Yves Van de Peer
A5070738091- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Microbial Community Ecology and Physiology
- Genetic diversity and population structure
- Plant Molecular Biology Research
- Bioinformatics and Genomic Networks
- Protist diversity and phylogeny
- Plant Pathogens and Fungal Diseases
- Plant Reproductive Biology
- Evolution and Genetic Dynamics
- Machine Learning in Bioinformatics
- Plant Disease Resistance and Genetics
- Gene expression and cancer classification
- Photosynthetic Processes and Mechanisms
- Plant Diversity and Evolution
- Genomics and Chromatin Dynamics
- Biomedical Text Mining and Ontologies
- Polar Research and Ecology
- Marine and coastal plant biology
- Plant-Microbe Interactions and Immunity
- RNA Research and Splicing
- Gene Regulatory Network Analysis
- Bacteriophages and microbial interactions
- Plant Gene Expression Analysis
Ghent University
2016-2025
VIB-UGent Center for Plant Systems Biology
2016-2025
University of Pretoria
2016-2025
Nanjing Agricultural University
2020-2025
Ghent University Hospital
2011-2025
Ecologie Microbienne Lyon
2019-2025
Planta
2024
Ministry of Agriculture and Rural Affairs
2023
Universiti Malaysia Terengganu
2019-2023
Vlaams Instituut voor Biotechnologie
2006-2022
This paper reports the genome sequence of domesticated tomato, a major crop plant, and draft for its closest wild relative; comparative genomics reveal very little divergence between two genomes but some important differences with potato genome, another food in genus Solanum. Tomato (Solanum lycopersicum) is plant model system fruit development. Solanum one largest angiosperm genera1 includes annual perennial plants from diverse habitats. Here we present high-quality relative,...
TREECON is a software package developed primarily for the construction and drawing of evolutionary trees based on distance data calculated from nucleic amino acid sequences (Van de Peer De Wachter, 1993).It implements several equations converting dissimilarity (fraction substitutions) into algorithms inferring tree topologies.Bootstrap analysis sequence (Felsenstein, 1985) also File Save Show Delete Scale Select Topology
We report the draft genome sequence of model moss Physcomitrella patens and compare its features with those flowering plants, from which it is separated by more than 400 million years, unicellular aquatic algae. This comparison reveals genomic changes concomitant evolutionary movement to land, including a general increase in gene family complexity; loss genes associated environments (e.g., flagellar arms); acquisition for tolerating terrestrial stresses variation temperature water...
Diatoms, a type of microscopic marine and freshwater alga, dominate the oceans are responsible for about fifth primary productivity on Earth. The complete genome sequence Phaeodactylum tricornutum is reported in this issue, second diatom to be sequenced. Comparisons with Thalassiosira pseudonana, first, reveal that hundreds genes have been acquired by gene transfer from bacteria — or vice versa. Gene appears common during evolution, creating unorthodox combinations including some plants...
Conifers have dominated forests for more than 200 million years and are of huge ecological economic importance. Here we present the draft assembly 20-gigabase genome Norway spruce (Picea abies), first available any gymnosperm. The number well-supported genes (28,354) is similar to >100 times smaller Arabidopsis thaliana, there no evidence a recent whole-genome duplication in gymnosperm lineage. Instead, large size seems result from slow steady accumulation diverse set long-terminal repeat...
Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in specialized structure known as the nodule. belong one of two main groups eurosids, Fabidae, which includes most species capable fixation. comprise several evolutionary lineages derived from common ancestor 60 million years ago (Myr ago). Papilionoids largest clade, dating nearly origin legumes and containing...
The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and extreme record of pesticide resistance. Here we present the completely sequenced annotated genome, representing first complete chelicerate genome. At 90 megabases T. has smallest arthropod Compared other arthropods, genome shows unique changes in hormonal environment organization Hox complex, also reveals evolutionary innovation silk production. We find strong signatures polyphagy...
The fungus Laccaria bicolor — seen in its above-ground fruiting body presence as the 'bicoloured deceiver' mushroom lives symbiotically on roots of trees. Its genome has now been sequenced, and key features characterized by transcript profiling. study throws light mechanism mycorrhizal symbiosis, union soil fungi that is vital important to plant productivity. And it will be keen interest evolutionary biologists for revelations about plant–fungus interactions shaping genomes over time....
Background Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become model for fruit trees genetics. Like many plant species, it is highly heterozygous, which an additional challenge modern whole genome shotgun sequencing. In this paper high quality draft sequence of clone V. Pinot Noir presented. Principal Findings We estimate the size be 504.6 Mb. Genomic sequences corresponding 477.1 Mb were assembled in 2,093...
Journal Article Compilation of small ribosomal subunit RNA sequences Get access Peter De Rijk, Rijk Departement Biochemie, Universiteit AntwerpenUIA, Universiteitsplein 1, B-2610 Antwerp, Belgium Search for other works by this author on: Oxford Academic PubMed Google Scholar Jean-Marc Neefs, Neefs Yves Van de Peer, Peer Rupert Wachter * To whom correspondence should be addressed Nucleic Acids Research, Volume 20, Issue suppl, 11 May 1992, Pages 2075–2089,...
Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication been rampant. Moreover, next to a continuous mode duplication, in many organisms the duplicated their evolutionary past. Such large-scale events have associated with important transitions or major leaps development and adaptive radiations species. Here, we present an model simulates dynamics genes, considering genome-wide duplication. Modeling evolution different functional categories genes assesses...
The genome of Ectocarpus, a model organism for brown algae, has been sequenced. Brown algae are complex photosynthetic organisms that have adapted to life in rocky coastal environments. Genome analysis sheds light on this adaptation and reveals an extended set light-harvesting pigment biosynthesis genes novel metabolic processes such as halide metabolism. Comparative genomic analyses highlight the likely importance family receptor kinases related molecules evolution multicellularity plants,...
Through phylogeny reconstruction we identified 49 genes with a single copy in man, mouse, and chicken, one or two copies the tetraploid frog Xenopus laevis , zebrafish ( Danio rerio ). For 22 of these genes, both duplicates had orthologs pufferfish Takifugu rubripes another 20 found only ortholog but each case it was more closely related to than other. Forty-three pairs duplicated map 24 25 linkage groups they are not randomly distributed; 10 regions genome that contain between five sets...
The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil complete genome sequence of an ancient member lineage, unicellular alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer world's smallest free-living eukaryote known date. Features likely reflecting optimization environmentally relevant pathways, including resource acquisition, unusual...
Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre energy. We sequenced assembled >94% 640-megabase genome Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, largest proportion thus far plant genomes. also shows highest diversity genes for specialized metabolites such as terpenes that act chemical defence provide unique...
Abstract Lignin, one of the most abundant terrestrial biopolymers, is indispensable for plant structure and defense. With availability full genome sequence, large collections insertion mutants, functional genomics tools, Arabidopsis constitutes an excellent model system to profoundly unravel monolignol biosynthetic pathway. In a genome-wide bioinformatics survey genome, 34 candidate genes were annotated that encode homologous 10 presently known enzymes biosynthesis pathway, nine which have...
We describe the genome sequence of protist Trichomonas vaginalis , a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds ∼160-megabase genome, reflecting recent massive expansion genetic material. This expansion, in conjunction with shaping metabolic pathways that likely transpired through lateral gene transfer from bacteria, amplification specific families implicated pathogenesis phagocytosis host proteins may exemplify adaptations parasite...
Different methods of data analysis (e.g. clustering and ordination) are based on distance matrices. In some cases, researchers may wish to compare several matrices with one another in order test a hypothesis concerning possible relationship between these However, this is not always self-evident. Usually, values are, way, correlated therefore the usual assumption independence objects violated classical tests approach. Furthermore, often, spurious correlations can be observed when comparing...
Rust fungi are some of the most devastating pathogens crop plants. They obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart their hosts. Their lifestyle has slowed dissection molecular mechanisms underlying host invasion avoidance or suppression innate immunity. We sequenced 101-Mb genome Melampsora larici - populina , causal agent poplar leaf rust, 89-Mb Puccinia graminis f. sp. tritici wheat barley stem rust. then compared 16,399 predicted...