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Publications (10 of 86) Show all publications
Sandell, F. L., Holzweber, T., Street, N., Dohm, J. C. & Himmelbauer, H. (2024). Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting. Plant Biotechnology Journal
Open this publication in new window or tab >>Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting
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2024 (English)In: Plant Biotechnology Journal, ISSN 1467-7644, E-ISSN 1467-7652Article in journal (Refereed) Epub ahead of print
Abstract [en]

Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.

Place, publisher, year, edition, pages
John Wiley & Sons, 2024
Keywords
betalain synthesis pathway, genome sequencing, genotype-phenotype relationships, machine learning, quinoa, seed colour
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-219822 (URN)10.1111/pbi.14267 (DOI)2-s2.0-85182144182 (Scopus ID)
Available from: 2024-01-22 Created: 2024-01-22 Last updated: 2024-01-22
Urbancsok, J., Donev, E. N., Sivan, P., van Zalen, E., Barbut, F. R., Derba-Maceluch, M., . . . Mellerowicz, E. J. (2023). Flexure wood formation via growth reprogramming in hybrid aspen involves jasmonates and polyamines and transcriptional changes resembling tension wood development. New Phytologist, 240(6), 2312-2334
Open this publication in new window or tab >>Flexure wood formation via growth reprogramming in hybrid aspen involves jasmonates and polyamines and transcriptional changes resembling tension wood development
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2023 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 240, no 6, p. 2312-2334Article in journal (Refereed) Published
Abstract [en]

Stem bending in trees induces flexure wood but its properties and development are poorly understood. Here, we investigated the effects of low-intensity multidirectional stem flexing on growth and wood properties of hybrid aspen, and on its transcriptomic and hormonal responses.

Glasshouse-grown trees were either kept stationary or subjected to several daily shakes for 5 wk, after which the transcriptomes and hormones were analyzed in the cambial region and developing wood tissues, and the wood properties were analyzed by physical, chemical and microscopy techniques.

Shaking increased primary and secondary growth and altered wood differentiation by stimulating gelatinous-fiber formation, reducing secondary wall thickness, changing matrix polysaccharides and increasing cellulose, G- and H-lignin contents, cell wall porosity and saccharification yields. Wood-forming tissues exhibited elevated jasmonate, polyamine, ethylene and brassinosteroids and reduced abscisic acid and gibberellin signaling. Transcriptional responses resembled those during tension wood formation but not opposite wood formation and revealed several thigmomorphogenesis-related genes as well as novel gene networks including FLA and XTH genes encoding plasma membrane-bound proteins.

Low-intensity stem flexing stimulates growth and induces wood having improved biorefinery properties through molecular and hormonal pathways similar to thigmomorphogenesis in herbaceous plants and largely overlapping with the tension wood program of hardwoods.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
flexure wood, jasmonic acid signaling, mechanostimulation, polyamines, Populus tremula × tremuloides, saccharification, thigmomorphogenesis, wood development
National Category
Botany Wood Science
Identifiers
urn:nbn:se:umu:diva-215853 (URN)10.1111/nph.19307 (DOI)001085559700001 ()37857351 (PubMedID)2-s2.0-85174386995 (Scopus ID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilBio4Energy
Available from: 2023-11-06 Created: 2023-11-06 Last updated: 2023-12-20Bibliographically approved
Escamez, S., Robinson, K. M., Luomaranta, M., Gandla, M. L., Mähler, N., Yassin, Z., . . . Tuominen, H. (2023). Genetic markers and tree properties predicting wood biorefining potential in aspen (Populus tremula) bioenergy feedstock. Biotechnology for Biofuels and Bioproducts, 16(1), Article ID 65.
Open this publication in new window or tab >>Genetic markers and tree properties predicting wood biorefining potential in aspen (Populus tremula) bioenergy feedstock
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2023 (English)In: Biotechnology for Biofuels and Bioproducts, E-ISSN 2731-3654, Vol. 16, no 1, article id 65Article in journal (Refereed) Published
Abstract [en]

Background: Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.

Results: We recorded 65 wood-related and growth traits in a population of 113 natural aspen genotypes from Sweden (https://doi.org/10.5061/dryad.gtht76hrd). These traits included three growth and field performance traits, 20 traits for wood chemical composition, 17 traits for wood anatomy and structure, and 25 wood saccharification traits as indicators of bioconversion potential. Glucose release after saccharification with acidic pretreatment correlated positively with tree stem height and diameter and the carbohydrate content of the wood, and negatively with the content of lignin and the hemicellulose sugar units. Most of these traits displayed extensive natural variation within the aspen population and high broad-sense heritability, supporting their potential in genetic improvement of feedstocks towards improved bioconversion. Finally, a genome-wide association study (GWAS) revealed 13 genetic loci for saccharification yield (on a whole-tree-biomass basis), with six of them intersecting with associations for either height or stem diameter of the trees.

Conclusions: The simple growth traits of stem height and diameter were identified as good predictors of wood saccharification yield in aspen trees. GWAS elucidated the underlying genetics, revealing putative genetic markers for bioconversion of bioenergy tree feedstocks.

Place, publisher, year, edition, pages
BioMed Central (BMC), 2023
Keywords
Bioenergy, Biomass, Biorefining, Feedstock recalcitrance, Forest feedstocks, Saccharification
National Category
Forest Science
Identifiers
urn:nbn:se:umu:diva-206938 (URN)10.1186/s13068-023-02315-1 (DOI)000967835900001 ()2-s2.0-85152632077 (Scopus ID)
Funder
Swedish Research Council Formas, 942-2015-84Swedish Research Council Formas, 2018-01381Knut and Alice Wallenberg Foundation, 2016.0341Knut and Alice Wallenberg Foundation, 2016.0352Vinnova, 2016-00504Bio4Energy
Available from: 2023-04-27 Created: 2023-04-27 Last updated: 2023-11-06Bibliographically approved
Schiffthaler, B., van Zalen, E., Serrano, A. R., Street, N. & Delhomme, N. (2023). Seiðr: Efficient calculation of robust ensemble gene networks. Heliyon, 9(6), Article ID e16811.
Open this publication in new window or tab >>Seiðr: Efficient calculation of robust ensemble gene networks
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2023 (English)In: Heliyon, E-ISSN 2405-8440, Vol. 9, no 6, article id e16811Article in journal (Refereed) Published
Abstract [en]

Gene regulatory and gene co-expression networks are powerful research tools for identifying biological signal within high-dimensional gene expression data. In recent years, research has focused on addressing shortcomings of these techniques with regard to the low signal-to-noise ratio, non-linear interactions and dataset dependent biases of published methods. Furthermore, it has been shown that aggregating networks from multiple methods provides improved results. Despite this, few useable and scalable software tools have been implemented to perform such best-practice analyses. Here, we present Seidr (stylized Seiðr), a software toolkit designed to assist scientists in gene regulatory and gene co-expression network inference. Seidr creates community networks to reduce algorithmic bias and utilizes noise corrected network backboning to prune noisy edges in the networks.

Using benchmarks in real-world conditions across three eukaryotic model organisms, Saccharomyces cerevisiae, Drosophila melanogaster, and Arabidopsis thaliana, we show that individual algorithms are biased toward functional evidence for certain gene-gene interactions. We further demonstrate that the community network is less biased, providing robust performance across different standards and comparisons for the model organisms.

Finally, we apply Seidr to a network of drought stress in Norway spruce (Picea abies (L.) H. Krast) as an example application in a non-model species. We demonstrate the use of a network inferred using Seidr for identifying key components, communities and suggesting gene function for non-annotated genes.

Place, publisher, year, edition, pages
Elsevier, 2023
Keywords
Functional genomics, Gene co-expression network, Gene network inference, Gene regulatory network, Systems biology
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-209556 (URN)10.1016/j.heliyon.2023.e16811 (DOI)001021913700001 ()2-s2.0-85160669474 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, 2016.0341Knut and Alice Wallenberg Foundation, 2016.0352Vinnova, 2016-00504
Available from: 2023-06-12 Created: 2023-06-12 Last updated: 2023-11-06Bibliographically approved
Estravis Barcala, M., van der Valk, T., Chen, Z., Funda, T., Chaudhary, R., Klingberg, A., . . . Wu, H. X. (2023). Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species. The Plant Journal
Open this publication in new window or tab >>Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species
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2023 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313XArticle in journal (Refereed) Epub ahead of print
Abstract [en]

Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.

Keywords
genome resequencing, genome-wide association studies, genomic selection, pines, Pinus sylvestris, SNP array
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-216873 (URN)10.1111/tpj.16535 (DOI)2-s2.0-85176314433 (Scopus ID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilSwedish Research Council Formas, 2019-00874
Available from: 2023-12-12 Created: 2023-12-12 Last updated: 2023-12-12
Akhter, S., Westrin, K. J., Zivi, N., Nordal, V., Kretzschmar, W. W., Delhomme, N., . . . Sundström, J. F. (2022). Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway. New Phytologist, 236(5), 1951-1963
Open this publication in new window or tab >>Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway
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2022 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 236, no 5, p. 1951-1963Article in journal (Refereed) Published
Abstract [en]

Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots.

We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees.

A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation.

In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.

Place, publisher, year, edition, pages
John Wiley & Sons, 2022
Keywords
cone-setting, flowering, gymnosperm, Picea abies, reproductive development, SPL-gene family, transcriptome
National Category
Plant Biotechnology Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-199915 (URN)10.1111/nph.18449 (DOI)000854207600001 ()36076311 (PubMedID)2-s2.0-85138178292 (Scopus ID)
Funder
Carl Tryggers foundation , CTS 18:367Royal Physiographic Society in Lund, 22309-000Swedish Foundation for Strategic Research, FID16-0030Swedish Foundation for Strategic Research, FFF20-0014Swedish Research Council Formas, 239-2013-650Swedish Research Council Formas, 2021-01026Swedish Research Council, 2018-05973Swedish National Infrastructure for Computing (SNIC)
Available from: 2022-10-06 Created: 2022-10-06 Last updated: 2022-12-30Bibliographically approved
Liu, S., Zhang, L., Sang, Y., Lai, Q., Zhang, X., Jia, C., . . . Wang, J. (2022). Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome. Molecular biology and evolution, 39(2), Article ID msac008.
Open this publication in new window or tab >>Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome
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2022 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 39, no 2, article id msac008Article in journal (Refereed) Published
Abstract [en]

Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.

Place, publisher, year, edition, pages
Oxford University Press, 2022
Keywords
Populus, adaptive introgression, genetic load, hybridization, natural selection
National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:umu:diva-192645 (URN)10.1093/molbev/msac008 (DOI)000767848900013 ()35022759 (PubMedID)2-s2.0-85124436552 (Scopus ID)
Available from: 2022-02-22 Created: 2022-02-22 Last updated: 2023-09-05Bibliographically approved
Curci, P. L., Zhang, J., Mähler, N., Seyfferth, C., Mannapperuma, C., Diels, T., . . . Vandepoele, K. (2022). Identification of growth regulators using cross-species network analysis in plants. Plant Physiology, 190(4), 2350-2365
Open this publication in new window or tab >>Identification of growth regulators using cross-species network analysis in plants
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2022 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 190, no 4, p. 2350-2365Article in journal (Refereed) Published
Abstract [en]

With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.

Place, publisher, year, edition, pages
Oxford University Press, 2022
National Category
Botany Plant Biotechnology
Identifiers
urn:nbn:se:umu:diva-201619 (URN)10.1093/plphys/kiac374 (DOI)000844537500001 ()35984294 (PubMedID)2-s2.0-85143141934 (Scopus ID)
Funder
The Research Council of Norway, 287465
Available from: 2022-12-14 Created: 2022-12-14 Last updated: 2022-12-14Bibliographically approved
Law, S. R., Serrano, A. R., Daguerre, Y., Sundh, J., Schneider, A. N., Stangl, Z. R., . . . Hurry, V. (2022). Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests. Proceedings of the National Academy of Sciences of the United States of America, 119(26), Article ID e2118852119.
Open this publication in new window or tab >>Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests
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2022 (English)In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 119, no 26, article id e2118852119Article in journal (Other academic) Published
Abstract [en]

Carbon storage and cycling in boreal forests-the largest terrestrial carbon store-is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree-microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host-microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions. 

Place, publisher, year, edition, pages
National Academy of Sciences, 2022
Keywords
carbon storage, ectomycorrhiza, fungal effectors, host–microbe, metatranscriptome
National Category
Other Biological Topics
Identifiers
urn:nbn:se:umu:diva-194524 (URN)10.1073/pnas.2118852119 (DOI)35727987 (PubMedID)2-s2.0-85132270803 (Scopus ID)
Available from: 2022-05-09 Created: 2022-05-09 Last updated: 2023-01-19Bibliographically approved
Ranjan, A., Perrone, I., Alallaq, S., Singh, R., Rigal, A., Brunoni, F., . . . Bellini, C. (2022). Molecular basis of differential adventitious rooting competence in poplar genotypes. Journal of Experimental Botany, 73(12), 4046-4064
Open this publication in new window or tab >>Molecular basis of differential adventitious rooting competence in poplar genotypes
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2022 (English)In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 73, no 12, p. 4046-4064Article in journal (Refereed) Published
Abstract [en]

Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotypes remains unknown. To address this, we generated cambium tissue-specific transcriptomic data from stem cuttings of hybrid aspen, T89 (difficult-to-root) and hybrid poplar OP42 (easy-to-root), and used transgenic approaches to verify the role of several transcription factors in the control of adventitious rooting. Increased peroxidase activity was positively correlated with better rooting. We found differentially expressed genes encoding reactive oxygen species scavenging proteins to be enriched in OP42 compared with T89. A greater number of differentially expressed transcription factors in cambium cells of OP42 compared with T89 was revealed by a more intense transcriptional reprograming in the former. PtMYC2, a potential negative regulator, was less expressed in OP42 compared with T89. Using transgenic approaches, we demonstrated that PttARF17.1 and PttMYC2.1 negatively regulate adventitious rooting. Our results provide insights into the molecular basis of genotypic differences in AR and implicate differential expression of the master regulator MYC2 as a critical player in this process.

Place, publisher, year, edition, pages
Oxford University Press, 2022
Keywords
Adventitious roots, cambium, hybrid aspen, hybrid poplar, Populus spp, stem cuttings
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-198225 (URN)10.1093/jxb/erac126 (DOI)000813477900001 ()35325111 (PubMedID)2-s2.0-85133797842 (Scopus ID)
Funder
Knut and Alice Wallenberg FoundationVinnovaSwedish Research CouncilSwedish Research Council FormasThe Kempe FoundationsCarl Tryggers foundation
Available from: 2022-07-21 Created: 2022-07-21 Last updated: 2022-07-21Bibliographically approved
Projects
Chromatin dynamics in the gigantic genome of Norway spruce [2019-05476_VR]; Umeå University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-6031-005x

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