A5088171003- Genomics and Phylogenetic Studies
- Wheat and Barley Genetics and Pathology
- Agriculture, Plant Science, Crop Management
- Chromosomal and Genetic Variations
- Genetics and Plant Breeding
- Genetic Mapping and Diversity in Plants and Animals
- Plant Pathogens and Resistance
- Plant Disease Resistance and Genetics
- Plant Reproductive Biology
- Plant Pathogenic Bacteria Studies
- Plant Gene Expression Analysis
- Plant-Microbe Interactions and Immunity
- Genetic diversity and population structure
- Plant Parasitism and Resistance
- Machine Learning in Bioinformatics
- Cocoa and Sweet Potato Agronomy
- Botanical Research and Chemistry
- Gene expression and cancer classification
- Plant biochemistry and biosynthesis
- Bioinformatics and Genomic Networks
- Phytoplasmas and Hemiptera pathogens
- Genetic and Environmental Crop Studies
- Plant Molecular Biology Research
- Carbohydrate Chemistry and Synthesis
- Protist diversity and phylogeny
Forschungszentrum Jülich
2016-2023
RWTH Aachen University
2013-2017
Universidade Federal de Viçosa
2014
Max Planck Institute of Molecular Plant Physiology
2011-2014
Hebrew University of Jerusalem
2011
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...
Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior this, sequencing was mainly used analyze microbial samples. Here, we describe the generation a comprehensive data set with median read length 11,979 bp for self-compatible accession wild tomato species Solanum pennellii We assembly its genome contig N50 2.5 MB. The pipeline comprised initial correction Canu and SMARTdenovo. resulting raw nanopore-based de novo is structurally highly similar that...
Cultivated potato is a clonally propagated autotetraploid species with highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome revealed extensive allelic diversity, altered coding and transcript sequences, preferential allele expression, structural variation that collectively result in complex transcriptome predicted proteome, which are distributed across the homologous chromosomes. Wild contribute to diversity tetraploid cultivars,...
Abstract A parasitic lifestyle, where plants procure some or all of their nutrients from other living plants, has evolved independently in many dicotyledonous plant families and is a major threat for agriculture globally. Nevertheless, no genome sequence been reported to date. Here we describe the field dodder, Cuscuta campestris . The contains signatures fairly recent whole-genome duplication lacks genes pathways superfluous lifestyle. Specifically, needed high photosynthetic activity are...
Background and Aims Leaf gas exchange is influenced by stomatal size, density, distribution between the leaf adaxial abaxial sides, as well pore dimensions. This study aims to quantify which of these traits mainly underlie genetic differences in operating conductance (gs) addresses possible links anatomical regulation width. Methods Stomatal responsiveness desiccation, gs-related each side estimated gs (based on traits) were determined for 54 introgression lines (ILs) generated introgressing...
Next-generation sequencing has triggered an explosion of available genomic and transcriptomic resources in the plant sciences. Although genome transcriptome become orders magnitudes cheaper more efficient, often functional annotation process is lagging behind. This might be hampered by lack a comprehensive enumeration simple-to-use tools to researcher. In this review, we present (i) typical ontologies used sciences, (ii) useful databases for annotation, (iii) what expect from annotated...
A bstract Gene structural annotation is a critical step in obtaining biological knowledge from genome sequences yet remains major challenge genomics projects. Current de novo Hidden Markov Models are limited their capacity to model complexity; while current pipelines resource-intensive and results vary quality with the available extrinsic data. Here, we build on our previous work applying Deep Learning gene calling make fully applicable, fast user friendly tool for predicting primary models...
Phosphatidylethanolamine-binding proteins (PEBPs) are a class of ancient plant involved in flowering, seed development and storage organ formation. The FLOWERING LOCUS T subgroup was shown to be the initiation flowering tuberization. We aimed characterize PEBP family tuber crop Chinese yam ( Dioscorea polystachya ) identify (FT) homologs potentially Based on de novo genome assembly yam, we investigated members silico . Expression analysis FT tissue revealed DpFT3a as candidate for inducing...
Advances in next-generation sequencing technologies over the last decade have substantially reduced cost and effort required to sequence plant genomes. Whereas early efforts focused primarily on economically important crops model species, attention has now turned a broader range of plants, including those with larger more complex In 2024, genomes 500 species were published, 370 sequenced for first time. Tracking providing access published (now covering than 1800 species) is an invaluable...
Wild relatives of tomato are a valuable source natural variation in breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed S. lycopersicum for development ordered introgression lines (ILs), facilitating breeding desirable traits. Despite utility these wild and their associated ILs, few finished genome sequences produced aid genetic genomic studies. Here we report chromosome-scale assembly...
Abstract Activities of 28 enzymes from central carbon metabolism were measured in pericarp tissue ripe tomato fruits field trials with an introgression line (IL) population generated by introgressing segments the genome wild relative Solanum pennellii (LA0716) into modern cultivar lycopersicum M82. Enzyme activities determined using a robotized platform optimized conditions, where largely reflect level corresponding proteins. Two experiments analyzed years markedly different climate...
Nonhost resistance (NHR) protects plants against a vast number of non-adapted pathogens which implicates potential exploitation as source for novel disease strategies. Aiming at fundamental understanding NHR global analysis transcriptome reprogramming in the economically important Triticeae cereals wheat and barley, comparing host nonhost interactions three major fungal pathosystems responsible powdery mildew (Blumeria graminis ff. ssp.), cereal blast (Magnaporthe sp.) leaf rust (Puccinia...
GlcNAc (N-acetylglucosamine) is an essential part of the glycan chain in N-linked glycoproteins. It a building block for polysaccharides such as chitin, and several glucosaminoglycans proteins can be O-GlcNAcylated. The deacetylated form, glucosamine, integral GPI (glycosylphosphatidylinositol) anchors. Both are incorporated into polymers by glycosyltransferases that utilize UDP-GlcNAc. This UDP-sugar synthesized short pathway comprising four steps starting from fructose 6-phosphate. GNA...
Recent updates in sequencing technology have made it possible to obtain Gigabases of sequence data from one single flowcell. Prior this update, the nanopore was mainly used analyze and assemble microbial samples 1-3 . Here, we describe generation a comprehensive dataset with median fragment size 11,979 bp for wild tomato species Solanum pennellii featuring an estimated genome ca 1.0 1.1 Gbases. We its assembly contig N50 2.5 MB using pipeline comprising Canu 4 pre-processing subsequent...
Abstract Recent massive growth in the production of sequencing data necessitates matching improve-ments bioinformatics tools to effectively utilize it. Existing suffer from limitations both scalability and applicability which are inherent their underlying algorithms structures. We identify key requirements for ideal structure sequence analy-ses: it should be informationally lossless, locally updatable, memory efficient; not met by structures major assembly strategies Overlap Layout Consensus...