Björn Usadel
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View article: Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model
Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model Open
The accurate identification of genes is vital for understanding biological function, yet this remains challenging across many newly sequenced or less-studied species. Here we present Helixer, an artificial intelligence-based tool for ab in…
View article: Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding
Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding Open
View article: Inheritance and enzymatic basis of anthocyanin malonylation in <i>Fragaria × ananassa</i>
Inheritance and enzymatic basis of anthocyanin malonylation in <i>Fragaria × ananassa</i> Open
SUMMARY The cultivated strawberry ( Fragaria × ananassa ) is highly valued for its attractive color and pleasant taste, which is due to the secondary metabolites it accumulates. To clarify which factors influence the content of secondary m…
View article: Chromosome-level genome assemblies of Thai cassava ecotypes (Manihot esculenta & Manihot glaziovii)
Chromosome-level genome assemblies of Thai cassava ecotypes (Manihot esculenta & Manihot glaziovii) Open
View article: Tomato and its relatives are breaking the genomics barriers
Tomato and its relatives are breaking the genomics barriers Open
Recent advances in high-quality genome sequencing have revolutionized research in the tomato clade (Solanum section Lycopersicon), enabling the generation of long-read and even chromosome-scale assemblies for cultivated tomato and its wild…
View article: PubPlant – a continuously updated online resource for sequenced and published plant genomes
PubPlant – a continuously updated online resource for sequenced and published plant genomes Open
Advances in next-generation sequencing technologies over the last decade have substantially reduced the cost and effort required to sequence plant genomes. Whereas early efforts focused primarily on economically important crops and model s…
View article: Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée
Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée Open
Cultivar Désirée is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of Désirée, achieved by assembling PacBio HiFi reads and Hi-C scaffolding, r…
View article: Molecular mechanisms underlying the early steps of floral initiation in seasonal flowering genotypes of cultivated strawberry
Molecular mechanisms underlying the early steps of floral initiation in seasonal flowering genotypes of cultivated strawberry Open
Floral initiation is essential for sexual reproduction in angiosperms and plays a critical role in determining crop yields. In cultivated strawberry, however, the molecular mechanisms underlying floral initiation remain poorly understood, …
View article: What can we learn from the ecophysiology of plants inhabiting extreme environments? From ‘sherplants’ to ‘shercrops’
What can we learn from the ecophysiology of plants inhabiting extreme environments? From ‘sherplants’ to ‘shercrops’ Open
In the 19th century it was proposed that ecophysiology was best studied in regions with extreme climatic conditions. In the present perspective, we argue that perhaps this is more timely than ever. The main reason is the need to improve cr…
View article: Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development
Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development Open
Grass inflorescences are composite structures, featuring complex sets of meristems as stem cell niches that are initiated in a repetitive manner. Meristems differ in identity and longevity, generate branches or split to form flower meriste…
View article: PubPlant: a continuously updated online resource for sequenced and published plant genomes
PubPlant: a continuously updated online resource for sequenced and published plant genomes Open
Advances in next-generation sequencing technologies over the last decade have substantially reduced the cost and effort required to sequence plant genomes. Whereas early efforts focused primarily on economically important crops and model s…
View article: Haplotype-resolved genome assembly of the tetraploid potato cultivar Desiree
Haplotype-resolved genome assembly of the tetraploid potato cultivar Desiree Open
Cultivar Desiree is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of Desiree, achieved by assembling PacBio HiFi reads and Hi-C scaffolding, r…
View article: Cultivar-by-environment interactions shape strawberry fruit quality: a multi-omics approach across European climates
Cultivar-by-environment interactions shape strawberry fruit quality: a multi-omics approach across European climates Open
View article: Taken to extremes: Loss of plastid rpl32 in Streptophyta and Cuscuta’s unconventional solution for its replacement
Taken to extremes: Loss of plastid rpl32 in Streptophyta and Cuscuta’s unconventional solution for its replacement Open
The evolution of plant genomes is riddled with exchanges of genetic material within one plant (endosymbiotic gene transfer/EGT) and between unrelated plants (horizontal gene transfer/HGT). These exchanges have left their marks on plant gen…
View article: A full genome assembly reveals drought stress effects on gene expression and metabolite profiles in blackcurrant (<i>Ribes nigrum</i> L.)
A full genome assembly reveals drought stress effects on gene expression and metabolite profiles in blackcurrant (<i>Ribes nigrum</i> L.) Open
Blackcurrant (Ribes nigrum L., family Grossulariaceae) is a perennial shrub that is widely cultivated for its edible berries. These are rich in antioxidants, vitamin C, and anthocyanins, making them a valuable ingredient in the food and be…
View article: A roadmap for a middleware as a federation service for integrative data retrieval of agricultural data
A roadmap for a middleware as a federation service for integrative data retrieval of agricultural data Open
Agriculture is confronted with several challenges such as climate change, the loss of biodiversity and stagnating productivity. The massive increasing amount of data and new digital technologies promise to overcome them, but they necessita…
View article: Potato Berries as a Valuable Source of Compounds Potentially Applicable in Crop Protection and Pharmaceutical Sectors: A Review
Potato Berries as a Valuable Source of Compounds Potentially Applicable in Crop Protection and Pharmaceutical Sectors: A Review Open
Potato (Solanum tuberosum) is a major agricultural crop cultivated worldwide. To meet market demand, breeding programs focus on enhancing important agricultural traits such as disease resistance and improvement of tuber palatability…
View article: In‐depth exploration of the genomic diversity in tea varieties based on a newly constructed pangenome of <i>Camellia sinensis</i>
In‐depth exploration of the genomic diversity in tea varieties based on a newly constructed pangenome of <i>Camellia sinensis</i> Open
SUMMARY Tea, one of the most widely consumed beverages globally, exhibits remarkable genomic diversity in its underlying flavour and health‐related compounds. In this study, we present the construction and analysis of a tea pangenome compr…
View article: Metabolomic and transcriptomic analyses of yellow-flowered crocuses to infer alternative sources of saffron metabolites
Metabolomic and transcriptomic analyses of yellow-flowered crocuses to infer alternative sources of saffron metabolites Open
View article: Metabolomic and transcriptomic analyses of yellow-flowered crocuses to infer alternative sources of saffron metabolites
Metabolomic and transcriptomic analyses of yellow-flowered crocuses to infer alternative sources of saffron metabolites Open
Background: The increasing demand for saffron metabolites in various commercial industries, including medicine, food, cosmetics, and dyeing, is driven by the discovery of their diverse applications. Saffron, derived from Crocus sativusstig…
View article: Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data
Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data Open
View article: Depicting the genetic and metabolic panorama of chemical diversity in the tea plant
Depicting the genetic and metabolic panorama of chemical diversity in the tea plant Open
Summary As a frequently consumed beverage worldwide, tea is rich in naturally important bioactive metabolites. Combining genetic, metabolomic and biochemical methodologies, here, we present a comprehensive study to dissect the chemical div…
View article: Ontologies for increasing the FAIRness of plant research data
Ontologies for increasing the FAIRness of plant research data Open
The importance of improving the FAIRness (findability, accessibility, interoperability, reusability) of research data is undeniable, especially in the face of large, complex datasets currently being produced by omics technologies. Facilita…
View article: Advances in fruit development and ripening
Advances in fruit development and ripening Open
Fruits originate from different tissues of the plant’s reproductive organs. They have evolved primarily to protect the developing seeds from the environment, and to act to facilitate seed dispersal and subsequently plant propagation. In or…
View article: DataPLAN: A Web-Based Data Management Plan Generator for the Plant Sciences
DataPLAN: A Web-Based Data Management Plan Generator for the Plant Sciences Open
Research data management (RDM) combines a set of practices for the organization, storage and preservation of data from research projects. The RDM strategy of a project is usually formalized as a data management plan (DMP)—a document that s…
View article: <scp>PLANTdataHUB</scp>: a collaborative platform for continuous <scp>FAIR</scp> data sharing in plant research
<span>PLANTdataHUB</span>: a collaborative platform for continuous <span>FAIR</span> data sharing in plant research Open
SUMMARY In modern reproducible, hypothesis‐driven plant research, scientists are increasingly relying on research data management (RDM) services and infrastructures to streamline the processes of collecting, processing, sharing, and archiv…
View article: Metabolomics and machine learning technique revealed that germination enhances the multi-nutritional properties of pigmented rice
Metabolomics and machine learning technique revealed that germination enhances the multi-nutritional properties of pigmented rice Open
View article: Ontologies for increasing the FAIRness of plant research data
Ontologies for increasing the FAIRness of plant research data Open
The importance of improving the FAIRness (findability, accessibility, interoperability, reusability) of research data is undeniable, especially in the face of large, complex datasets currently being produced by omics technologies. Facilita…
View article: Characterization of Bioactive Phenolic Compounds in Seeds of Chilean Quinoa (Chenopodium quinoa Willd.) Germplasm
Characterization of Bioactive Phenolic Compounds in Seeds of Chilean Quinoa (Chenopodium quinoa Willd.) Germplasm Open
In recent years, quinoa (Chenopodium quinoa Willd.), an ancient Andean region crop, has received increased research attention because it is an excellent source of nutrients and also of bioactive phenolic compounds, which are potentially be…
View article: DataPLAN: a web-based data management plan generator for the plant sciences
DataPLAN: a web-based data management plan generator for the plant sciences Open
Research Data Management (RDM) is a system for the effective handling of research data that enables scientists to structure their research questions and ensure best practices throughout the data lifecycle, from acquisition, computation and…