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Bioinformatics & Cell Walls

Integrating multiple omics data to improve plant resilience and performance and improving the material and energetic use of plants.

We are integrating mulitple large data streams (genomes, transcritpomes, metabolomes and phenotypes) to predict and understand plant performance and  resilience. In addition we are interested in unravelling cell wall biosynthesis and plant natural product induction and adaptation for material and energetic uses.

Focus Areas

Network reconstruction, network learning and biological pathways

Given the ample amount of “omics” data that is being generated, it becomes more and more important to devise schemes to best profit from the mass of generated data and to extract the most likely biological interpretation. The group is thus aiming to develop methods and tools to abstract, visualize and interpret high throughput data. Here the group is focussing specifically on metabolomics and transcriptomic data sets but as proteomics matures more and more data is being integrated as well. These tools are applied to data that is generated in the group to find new candidate genes for cell wall synthesis and the response to carbon limitation. Furthermore these approaches are used to build predictive models.

References

Mutwil, M., Klie, S., Tohge, T.,Giorgi, FM., Wilkins, O.,Campbell, MM., Fernie, AR.,Usadel, B., Nikoloski, Z.,Persson, S. (2011) PlaNet: Combined sequence and expression comparisons across plant networks derived from seven even species. Plant Cell 23:895-910.

Vasilevski, A., Giorgi, FM., Bertinetti, L.,Usadel, B. (2012) LASSO modeling of the Arabidopsis thaliana seed/seedling Transcriptome: a model case for detection of novel mucilage and pectin metabolism genes. Molecular Biosystems 8:2566-74.

Team

Prof. Björn Usadel

Dr. Marie Bolger
Aziz Hallab

Network AnalysisNetwork Analysis

Identifying cell wall biosynthesis genes using a simple model

The plant cell wall is complex consisting of cellulosic fibres embedded into a matrix of pectins and hemicelluloses. Whilst a tremendous amount of data was generated using mutant collections, not all cell wall mutants are viable and not in all cases is it possible to directly determine changes in the cell wall composition without a fractionation of the cell wall. Interestingly Arabidopsis thaliana seeds extrude a substance called mucilage upon contact with water. As it turns out a major component of the mucilage is rhamnogalacturonan-I which is also one of the major components in cell wall pectin.

References

Voiniciuc, C., Zimmermann, E., Schmidt,MHW., Günl, M., Fu, L.,North, H., Usadel, B. (2016)Extensive Natural Variation in Arabidopsis Seed Mucilage Structure. Frontiers in Plant Sciences 7:803.

Voiniciuc, C., Guenl, M., Schmidt, MH.,Usadel, B. (2015) Highly Branched Xylan Made by IRX14 and MUCI21 Links Mucilage to Arabidopsis Seeds. Plant Physiol. 169(4):2481-95.

Voiniciuc, C., Schmidt, MH., Berger, A.,Yang, B., Ebert, B., Scheller,HV., North, HM., Usadel, B.,Guenl, M. (2015) MUCI10 Produces Galactoglucomannan That Maintains Pectin and Cellulose Architecture in Arabidopsis Seed Mucilage. Plant Physiol. 169(1):403-20.

Team

Prof. Björn Usadel

Cell Wall Bio-SynthesisCell Wall Bio-Synthesis

Identifying beneficial cell wall traits in natural populations

Plant cell walls are a major resource which can be used for biofuels or for a material use. Whilst the last few years have seen major advances in our understanding of how the plant cell walls are constructed and plant cell walls can be decomposed, we are still far away from tailoring plants to our needs. We therefore investigate the cell wall composition of naturally occurring plant species or variants (e.g. wild relatives) to identify potentially beneficial traits that could be introduced into modern breeding varieties. In addition we analyze how cell walls from plants not competing with food/feed use and having no incurred indirect land use change can be used for biomass generation.Specifically we focus on the use of residual material and perennial plants.

References

Damm, T., Pattathil, S., Günl, M., Jablonowski, ND., O'Neill, M., Grün, KS., Grande, PM., Leitner, W., Schurr, U., Usadel, B., Klose, H.  (2017) Insights into cell wall structure of Sida hermaphrodita and its influence on recalcitrance. Carbohydrate Polymers 168, 94–102.

Damm, T., Commandeur, U., Fischer, R., Usadel, B., Klose, H. (2016) Improving the utilization of lignocellulosic biomass by polysaccharide modification. Process Biochemistry 51:288-296.

Klose, H., Günl, M., Usadel, B., Fischer, R., Commandeur, U. (2015) Cell wall modification in tobacco by differential targeting of recombinant endoglucanase from Trichoderm reesei. BMC Plant Biol. 15:54

Team

Prof. Björn Usadel

Dr. Marie Bolger

Cell Wall TraitsCell Wall Traits

Using Next Generation Sequencing to answer biological problems

Currently the group is involved in various RNASeq projects (Illumina Solexa), the assembly of several Solanacaeous plants and in using sequencing to pinpoint mutations. Here the group is interested in developing new tools and algorithms that expedite the analysis of data and which help a biologist to find answers to biologically relevant questions. The group thus tries to enable biologists to e.g. find new candidate genes.
A first release tool is Trimmomatic which can be used to quality trim and adapter clip NGS data (Illumina Solexa). Also the group has pioneered Oxford nanopore single molecule sequencing in the plant field.

References

Kranz, A., Vogel, A., Degner, U.,Kiefler, I., Bott, M., Usadel,B., Polen, T. (2017) High precision genome sequencing of engineered G. oxydans 621H by combining long nanopore and short accurate Illumina reads. J Biotechnol.2017 Apr 19. pii:S0168-1656(17)30170-0.

Bolger, AM., Lohse, M., Usadel, B.(2014) Trimmomatic: A flexible trimmer for Illumina Sequence Data, Bioinformatics,30 (15): 2114-2120

Bolger,A., Scossa, F., Bolger, ME.,Lanz, C., Maumus, F., et al., (2014) The genome of the stress-tolerant wild tomato species Solanum pennellii Nature Genetics ,46(9):1034-8

Li, J-W., Robison, K., Martin, M.,Sjödin, A., Usadel, B., Young,M., Olivares, EC., Bolser. DM,(2011) The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis.Nucleic acid research 40:D1313-D1317

Team

Prof. Björn Usadel

Dr. Marie Bolger
Dr. Alexandra Olarte
Dr. Claudio Cerboncini

SequencingSequencing

Databases, ontology and tool development

The group is involved in develop tools to faster evaluate, interpret and visualize omics data. The group is involved in develop tools to faster evaluate, interpret and visualize omics data. Major tools the group has developed are MapMan a GUI application to visualize omics data on biological pathways. ROBINa is a graphical frontend to BioConductor/R. It allows you to quality control and visualize microarray and RNASeq data. In addition experimental questions can be formulated by visually drawing experiments and the data is then statistically evaluated using state-of-the-art statistical algorithms developed in R. All these tools are supported by forums. Within the MapMan tool we have also developed a specific ontology to support the annotation of genes and metabolites for plant omics data. This onotology has been expanded to more than 10 plant species and can be applied to any plant species where transcript data is available based on sequence similarity searches. We thus provide an easy way to learn about plant transcriptome projects.
Also the group hosts the GABI PRIMARY database. A database for primary data generated within the BMBF financed German GABI programs.

References

Bolger, M., Arsova, B., Usadel, B.(2017) Plant Genome and Transcriptome Annotations: from misconceptions to simple solutions. Briefings in Bioinformatics https://doi.org/10.1093/bib/bbw135

Jaiswal, P., Usadel, B. (2016) Plant Pathway Databases. Methods Mol Biol.1374:71-87. doi: 10.1007/978-1-4939-3167-5_4

Lohse, M., Nagel, A., Herter, T.,May, P., Schroda, M., Zrenner,R., Tohge, T., Fernie, AR.,Stitt, M., Usadel, B. (2014) Mercator: A fast and simple web server for genome scale functional annotation of plant sequence data. Plant Cell Environ. 37(5):1250-8.

Team

Prof. Björn Usadel

Rainer Schwacke
Aziz Hallab

Cell Wall Bio-SynthesisCell Wall Bio-Synthesis

Plant Natural Product Pathways Mining

More than 200.000 natural products are said to be synthesized by plants and many are of nutritional, nutraceutical, and pharmacological relevance. However, despite their importance for food, feed and/or human health, extracting these compounds from plants is often not economically feasible due to low contents, and a total chemical synthesis is neither sustainable nor cost-competitive. This is asking for innovative solutions bringing together plant research and biotechnology where pathways are mined in plants and transferred to (microbial) production organisms. In addition we explore how plant natural product production can be increased or improved.

References

Härtl, K., Denton, A., Franz-Oberdorf, K., Hoffmann, T., Spornraft, M., Usadel, B., Schwab, W. (2017) Early metabolic and transcriptional variations in fruit of natural white-fruited Fragaria vesca genotypes. Scientific reports doi: 10.1038/srep45113

Matsuba, Y., Nguyena, THH., Wiegert, K., Falara, V., Gonzales-Vigil, E., Leong, B., Schäfer, P., Kudrna, D., Wing, RA., Bolger, AM., Usadel, B., Tissier, A., Fernie, AR., Barry, CS., Pichersky, E. (2013) Evolution of a Complex Locus for Terpene Biosynthesis in Solanum. Plant Cell 25:2022-2036

Team

Prof. Björn Usadel

Dr. Anika Wiese-Klinkenberg
Dr. Claudio Cerboncini
Prof. Dr. Ingar Janzik
Andrea Neuwohner
Sabine Preiskowski
Jan-Phillip Rusteberg



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