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Schiffthaler, Bastian
Publications (9 of 9) 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
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: 2019-08-30Bibliographically 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: 2019-01-07Bibliographically 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: 2019-08-30Bibliographically 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: 2018-06-09Bibliographically approved
Schiffthaler, B., Bernhardsson, C., Ingvarsson, P. K. & Street, N. R. (2017). BatchMap: A parallel implementation of the OneMap R package for fast computation of F-1 linkage maps in outcrossing species. PLoS ONE, 12(12), Article ID e0189256.
Open this publication in new window or tab >>BatchMap: A parallel implementation of the OneMap R package for fast computation of F-1 linkage maps in outcrossing species
2017 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 12, article id e0189256Article in journal (Refereed) Published
Abstract [en]

With the rapid advancement of high throughput sequencing, large numbers of genetic markers can be readily and cheaply acquired, but most current software packages for genetic map construction cannot handle such dense input. Modern computer architectures and server farms represent untapped resources that can be used to enable higher marker densities to be processed in tractable time. Here we present a pipeline using a modified version of OneMap that parallelizes over bottleneck functions and achieves substantial speedups for producing a high density linkage map (N = 20,000). Using simulated data we show that the outcome is as accurate as the traditional pipeline. We further demonstrate that there is a direct relationship between the number of markers used and the level of deviation between true and estimated order, which in turn impacts the final size of a genetic map.

National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-144110 (URN)10.1371/journal.pone.0189256 (DOI)000418564200037 ()29261725 (PubMedID)
Available from: 2018-01-23 Created: 2018-01-23 Last updated: 2018-06-09Bibliographically 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: 2018-06-09Bibliographically approved
Schiffthaler, B., Kostadima, M., Delhomme, N. & Rustici, G. (2016). Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability. PloS Computational Biology, 12(6), Article ID e1004937.
Open this publication in new window or tab >>Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability
2016 (English)In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 12, no 6, article id e1004937Article in journal (Refereed) Published
Abstract [en]

The advancement of high-throughput sequencing (HTS) technologies and the rapid development of numerous analysis algorithms and pipelines in this field has resulted in an unprecedentedly high demand for training scientists in HTS data analysis. Embarking on developing new training materials is challenging for many reasons. Trainers often do not have prior experience in preparing or delivering such materials and struggle to keep them up to date. A repository of curated HTS training materials would support trainers in materials preparation, reduce the duplication of effort by increasing the usage of existing materials, and allow for the sharing of teaching experience among the HTS trainers' community. To achieve this, we have developed a strategy for materials' curation and dissemination. Standards for describing training materials have been proposed and applied to the curation of existing materials. A Git repository has been set up for sharing annotated materials that can now be reused, modified, or incorporated into new courses. This repository uses Git; hence, it is decentralized and self-managed by the community and can be forked/built-upon by all users. The repository is accessible at http://bioinformatics.upsc.se/htmr.

National Category
Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:umu:diva-124349 (URN)10.1371/journal.pcbi.1004937 (DOI)000379349700027 ()27309738 (PubMedID)
Available from: 2016-10-12 Created: 2016-08-04 Last updated: 2018-06-09Bibliographically approved
Schiffthaler, B., Terebieniec, B. K., Mähler, N., Robinson, K. M., Mannapperuma, C., Jansson, S. & Street, N. R.An integrated functional genomics and systems genetics analysis of leaf shape in Populus tremula .
Open this publication in new window or tab >>An integrated functional genomics and systems genetics analysis of leaf shape in Populus tremula 
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Leaf shape is an important component of our relationship with the living world, representing a defining feature of how we recognise and classify plant species. There is extensive variation in the form and function of leaves within and between species. In the current study we utilised variation in leaf shape represented among individuals of a collection of Eurasian aspen (Populus tremula L.) sampled across Sweden and the remarkable extent of heterophylly present to establish morphological, cellular and transcriptional developmental time lines. We performed gene expression network and phenotypical regression analyses to identify genes of central importance or that were highly predictive of shape and size phenotypes during leaf development using a systems biology approach. We complemented this developmental study with a genome wide association study of leaf shape variation to identify single nucleotide polymorphisms associated with leaf shape and size, their genomic context and the biological role of associated genes. We then compared these association candidate genes to differentially expressed genes between groups of genotypes with highly contrasting leaf shapes, also considering whether there were expression quantitative trait loci associated with the genes. We demonstrate that our developmental gene expression series captured known biology for homologs of functionally characterised Arabidopsis thaliana genes and biological processes of importance during leaf development. We identified genes of high importance from the developmental series and natural variation analyses. These included genes with characterised functions in leaf development in addition to many novel candidates. Our systems genetics approach identified numerous genes supported by the developmental time series, phenotypic and expression association mapping and differential expression between phenotypic extremes. As such, we describe a rich resource for directing future functional characterisation studies and a comprehensive data resource characterising the role of gene expression during leaf development in aspen.

Keywords
leaf shape, RNA-Sequencing, expression network, Populus tremula, natural variation, GWAS
National Category
Bioinformatics and Systems Biology Biochemistry and Molecular Biology
Research subject
Molecular Biology; Genetics
Identifiers
urn:nbn:se:umu:diva-156461 (URN)
Available from: 2019-02-15 Created: 2019-02-15 Last updated: 2019-02-19
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