A5016406116- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Plant Virus Research Studies
- Parasite Biology and Host Interactions
- Plant Pathogenic Bacteria Studies
- Photosynthetic Processes and Mechanisms
- Plant Pathogens and Fungal Diseases
- Plant Disease Resistance and Genetics
- Entomopathogenic Microorganisms in Pest Control
- Plant-Microbe Interactions and Immunity
- RNA Research and Splicing
- Species Distribution and Climate Change
- Legume Nitrogen Fixing Symbiosis
- Evolution and Genetic Dynamics
- Plant Stress Responses and Tolerance
- Bacteriophages and microbial interactions
- Actinomycetales infections and treatment
- Data Visualization and Analytics
- Infectious Diseases and Mycology
- Genetic diversity and population structure
- Insect symbiosis and bacterial influences
- Tuberculosis Research and Epidemiology
- Pneumonia and Respiratory Infections
Wageningen University & Research
2016-2025
Eindhoven University of Technology
2022-2023
Vrije Universiteit Amsterdam
2008-2023
Amsterdam University Medical Centers
2023
Western Cape Department of Health
2016-2017
University of Colorado Boulder
2005-2009
Centre for Medical Systems Biology
2008
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...
Significance Fixed nitrogen is essential for plant growth. Some plants, such as legumes, can host nitrogen-fixing bacteria within cells in root organs called nodules. Nodules are considered to have evolved parallel different lineages, but the genetic changes underlying this evolution remain unknown. Based on gene expression nonlegume Parasponia andersonii and legume Medicago truncatula , we find that nodules these lineages may share a single origin. Comparison of genomes with those related...
Abstract We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized techniques working with controllers third-party applications. The toolkit takes advantage parallel architectures runs on range hardware operating systems, is available under general...
Folsomia candida is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically presence Wolbachia, and exhibits remarkable physiological adaptations stress. To better understand these features life soil, we studied its genome context parthenogenetic lifestyle.We applied Pacific Bioscience sequencing assembly generate reference for F. 221.7 Mbp, comprising only 162 scaffolds. The complete endosymbiont was also assembled turned out be...
Understanding patterns of rRNA evolution is critical for a number fields, including structure prediction and phylogeny. The standard model RNA that compensatory mutations in stems make up the bulk changes between homologous sequences, while unpaired regions are relatively homogeneous. We show considerable heterogeneity exists relative rates different secondary categories (stems, loops, bulges, etc.) within rRNA, eukaryotes, loops actually evolve much faster than stems. Both abundance...
The order and orientation (arrangement) of all 91 sequenced scaffolds in the 12 pseudomolecules recently published tomato (Solanum lycopersicum, 2n = 2x 24) genome sequence were positioned based on marker a high-density linkage map. Here, we report arrangement these determined by two independent physical methods, bacterial artificial chromosome-fluorescence situ hybridization (BAC-FISH) optical mapping. By localizing BACs at ends to spreads synaptonemal complexes (pachytene chromosomes),...
The winter moth (Operophtera brumata) belongs to one of the most species-rich families in Lepidoptera, Geometridae (approximately 23,000 species). This family is great economic importance as species are herbivorous and capable defoliating trees. Genome assembly allows study genes gene families, such cytochrome P450 family, which known be vital plant secondary metabolite detoxification host-plant selection. It also enables exploration genomic basis for female brachyptery (wing reduction), a...
From prokaryotes to eukaryotes, phenotypic variation, adaptation and speciation has been associated with structural variation between genomes of individuals within the same species. Many computer algorithms detecting such variations (callers) have recently developed, spurred by advent next-generation sequencing technology. Such callers mainly exploit split-read mapping or paired-end read mapping. However, as different are geared towards types there is still no single caller that can be...
Abstract Many disciplines, from human genetics and oncology to plant breeding, microbiology virology, commonly face the challenge of analyzing rapidly increasing numbers genomes. In case Homo sapiens , number sequenced genomes will approach hundreds thousands in next few years. Simply scaling up established bioinformatics pipelines not be sufficient for leveraging full potential such rich genomic datasets. Instead, novel, qualitatively different computational methods paradigms are needed. We...
Next-generation sequencing technology is generating a wealth of highly similar genome sequences for many species, paving the way transition from single-genome to pan-genome analyses. Accordingly, genomics research going switch reference-centric pan-genomic approaches. We define as comprehensive representation multiple annotated genomes, facilitating analyses on similarity and divergence constituent genomes at nucleotide, gene structure level. Current approaches do not thoroughly address...
Collembola (springtails) are detritivorous hexapods that inhabit the soil and its litter layer. The ecology of springtail Orchesella cincta is extensively studied in context adaptation to anthropogenically disturbed areas. Here, we present a draft genome an O. reference strain with estimated size 286.8 Mbp, containing 20,249 genes. In total, 446 gene families expanded 1,169 evolved specific this lineage. Besides these involved general biological processes, observe clusters participating...
Bacterial plant pathogens of the Pectobacterium genus are responsible for a wide spectrum diseases in plants, including important crops such as potato, tomato, lettuce, and banana. Investigation genetic diversity underlying virulence host specificity can be performed at genome level by using comprehensive comparative approach called pangenomics. A pangenomic approach, newly developed functionalities PanTools, was applied to analyze complex phylogeny genus. We specifically used pangenome...
Abstract Summary The ever-increasing number of sequenced genomes necessitates the development pangenomic approaches for comparative genomics. Introduced in 2016, PanTools is a platform that allows pangenome construction, homology grouping and read mapping. use graph database technology makes versatile, applicable from small viral like SARS-CoV-2 up to large plant or animal tomato human. Here, we present our third major update enables integration functional annotations provides both...
We have encountered an unexpected property of rRNA secondary structures that may generalize to all RNAs. Analysis 8892 ribosomal RNA sequences and from a wide range species revealed universal compositional trends. First, different categories structure (stems, loops, bulges, junctions) distinct, characteristic base compositions. Second, the observed patterns variation are similar among large small subunits domains life, despite extensive evolutionary divergence. Surprisingly, these...
Pseudoknots are abundant in RNA structures. Many computational analyses require pseudoknot-free structures, which means that some of the base pairs knotted structure must be disregarded to obtain a nested structure. There is surprising diversity methods perform this pseudoknot removal task, but these often poorly described and studies can therefore difficult reproduce (in part, because different procedures may intuitively obvious investigators). Here we provide variety algorithms for...
Entomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. reduces the lifespan mosquitoes in laboratory and field. Natural isolates show up to 10-fold differences virulence between most least virulent isolate. In this study, we sequenced genomes five representing extremes low/high three RNA libraries, applied a genome comparison approach uncover genetic mechanisms underpinning virulence.A high-quality,...
Grain legume improvement is currently impeded by a lack of genomic resources. The paucity genome information for faba bean can be attributed to the intrinsic difficulties assembling/annotating its giant (~13 Gb) genome. In order address this challenge, RNA-sequencing analysis was performed on (cv. Wizard) leaves. Read alignment reference transcriptome identified 16 300 high quality unigenes. addition, Illumina paired-end sequencing used establish baseline assembly. Genomic reads were...
Abstract Plant immune responses are triggered during the interaction with pathogens. The fungus Botrytis cinerea has previously been reported to use small RNAs (sRNAs) as effector molecules capable of interfering host response. Conversely, a plant produces sRNAs that may interfere infection mechanism an intruder. We used high‐throughput sequencing identify produced by B. and Solanum lycopersicum (tomato) early phases examine expression their predicted mRNA targets in other organism. A total...
Summary With advances in long‐read sequencing and assembly techniques, haplotype‐resolved (phased) genome assemblies are becoming more common, also the field of plant genomics. Computational tools to effectively explore these phased genomes, particularly for polyploid currently limited. Here we describe a new strategy adopting pangenome approach. To analyse both intra‐ intergenomic variation assemblies, have made software package PanTools ploidy‐aware by updating graph representation adding...
Abstract Background Adaptive laboratory evolution (ALE) is a powerful method for strain optimization towards abiotic stress factors and identifying adaptation mechanisms. In this study, the green microalga Picochlorum sp. BPE23 was cultured under supra-optimal temperature to force genetic adaptation. The robustness adaptive capacity of strains turned them into an emerging model evolutionary studies on stressors such as temperature, salinity, light. Results Mutant showed expanded maximal...
Fusarium head blight (FHB) is one of the most destructive wheat diseases worldwide. To understand impact human migration and changes in agricultural practices on crop pathogens, here population genomic analysis with 245 representative strains from a collection 4,427 field isolates asiaticum, causal agent FHB Southern China conducted. Three populations distinct evolution trajectories are identifies over last 10,000 years that can be correlated historically documented due to caused by...
Automated RNA alignment algorithms often fail to recapture the essential conserved sites that are critical for function. To assist in refinement of these algorithms, we manually curated a set 148 alignments with total 9600 unique sequences, which each was backed by at least one crystal or NMR structure. These included both naturally and artificially selected molecules. We used principles isostericity improve from an average 83%–94% isosteric base pairs. expect this collection will wide range...
ABSTRACT We present the first genome sequence for a strain of main mycetoma causative agent, Madurella mycetomatis . This 36.7-Mb will offer new insights into pathogenesis mycetoma, and it contribute to development better therapies this neglected tropical disease.
Tuberculosis (TB) continues to be a major global health problem. While progress has been made improve TB cure rates, South Africa's 76 % smear-positive pulmonary (PTB) case rate remains below the WHO target of 85 %. We report on trends smear non-conversion and their predictors at end an intensive phase treatment, how this impacted treatment outcomes PTB cases in Eden District, Western Cape Province, Africa.Routinely collected, retrospective data from electronic register District between 2007...