Wageningen University & Research
Droevendaalsesteeg 1 6708 PB Wageningen
Dr. Sara Diaz Trivino, Dr. H.J. Finkers, Prof. dr. M.A.M. Groenen, Prof. dr. J. Molenaar, Prof. dr. F.A. van Eeuwijk, Prof. dr. ir. D. de Ridder
0031 (0)317 480441
Applied Bioinformatics (AB) at Plant Research International, together with the Chair Group of Bioinformatics (CGB), have played a leading role in the international initiatives that recently published the genomic sequences of the Solanaceous crops tomato and potato. Also they are involved in several genomic, transcriptomic and epigenomic projects from different crop species. AB hosts state-of-art sequencing facilities including PacBio SEQUEL, Illumina Hiseq2500, Illumina MiSeq, BioNanoGenomics IRYS, MinION and 10x Chromium. The group also develop standardized and generic systems for the management, analysis and integration of (plant) omics data, in support of the technology platforms of the Wageningen Omics Facility (sequencing, proteomics and metabolomics).
Animal Breeding and Genomics Centre (ABGC) is a world leading group in the mapping, sequencing and analysis of animal genomes. Prof. Groenen was involved in the overall coordination of the sequencing of the chicken and pig genomes (published in Nature in 2004 and 2012). The group has a strong focus in livestock species (pig, poultry, cattle) but is also actively involved in genome projects in many other species (e.g. Great tit, Mallard (duck), African and South-East Asian Suids, winter moth).
Plant Breeding (PB) is focused on integration of ~omics datasets using state-of-the art methodology, such as penalized linear regression methodology (e.g. lasso and ridge regression) and machine learning techniques (such as support vector machine and random forest) and network reconstruction approaches. PB combines this metrology with semantic data integration to post-hoc add biological meaning to the analysed datasets.
Biometris consists of ~70 academic mathematicians and statisticians, integrating academic and contract research, making them an interesting partner for both industry and governmental (national & EU) collaborative projects. Biometris is renowned as centre of expertise for teaching, development and application of quantitative methods in the life sciences. Their focus is on five themes: Systems Biology, Statistical Genetics and Genomics, Food and Health, Pattern Recognition and Education & Consultation.
- Biomedical & health
- Agri & Food
- Genome-wide variation analysis by means of high-throughput sequencing (NGS)
- De novo assembly of plant and animal genome
- Transcriptome analysis based on RNAseq
- Population genetics and phylogeny based on whole genome sequence data
- Epigenetics (imprinting, whole genome methylation studies, RNA editing)
- Plant and animal bioinformatics focused on genome and genetic analysis
- Statistical methods for -omics data integration and data mining
- Methematical modelling (ODE and boolean systems, parameter identification, network reconstruction, prediction uncertainty)
- Complex traits in crops and livestock (GWAS, QTL)
- Evolutionary and population genomics
Expertise and Track Record
43500985054 Unlocking high throughput single nucleus RNA sequencing in diverse plant tissues with W. Kohlen (Wageningen University). 43500985040 Deciphering the temperature-dependent dynamics of the DNA methylome in Arabidopsis using BioNano sequencing with R. Immink (Wageningen University). 43500985038 Resolution of resistance genes within melon QTL regions by optical mapping with D. de Ridder (Wageningen University). 43500985025 Detecting meiotic recombination events by sequencing genomic DNA of pollen in Zea mays with P.F. Fransz (Universiteit van Amsterdam). 43500984107 Elucidation of the genomic organization of wild tomatoes to allow the mapping of resistance traits aiding the creation of insect resistant varieties with P.M. Bleeker (UvA). 43500984062 Global analysis of the salt stress-induced transcriptome and RNA degradome in Arabidopsis roots with Y. Zhang (University of Amsterdam). 43500984052 Targets of mRNA decay affecting seed dormancy and seed longevity with L. Bentsink (Wageningen University). 43500984025 Uncovering hidden genetic variation in the human genome with C.F.H.A. Gilissen (Radboudumc). 43500984001 Genome structural architecture of representative species in the Lactuca genus with dr. M.E. Schranz (WUR). 4350098200 Assessing the effect of genome structural differences on cross-over recombination with dr.ir. S.A. Peters (WUR). 4350098201 Discovering and analysing the 'dark-matter' of the tomato reference genome with long-read sequencing and genome mapping technology with dr. M.E. Schranz (WUR). 4350098210 Mapping specialized metabolic diversity in complex plant microbiomes through computation wit prof.dr. J.M. Raaijmakers (NIOO-KNAW). 4350098225 The Azolla filiculoides metagenome: towards evaluating biomass safety with dr. H. Schluepmann (U Utrecht). 4350098207 Bioinformatic identification of novel enzymology for the posttranslational modification of bioactive peptides with prof.dr. G. van Wezel (U Leiden). 4350098239 Genome-resolved metagenomics of bioremediation bacteria in the Griftpark with dr. M.C. Koster (Utrecht University). 4350098246 Transcriptomics of terpene producing Rhodobacter with dr. M.J. Beekwilder (DLO). 4350098206 Finding functional homologs of transcription factors in crop species with prof.dr.ir. G.C. Angenent. 4350098217 Resequencing of the potatoe blight pathogen Phytophtera infestans; from a fragmented genome to a more complete assembly with prof.dr. F. Govers (WUR). 4350098235 Arabidopsis transcript isoform identification using PacBio sequencing technology with dr.ing M.A. Fiers (WUR). 4350098250 Sequencing the giant tulip genome with dr. C.V. Henkel (Generade). 4350098209 Metagenomic identification of biosynthetic gene clusters involved in disease suppression in aquaculture with prof.dr. G. Wiegertjes (NIOO-KNAW). 4350098219 A genomic view on the effects of photoperiod on winter moths with dr. M.E. Visser (NIOO-KNAW). 435000025 Exploitation of sequence diversity in potato NB-LRR resistance gene clusters to determine the genomic location of novel nematode resistance loci in potato with dr. ir. A. Goverse (WUR). 435000023 Unveiling the Banana-Fusarium oxysporum interaction with dr. ir. G.H.J. Kema (WUR). 435000022 Development of tools for an RNAseq based advanced eQTL approach to study seedling quality in Arabidopsis with dr. ir. W. Ligterink (WUR). 435000020 Effect of organellar genomes on the transcriptome of Arabidopsis thaliana with dr. ing. J.J.B. Keurentjes (WUR). 435000017 Gene expression related to aphid resistance with prof. dr. M. Dicke (WUR). 435000015 Role of chromosomal interactions on flowering time regulation with prof. dr. ir. G.C. Angenent (WUR). 435000009 Transcriptomics analysis of strigolactone downstream signalling with prof. dr. ir. H.J. Bouwmeester (WUR). 435000005 A role for antisense RNA in ambient temperature-mediated flowering time control? With dr. Ir. R.G.H. Immink (WUR). 435002001 Optimal mapping assisted accelerated assembly of genomes of non-conventional yeast species isolated from fermented massau fruit With Smid (WUR). 435002004 Improving chromosomal structure in the natural interspecific hybrid lager brewing yeast Sacchoraromyces Pastorianonus with Daran (Delft University of Technology). 435002006 Assessing allelic variation in tetraploid potatoe with long-read genome sequencing With Nap (Hanzehogeschool Groningen). 435002007 What makes cauliflower (in-)sensitive to ambient temparature fluctuations: analysis of differential gene expression and splicing profiles With Bonnema (WUR). 435002010 Transcript proflling for light/temperature control of plant growth in greenhouses With Van der Krol (WUR). 435002011 Haplotype sequencing in tetraploid potatoe With Schaart (WUR). 435002012 Hunting for strigolactone diversification genes in tomato With Ruyter-Spira (WUR). 435002013 Cold responsive networks in natural variants of Brassica rapa With Harbinson (WUR). 435002028 Characterizatoin of critical DNA binding specificities of PLETHORA proteins With Scheres (WUR). 435002032 Optical mapping towards assembling the first fern genome With Schluepmann (WUR).
AB and CGB have already extensive experience supporting plant next-generation sequencing projects within Hotel calls, providing access to state-of-art sequencing technologies and guidance at the bioinformatics analyses to the desired results. Their in-house sequencing facilities (including HiSeq, MiSeq, 10x and PacBio) provides them with unique insight on how to select the best strategy according to the biological question the plant researcher. Together with PB, they have experience integrating all sorts of –omics data from different plants (Arabidopsis, tomato, potato…) with different scientific outputs (protein function prediction, alternative splicing genome-wide analysis…).
ABGC is the only group in the Netherlands dedicated to livestock genomics. Their long-term international leading role in livestock genomics, extensive expertise in the use of NGS data to address research questions in population genetics, phylogenomics and evolution, and their large variation database for several livestock species (e.g. >220 sequenced pig genomes, high-density genotype data on many thousands individual pigs, wild boar, chicken, turkey, and songbirds) makes them a unique partner in this research area.
Biometris is the biggest group in the Netherlands with such expertise in Systems Biology and Statistical Genetics.
- CBSG Hotel calls 2012 and 2013 – Hotel manager for 5 Bioinformatics hotel projects and 20 hotel plant NGS projects granted in our sequencing facilities (~20 K€ each).
- 150 tomato genome project – TTI-GG project with 12 tomato seed companies. We managed the coordination of the project and together with BGI we provided NGS sequencing (454 and HiSeq), and we performed the de novo assembly of 3 wild-type tomato varieties.
- Visiting PhD student from Barcelona, Spain (Anna Esteve-Codina) for the analysis of genetic variation (SNP, CNV) in Iberian pigs based on whole genome NGS data. This resulted in two joint publications.
- Strong links with industry, on food safety (RIVM, VWA (Voedsel en Warenautoriteit), Bayer, BASF, Syngenta, Monsanto) and nearly all breeding companies (Rijk Zwaan, Keygene, Pioneer, Monsanto, SES van der Have ….)
- Bolger, A. et al. The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics 46, 1034-1038 (2014).
- Sato, S. et al. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635-641 (2012).
- Bargsten, J.W. Nap, J.P., Sanchez-Perez, G.F. & van Dijk, A.D.J. Prioritization of candidate genes in QTL regions based on associations between traits and biological processes. BMC Plant Biology 14, 330 (2014)
- Szakonyi, D. et al. The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining. Current Plant Biology 2, 1-11 (2015).
- Aflitos, S.A. et al. Introgression browser: High-throughput whole-genome SNP visualization. Plant Journal 82, 174-182 (2015).
- Lin, K., Bonnema, G., Sanchez-Perez, G. & De Ridder, D. Making the difference: Integrating structural variation detection tools. Briefings in Bioinformatics 16, 852-864 (2014).
- Muiño, J.M., Hoogstraat, M., Van Ham, R.C.H.J. & Van Dijk, A.D.J. PRI-CAT: A web-tool for the analysis, storage and visualization of plant ChIP-seq experiments. Nucleic Acids Research 39, W524-W527 (2011).
- Bargsten, J.W., Severing, E.I., Nap, J.P., Sanchez-Perez, G.F. & van Dijk, A.D.J. Biological process annotation of proteins across the plant kingdom. Current Plant Biology 1, 73-82 (2014).
- Xu, X. et al. Genome sequence and analysis of the tuber crop potato. Nature 475, 189-195 (2011).
- Aflitos, S. et al. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant Journal (2014).
- Currently involved in establishing a DTL for Agrogenomics and Sector integrator in DTL for the ‘Green’ sector
- Members of NBIC, NCSB, SB&NL
- Participant in FP7-EU-Transplant project, initiative dedicated to provide adequate infrastructure for genomic data to the plant community
- Participant in Virtual Lab of Plant Breeding (TTI-GG & NWO eScience)
- WP leader in Infrastructure for Systems Biology (ISBE)
- Working Group Leader in European Food Safety Authority (EFSA)
- Board Member of European Statististical Association
- Board Member of Society for Statistics and Operations Research (VvS)
- National deputy at FAO
- Member of the EU-US working group on animal biotechnology