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Schiffthaler, BastianORCID iD iconorcid.org/0000-0002-9771-467x
Publications (10 of 17) Show all publications
Schiffthaler, B. (2020). Embracing the data flood: integrating diverse data to improve phenotype association discovery in forest trees. (Doctoral dissertation). Umeå: Umeå University
Open this publication in new window or tab >>Embracing the data flood: integrating diverse data to improve phenotype association discovery in forest trees
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Complex traits represent valuable research targets as many highly desirable properties of plants and animals (such as growth rate and height) fall into this group. However, associating biological markers with these traits is incredibly challenging, in part due to their small effect sizes. For the two species at the core of our research, European aspen (Populus tremula) and Norway spruce (Picea abies), association studies are even more challenging, primarily due to the fragmented state of their genome assemblies. These assemblies represent the gene space well, but poorly represented inter-genic regions hinder variant discovery and large scale association studies.

In this thesis, I present my work to improve association discovery of complex traits in forest trees. Firstly, to overcome the issues with assembly fragmentation, I have created an updated version of the P. tremula genome, which is highly contiguous and anchored in full chromosomes. To calculate the dense linkage map required to order and orient the aspen assembly, I developed "BatchMap", a parallel implementation of linkage mapping software. BatchMap has been successfully applied to several dense linkage maps, including aspen and Norway spruce, and was essential to the progress in improving the aspen genome assembly. Further, I developed seidr, which represents a starting point in multi-layer, network-based systems biology, an analysis technique with promising prospects for complex trait association analysis. As a case study, I applied some of the methods developed to the analysis of leaf shape in natural populations of European aspen, a complex, omnigenic trait.

The multi-layer model of systems biology and related analysis techniques offer promise in the analysis of complex traits, and this thesis represents a starting point toward an intricate, holistic model of systems biology that may help to unravel the overwhelmingly complicated nature of complex traits.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2020. p. 83
Keywords
Systems Biology, Association Discovery, Genomics, Transcriptomics, Genome Assembly, Gene Networks, Forest Tree, Aspen, Spruce
National Category
Biological Sciences
Research subject
biology
Identifiers
urn:nbn:se:umu:diva-170643 (URN)978-91-7855-273-3 (ISBN)978-91-7855-274-0 (ISBN)
Public defence
2020-06-12, Carl Kempe Salen, Linnaeus Väg 6, Umeå, 13:00 (English)
Opponent
Supervisors
Available from: 2020-05-20 Created: 2020-05-13 Last updated: 2020-05-13Bibliographically approved
Apuli, R.-P., Bernhardsson, C., Schiffthaler, B., Robinson, K. M., Jansson, S., Street, N. & Ingvarsson, P. K. (2020). Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula). G3: Genes, Genomes, Genetics, 10(1), 299-309
Open this publication in new window or tab >>Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula)
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2020 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 10, no 1, p. 299-309Article in journal (Refereed) Published
Abstract [en]

The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.

Place, publisher, year, edition, pages
GENETICS SOCIETY AMERICA, 2020
Keywords
linkage disequilibrium, linkage map, linked selection, methylation, nucleotide diversity, recombination
National Category
Genetics Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-167954 (URN)10.1534/g3.119.400504 (DOI)000506031000027 ()31744900 (PubMedID)
Available from: 2020-02-25 Created: 2020-02-25 Last updated: 2020-02-25Bibliographically approved
Mannapperuma, C., Liu, H., Bel, M., Delhomme, N., Serrano, A., Schiffthaler, B., . . . Street, N. (2020). PlantGenIE-PLAZA: integrating orthology into the PlantGenIE.org resource using the PLAZA pipeline.
Open this publication in new window or tab >>PlantGenIE-PLAZA: integrating orthology into the PlantGenIE.org resource using the PLAZA pipeline
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2020 (English)In: Article in journal (Other academic) In press
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-170114 (URN)
Available from: 2020-04-27 Created: 2020-04-27 Last updated: 2020-05-25
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
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
Creel, S., Spong, G., Becker, M., Simukonda, C., Norman, A., Schiffthaler, B. & Chifunte, C. (2019). Carnivores, competition and genetic connectivity in the Anthropocene. Scientific Reports, 9, Article ID 16339.
Open this publication in new window or tab >>Carnivores, competition and genetic connectivity in the Anthropocene
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2019 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 16339Article in journal (Refereed) Published
Abstract [en]

Current extinction rates are comparable to five prior mass extinctions in the earth's history, and are strongly affected by human activities that have modified more than half of the earth's terrestrial surface. Increasing human activity restricts animal movements and isolates formerly connected populations, a particular concern for the conservation of large carnivores, but no prior research has used high throughput sequencing in a standardized manner to examine genetic connectivity for multiple species of large carnivores and multiple ecosystems. Here, we used RAD SNP genotypes to test for differences in connectivity between multiple ecosystems for African wild dogs (Lycaon pictus) and lions (Panthera leo), and to test correlations between genetic distance, geographic distance and landscape resistance due to human activity. We found weaker connectivity, a stronger correlation between genetic distance and geographic distance, and a stronger correlation between genetic distance and landscape resistance for lions than for wild dogs, and propose a new hypothesis that adaptations to interspecific competition may help to explain differences in vulnerability to isolation by humans.

Place, publisher, year, edition, pages
Nature Publishing Group, 2019
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-165772 (URN)10.1038/s41598-019-52904-0 (DOI)000495371900015 ()31705017 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation
Available from: 2019-12-05 Created: 2019-12-05 Last updated: 2019-12-05Bibliographically approved
Ratke, C., Terebieniec, B. K., Winestrand, S., Derba-Maceluch, M., Grahn, T., Schiffthaler, B., . . . Mellerowicz, E. J. (2018). Downregulating aspen xylan biosynthetic GT43 genes in developing wood stimulates growth via reprograming of the transcriptome. New Phytologist, 219(1), 230-245
Open this publication in new window or tab >>Downregulating aspen xylan biosynthetic GT43 genes in developing wood stimulates growth via reprograming of the transcriptome
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2018 (English)In: New Phytologist, ISSN 0028-646X, Vol. 219, no 1, p. 230-245Article in journal (Refereed) Published
Abstract [en]

Xylan is one of the main compounds determining wood properties in hardwood species. The xylan backbone is thought to be synthesized by a synthase complex comprising two members of the GT43 family. We downregulated all GT43 genes in hybrid aspen (Populus tremulaxtremuloides) to understand their involvement in xylan biosynthesis.

All three clades of the GT43 family were targeted for downregulation using RNA interference individually or in different combinations, either constitutively or specifically in developing wood.

Simultaneous downregulation in developing wood of the B (IRX9) and C (IRX14) clades resulted in reduced xylan Xyl content relative to reducing end sequence, supporting their role in xylan backbone biosynthesis. This was accompanied by a higher lignocellulose saccharification efficiency. Unexpectedly, GT43 suppression in developing wood led to an overall growth stimulation, xylem cell wall thinning and a shift in cellulose orientation. Transcriptome profiling of these transgenic lines indicated that cell cycling was stimulated and secondary wall biosynthesis was repressed. We suggest that the reduced xylan elongation is sensed by the cell wall integrity surveying mechanism in developing wood.

Our results show that wood-specific suppression of xylan-biosynthetic GT43 genes activates signaling responses, leading to increased growth and improved lignocellulose saccharification.

Keywords
cellulose microfibril angle, GT43, Populus, saccharification, secondary wall, wood development, xylan biosynthesis
National Category
Plant Biotechnology
Identifiers
urn:nbn:se:umu:diva-150384 (URN)10.1111/nph.15160 (DOI)000434153200026 ()29708593 (PubMedID)2-s2.0-85046148362 (Scopus ID)
Projects
Bio4Energy
Available from: 2018-08-06 Created: 2018-08-06 Last updated: 2020-01-30Bibliographically 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: 2020-05-13Bibliographically approved
Jokipii-Lukkari, S., Delhomme, N., Schiffthaler, B., Mannapperuma, C., Prestele, J., Nilsson, O., . . . Tuominen, H. (2018). Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce. Plant Physiology, 176(4), 2851-2870
Open this publication in new window or tab >>Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce
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2018 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 176, no 4, p. 2851-2870Article in journal (Refereed) Published
Abstract [en]

Seasonal cues influence several aspects of the secondary growth of tree stems, including cambial activity, wood chemistry, and transition to latewood formation. We investigated seasonal changes in cambial activity, secondary cell wall formation, and tracheid cell death in woody tissues of Norway spruce (Picea abies) throughout one seasonal cycle. RNA sequencing was performed simultaneously in both the xylem and cambium/phloem tissues of the stem. Principal component analysis revealed gradual shifts in the transcriptomes that followed a chronological order throughout the season. A notable remodeling of the transcriptome was observed in the winter, with many genes having maximal expression during the coldest months of the year. A highly coexpressed set of monolignol biosynthesis genes showed high expression during the period of secondary cell wall formation as well as a second peak in midwinter. This midwinter peak in expression did not trigger lignin deposition, as determined by pyrolysis-gas chromatography/mass spectrometry. Coexpression consensus network analyses suggested the involvement of transcription factors belonging to the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES and MYELOBLASTOSIS-HOMEOBOX families in the seasonal control of secondary cell wall formation of tracheids. Interestingly, the lifetime of the latewood tracheids stretched beyond the winter dormancy period, correlating with a lack of cell death-related gene expression. Our transcriptomic analyses combined with phylogenetic and microscopic analyses also identified the cellulose and lignin biosynthetic genes and putative regulators for latewood formation and tracheid cell death in Norway spruce, providing a toolbox for further physiological and functional assays of these important phase transitions.

Place, publisher, year, edition, pages
American Society of Plant Biologists, 2018
National Category
Cell Biology
Identifiers
urn:nbn:se:umu:diva-148642 (URN)10.1104/pp.17.01590 (DOI)000429089100021 ()29487121 (PubMedID)
Projects
Bio4Energy
Funder
Knut and Alice Wallenberg Foundation, KAW 2013.0305The Kempe Foundations, SMK-1340Swedish Research Council, 621-2013-4949Vinnova, 2015-02290
Available from: 2018-06-21 Created: 2018-06-21 Last updated: 2020-05-05Bibliographically approved
Laitinen, T., Morreel, K., Delhomme, N., Gauthier, A., Schiffthaler, B., Nickolov, K., . . . Kärkönen, A. (2017). A Key Role for Apoplastic H2O2 in Norway Spruce Phenolic Metabolism. Plant Physiology, 174(3), 1449-1475
Open this publication in new window or tab >>A Key Role for Apoplastic H2O2 in Norway Spruce Phenolic Metabolism
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2017 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 174, no 3, p. 1449-1475Article in journal (Refereed) Published
Abstract [en]

Apoplastic events such as monolignol oxidation and lignin polymerization are difficult to study in intact trees. To investigate the role of apoplastic hydrogen peroxide (H2O2) in gymnosperm phenolic metabolism, an extracellular lignin-forming cell culture of Norway spruce (Picea abies) was used as a research model. Scavenging of apoplastic H2O2 by potassium iodide repressed lignin formation, in line with peroxidases activating monolignols for lignin polymerization. Time-course analyses coupled to candidate substrate-product pair network propagation revealed differential accumulation of low-molecular-weight phenolics, including (glycosylated) oligolignols, (glycosylated) flavonoids, and proanthocyanidins, in lignin-forming and H2O2-scavenging cultures and supported that monolignols are oxidatively coupled not only in the cell wall but also in the cytoplasm, where they are coupled to other monolignols and proanthocyanidins. Dilignol glycoconjugates with reduced structures were found in the culture medium, suggesting that cells are able to transport glycosylated dilignols to the apoplast. Transcriptomic analyses revealed that scavenging of apoplastic H2O2 resulted in remodulation of the transcriptome, with reduced carbon flux into the shikimate pathway propagating down to monolignol biosynthesis. Aggregated coexpression network analysis identified candidate enzymes and transcription factors for monolignol oxidation and apoplastic H2O2 production in addition to potential H2O2 receptors. The results presented indicate that the redox state of the apoplast has a profound influence on cellular metabolism.

Place, publisher, year, edition, pages
American Society of Plant Biologists, 2017
National Category
Cell Biology Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-138557 (URN)10.1104/pp.17.00085 (DOI)000404233000014 ()28522458 (PubMedID)
Available from: 2017-09-14 Created: 2017-09-14 Last updated: 2020-02-17Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0002-9771-467x

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