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Schiffthaler, BastianORCID iD iconorcid.org/0000-0002-9771-467x
Publications (10 of 21) Show all publications
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
Spitzer, R., Norman, A. J., Konigsson, H., Schiffthaler, B. & Spong, G. (2020). De novo discovery of SNPs for genotyping endangered sun parakeets (Aratinga solstitialis) in Guyana. Conservation Genetics Resources, 12, 631-641
Open this publication in new window or tab >>De novo discovery of SNPs for genotyping endangered sun parakeets (Aratinga solstitialis) in Guyana
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2020 (English)In: Conservation Genetics Resources, ISSN 1877-7252, E-ISSN 1877-7260, Vol. 12, p. 631-641Article in journal (Refereed) Published
Abstract [en]

Parrots (Psittaciformes) are among the most endangered groups of birds today and remain threatened by habitat loss and exploitation for the live bird trade. Under such conditions, reliable and non-invasive monitoring techniques are crucial for successful conservation measures. In this study, we developed a panel of 86 high quality SNPs for genotyping endangered sun parakeets (Aratinga solstitialis) in Guyana, which form one of the last known breeding populations of this South American species in the wild. Genotyping was tested on different types of samples (blood, feathers, feces, beak and cloacal swabs). While blood performed best, feathers and feces also yielded reliable results and could thus be used as non-invasive sources of DNA for future population monitoring. Discriminant Analysis of Principal Components (DAPC) on genotypes revealed that Guyanese sun parakeets clustered separately from other psittacine species as well as conspecifics from a captive population. A priori known first-order kinships were also adequately detected by the SNP panel. Using a series of experimental contaminations, we found that contamination from other psittacine species and slight contamination ( 10%) from conspecifics did not prevent successful genotyping and recognition of individuals. We show that instances of higher conspecific contamination ( 50%) can be detected through an increased level of heterozygosity that falls outside the distribution of uncontaminated samples.

Place, publisher, year, edition, pages
Springer, 2020
Keywords
SNP, Sun parakeet, Conservation, Relatedness, Non-invasive sampling, Contamination
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-171952 (URN)10.1007/s12686-020-01151-x (DOI)000533022100001 ()2-s2.0-85084836422 (Scopus ID)
Available from: 2020-06-18 Created: 2020-06-18 Last updated: 2023-03-24Bibliographically approved
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, KBE303 - Stora hörsalen, Umeå, 10:00 (English)
Opponent
Supervisors
Note

2020-06-10: Errata spikblad - Ny tid för disputation. 

Available from: 2020-05-20 Created: 2020-05-13 Last updated: 2020-06-10Bibliographically 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, 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)2-s2.0-85077669677 (Scopus ID)
Available from: 2020-02-25 Created: 2020-02-25 Last updated: 2024-01-17Bibliographically approved
Mähler, N., Schiffthaler, B., Robinson, K. M., Terebieniec, B. K., Vucak, M., Mannapperuma, C., . . . Street, N. R. (2020). Leaf shape in Populus tremula is a complex, omnigenic trait. Ecology and Evolution, 10(21), 11922-11940
Open this publication in new window or tab >>Leaf shape in Populus tremula is a complex, omnigenic trait
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2020 (English)In: Ecology and Evolution, E-ISSN 2045-7758, Vol. 10, no 21, p. 11922-11940Article in journal (Refereed) Published
Abstract [en]

Leaf shape is a defining feature of how we recognize and classify plant species. Although there is extensive variation in leaf shape within many species, few studies have disentangled the underlying genetic architecture. We characterized the genetic architecture of leaf shape variation in Eurasian aspen (Populus tremula L.) by performing genome‐wide association study (GWAS) for physiognomy traits. To ascertain the roles of identified GWAS candidate genes within the leaf development transcriptional program, we generated RNA‐Seq data that we used to perform gene co‐expression network analyses from a developmental series, which is publicly available within the PlantGenIE resource. We additionally used existing gene expression measurements across the population to analyze GWAS candidate genes in the context of a population‐wide co‐expression network and to identify genes that were differentially expressed between groups of individuals with contrasting leaf shapes. These data were integrated with expression GWAS (eQTL) results to define a set of candidate genes associated with leaf shape variation. Our results identified no clear adaptive link to leaf shape variation and indicate that leaf shape traits are genetically complex, likely determined by numerous small‐effect variations in gene expression. Genes associated with shape variation were peripheral within the population‐wide co‐expression network, were not highly connected within the leaf development co‐expression network, and exhibited signatures of relaxed selection. As such, our results are consistent with the omnigenic model.

Place, publisher, year, edition, pages
John Wiley & Sons, 2020
Keywords
complex trait, GWAS, leaf shape, natural variation, omnigenic, Populus tremula
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-170641 (URN)10.1002/ece3.6691 (DOI)000578291300001 ()2-s2.0-85092478395 (Scopus ID)
Note

Originally included in thesis in manuscript form.

Available from: 2020-05-12 Created: 2020-05-12 Last updated: 2024-01-17Bibliographically 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)Manuscript (preprint) (Other academic)
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: 2022-03-09
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)000522860800005 ()2-s2.0-85077489986 (Scopus ID)
Available from: 2020-02-14 Created: 2020-02-14 Last updated: 2023-09-05Bibliographically 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, 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)2-s2.0-85065783386 (Scopus ID)
Projects
Bio4Energy
Funder
Knut and Alice Wallenberg FoundationBio4Energy
Available from: 2019-06-10 Created: 2019-06-10 Last updated: 2024-01-17Bibliographically 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, 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)2-s2.0-85074719121 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation
Available from: 2019-12-05 Created: 2019-12-05 Last updated: 2023-03-24Bibliographically 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
Funder
Bio4Energy
Available from: 2018-08-06 Created: 2018-08-06 Last updated: 2023-11-06Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-9771-467x

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