tab >>Landscape genomics predicts climate change-related genetic offset for the widespread Platycladus orientalis (Cupressaceae)
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2019 (English)In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571Article in journal (Refereed) Epub ahead of print
Abstract [en]

Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome-wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high-quality variants from Platycladus orientalis range-wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. Platycladus orientalis is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature-related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for P. orientalis.

Place, publisher, year, edition, pages
WILEY, 2019
Keywords
adaptation, climate change, genetic offset, genotyping by sequencing, Platycladus orientalis, population structure
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-166574 (URN)10.1111/eva.12891 (DOI)000497989300001 ()
Available from: 2019-12-19 Created: 2019-12-19 Last updated: 2019-12-19
Xia, H., Wang, B., Zhao, W., Pan, J., Mao, J.-F. & Wang, X.-R. (2018). Combining mitochondrial and nuclear genome analyses to dissect the effects of colonization, environment, and geography on population structure in Pinus tabuliformis. Evolutionary Applications, 11(10), 1931-1945
Open this publication in new window or tab >>Combining mitochondrial and nuclear genome analyses to dissect the effects of colonization, environment, and geography on population structure in Pinus tabuliformis
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2018 (English)In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 11, no 10, p. 1931-1945Article in journal (Refereed) Published
Abstract [en]

The phylogeographic histories of plants in East Asia are complex and shaped by both past large‐scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. Pinus tabuliformis is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping‐by‐sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among‐population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in P. tabuliformis is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for P. tabuliformis.

Place, publisher, year, edition, pages
John Wiley & Sons, 2018
Keywords
demographic history, genotyping-by-sequencing, local adaptation, niche modeling, population structure
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-154936 (URN)10.1111/eva.12697 (DOI)000449942900012 ()30459839 (PubMedID)
Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2019-01-07Bibliographically approved
Olajos, F., Bokma, F., Bartels, P., Myrstener, E., Rydberg, J., Öhlund, G., . . . Englund, G. (2018). Estimating species colonization dates using DNA in lake sediment. Methods in Ecology and Evolution, 9(3), 535-543
Open this publication in new window or tab >>Estimating species colonization dates using DNA in lake sediment
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2018 (English)In: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 9, no 3, p. 535-543Article in journal (Refereed) Published
Abstract [en]
  1. Detection of DNA in lake sediments holds promise as a tool to study processes like extinction, colonization, adaptation and evolutionary divergence. However, low concentrations make sediment DNA difficult to detect, leading to high false negative rates. Additionally, contamination could potentially lead to high false positive rates. Careful laboratory procedures can reduce false positive and negative rates, but should not be assumed to completely eliminate them. Therefore, methods are needed that identify potential false positive and negative results, and use this information to judge the plausibility of different interpretations of DNA data from natural archives.
  2. We developed a Bayesian algorithm to infer the colonization history of a species using records of DNA from lake-sediment cores, explicitly labelling some observations as false positive or false negative. We illustrate the method by analysing DNA of whitefish (Coregonus lavaretus L.) from sediment cores covering the past 10,000 years from two central Swedish lakes. We provide the algorithm as an R-script, and the data from this study as example input files.
  3. In one lake, Stora Lögdasjön, where connectivity with the proto-Baltic Sea and the degree of whitefish ecotype differentiation suggested colonization immediately after deglaciation, DNA was indeed successfully recovered and amplified throughout the post-glacial sediment. For this lake, we found no loss of detection probability over time, but a high false negative rate. In the other lake, Hotagen, where connectivity and ecotype differentiation suggested colonization long after deglaciation, DNA was amplified only in the upper part of the sediment, and colonization was estimated at 2,200 bp based on the assumption that successful amplicons represent whitefish presence. Here the earliest amplification represents a false positive with a posterior probability of 41%, which increases the uncertainty in the estimated time of colonization.
  4. Complementing careful laboratory procedures aimed at preventing contamination, our method estimates contamination rates from the data. By combining these results with estimates of false negative rates, our models facilitate unbiased interpretation of data from natural DNA archives.
Place, publisher, year, edition, pages
British Ecological Society, 2018
Keywords
ancient DNA, colonization, Coregonus lavaretus, detection probability, divergence, environmental DNA, lake sediment, population age
National Category
Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-143248 (URN)10.1111/2041-210X.12890 (DOI)000426867600010 ()
Funder
Swedish Research Council, 2013-5110
Available from: 2017-12-19 Created: 2017-12-19 Last updated: 2018-08-07Bibliographically approved
Zale, R., Huang, Y.-T. -., Bigler, C., Wood, J. R., Dalén, L., Wang, X.-R., . . . Klaminder, J. (2018). Growth of plants on the Late Weichselian ice-sheet during Greenland interstadial-1?. Quaternary Science Reviews, 185, 222-229
Open this publication in new window or tab >>Growth of plants on the Late Weichselian ice-sheet during Greenland interstadial-1?
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2018 (English)In: Quaternary Science Reviews, ISSN 0277-3791, E-ISSN 1873-457X, Vol. 185, p. 222-229Article in journal (Refereed) Published
Abstract [en]

Unglaciated forelands and summits protruding from ice-sheets are commonly portrayed as areas where plants first establish at the end of glacial cycles. But is this prevailing view of ice-free refugia too simplistic? Here, we present findings suggesting that surface debris supported plant communities far beyond the rim of the Late Weichselian Ice-sheet during Greenland interstadial 1 (GI-1 or Bolling-Altered interstadial). We base our interpretations upon findings from terrigenous sediments largely resembling 'plant-trash' deposits in North America (known to form as vegetation established on stagnant ice became buried along with glacial debris during the deglaciation). In our studied deposit, we found macrofossils (N = 10) overlapping with the deglaciation period of the area (9.5-10 cal kyr BP) as well as samples (N = 2) with ages ranging between 12.9 and 13.3 cal kyr BP. The latter ages indicate growth of at least graminoids during the GI-1 interstadial when the site was near the geographic center of the degrading ice-sheet. We suggest that exposure of englacial material during GI-1 created patches of supraglacial debris capable of supporting vascular plants three millennia before deglaciation. The composition and resilience of this early plant community remain uncertain. Yet, the younger group of macrofossils, in combination with pollen and ancient DNA analyses of inclusions, imply that shrubs (Salix sp., Betula sp. and Ericaceae sp) and even tree species (Larix) were present in the debris during the final deglaciation stage. 

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
Holocene, Pleistocene, Glaciology, Paleolimnology, Scandinavia, Vegetation dynamics, MIS-3
National Category
Geology Physical Geography
Identifiers
urn:nbn:se:umu:diva-148634 (URN)10.1016/j.quascirev.2018.02.005 (DOI)000428830400015 ()
Funder
Knut and Alice Wallenberg FoundationCarl Tryggers foundation
Available from: 2018-06-26 Created: 2018-06-26 Last updated: 2018-08-17Bibliographically approved
Sullivan, A. R., Schiffthaler, B., Thompson, S. L., Street, N. R. & Wang, X.-R. (2017). Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae). Molecular biology and evolution, 34(7), 1689-1701
Open this publication in new window or tab >>Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)
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2017 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 34, no 7, p. 1689-1701Article in journal (Refereed) Published
Abstract [en]

Plastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. Using advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of similar to 35 coniferous forest tree species, to test for deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for chimeric plastomes generated by interspecific hybridization and recombination in the clade comprising Norway spruce (P. abies) and 10 other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results reconcile previous conflicting plastid-based phylogenies and strengthen the mounting evidence of reticulate evolution in Picea. Given the relatively high frequency of hybridization and biparental plastid inheritance in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2017
Keywords
hybridization, chloroplast genomes, phylogenetic incongruence, recombination, reticulate evolution
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-137034 (URN)10.1093/molbev/msx111 (DOI)000402754400012 ()28383641 (PubMedID)
Available from: 2017-06-29 Created: 2017-06-29 Last updated: 2020-02-14Bibliographically approved
Projects
Importance of allelic variation in homoploid hybrid speciation in plants [2008-05709_VR]; Umeå UniversityIn-depth evaluation of the function of an advanced Scots pine seed orchard [2010-591_Formas]; Umeå UniversityEcological and genetic dynamics in species boundaries [2011-03195_VR]; Umeå UniversityLong-term sustainable forest production: knowledge-based strategies in seed orchard and reforestation operations [2015-67_Formas]; Umeå UniversityDynamics of hybrid speciation and adaptation to extreme habitats [2017-04686_VR]; Umeå University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-6150-7046

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