A5011330514- Coastal wetland ecosystem dynamics
- Coral and Marine Ecosystems Studies
- Plant Virus Research Studies
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Plant Molecular Biology Research
- Genetic diversity and population structure
- Plant Pathogens and Resistance
- Plant Reproductive Biology
- Agricultural Practices and Plant Genetics
- Advances in Cucurbitaceae Research
- Plant Pathogenic Bacteria Studies
- Soybean genetics and cultivation
- Seed Germination and Physiology
- Plant-Microbe Interactions and Immunity
- Land Rights and Reforms
- Advanced Proteomics Techniques and Applications
- Agriculture, Land Use, Rural Development
- Plant and Fungal Species Descriptions
- Scientific Computing and Data Management
- CRISPR and Genetic Engineering
- Genetics, Bioinformatics, and Biomedical Research
- Potato Plant Research
- Cocoa and Sweet Potato Agronomy
- Plant Disease Resistance and Genetics
Bejo Zaden (Netherlands)
2020
Wageningen University & Research
2014-2020
Institute of Bioinformatics and Applied Biotechnology
2015-2016
Centre for BioSystems Genomics
2014
BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. allows labs of all sizes to easily install software, maintain multiple versions the same software combine tools into powerful analysis pipelines. based on popular projects Docker rkt frameworks, that allow be installed executed under isolated controlled environment. Also, it infrastructure basic guidelines create, manage...
Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved thrive arid habitats. Because of its extreme stress tolerance and unusual morphology, an important donor germplasm for the cultivated lycopersicum. Introgression lines (ILs) which large genomic S. lycopersicum are replaced with corresponding segments from can show remarkably superior agronomic performance. Here we describe high-quality genome assembly parents IL population. By...
Genetic variation in the tomato clade was explored by sequencing a selection of 84 accessions and related wild species representative for Lycopersicon, Arcanum, Eriopersicon, Neolycopersicon groups. We present reconstruction three new reference genomes support our comparative genome analyses. Sequence diversity commercial breeding lines appears extremely low, indicating dramatic genetic erosion crop tomatoes. This is reflected SNP count which can exceed 10 million i.e. 20 fold higher than...
Summary Chromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate paracentric 1.17‐Mb inversion on chromosome 4 Arabidopsis thaliana with nucleotide precision its borders. The is created by Vandal transposon activity, splitting an F‐box relocating pericentric heterochromatin segment in juxtaposition euchromatin without affecting epigenetic landscape. Examination RegMap panel 1001 genomes revealed more...
Summary We determined the crossover ( CO ) distribution, frequency and genomic sequences involved in interspecies meiotic recombination by using parent‐assigned variants of 52 F 6 recombinant inbred lines obtained from a cross between tomato, Solanum lycopersicum , its wild relative, pimpinellifolium . The interspecific was 80% lower than reported for intraspecific tomato crosses. detected regions showing relatively high low frequency, so‐called hot cold regions. Cold coincide to large...
Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, desired traits are monitored in consecutive crossing generations marker-assisted selection, but their analyses fail chromosome regions where crossover recombinants rare or not viable. Here, we present Introgression Browser (iBrowser), bioinformatics tool aimed at visualizing introgressions nucleotide SNP (Single Nucleotide Polymorphisms) accuracy. The software selects homozygous SNPs...
Background: Identification of biological specimens is a major requirement for range applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but generally do not scale to arbitrarily large genomes and phylogenetic distances. Results: We present Cnidaria, practical tool clustering genomic transcriptomic with no limitation genome size or successfully simultaneously clustered 169 datasets from 4 kingdoms, achieving 100% identification accuracy...
Cucumis melo (melon or muskmelon) is an important crop in the family of Cucurbitaceae. Melon cross pollinated and domesticated at several locations throughout breeding history, resulting highly diverse genetic structure germplasm. Yet, relations among groups cultivars are still incomplete. We shed light on melonbreeding analyzing structural variations ranging from 50 bp up to 100 kb, identified whole genome sequences selected melon accessions wild relatives. Phylogenetic trees based SV types...
Abstract A common problem in the cultivation and breeding of cauliflower ( Brassica oleracea L. var. botrytis ) is occurrence aneuploids offspring families. To reveal chromosomal cause such numerical variants, it was necessary to develop karyotype tools with which chromosomes can be easily identified. Since mitotic this crop are morphologically similar lack differentiating banding patterns, we tested two Fluorescent situ Hybridization (FISH) procedures for chromosome identification: (1) FISH...
Osmopriming of seeds can increase seed vigour, allowing faster germination and field emergence, especially under adverse conditions. The restricted imbibition during priming treatments reactivates metabolism although will be prevented. In order to identify characterize genes that are involved in the improvement vigour Poincianella pyramidalis (Catingueira) upon priming, we produced two different Suppression Subtractive Hybridization (SSH) cDNA libraries. These were a Forward Reverse...