2. ELIXIR plant sciences community roadmap 2024-2029Sebastian Beier, Kristina Gruden, Cyril Pommier, Stéphanie Sidibe-Bocs, Sarah Dyer, Pedro Miguel Barros, Keywan Hassani-Pak, Bruno Contreras-Moreira, Carissa Bleker, 2025, strokovni članek Povzetek: The ELIXIR Plant Sciences Community is an interdisciplinary group of researchers with diverse backgrounds from computer science to different fields of plant biology. We answer the needs of both bioinformaticians and plant biologists. The Community objective is to develop services supporting the integration and linking of phenotypic, genotypic, omics (e.g. expression, metabolomics, etc.), environmental, and bibliographic data. The underlying scientific use cases encompass fundamental and applied plant sciences, including genetics, system biology and omics approaches, within the broader context of climate change, agroecology, food security, and sustainable agriculture. To meet the current challenges in agriculture, the ELIXIR Community promotes tools, databases, standards, and best practices for plant research while developing joint initiatives such as international projects and events in collaboration with European infrastructures (EMPHASIS, AnaEE-ERIC, Euro-Bioimaging, METROFOOD-RI). The ELIXIR Community also supports the establishment of links to structuring national projects and initiatives such as NFDI in Germany, or the french Agroecology and ICT program. Despite ongoing efforts, challenges remain, such as the continued scattering of plant molecular and cellular data, which hampers efficient data integration and reuse. Additionally, progressing toward a comprehensive agriculture data space is essential to address the interdisciplinary challenges that modern agriculture faces. Strengthening engagement with related research communities, such as those working on plant pathogens, is also a priority to ensure a holistic approach to plant science and agricultural research. Finally the Plant Sciences Community links with other ELIXIR Communities and Focus Groups, in particular to contribute to the objectives and priority of the Biodiversity, Food Security and Pathogens and of the Cellular and Molecular Research scientific priority areas.
Ključne besede: system biology, genotyping, plant
Objavljeno v DiRROS: 04.04.2025; Ogledov: 205; Prenosov: 54
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3. Haplotype-resolved genome assembly of the tetraploid potato cultivar DésiréeTim Godec, Sebastian Beier, Natalia Yaneth Rodriguez-Granados, Rashmi Sasidharan, Lamis Abdelhakim, Markus Teige, Björn Usadel, Kristina Gruden, Marko Petek, 2025, drugi sestavni deli Povzetek: 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, resulting in a high-contiguity chromosome-level assembly. We implemented a comprehensive annotation pipeline incorporating gene models and functional annotations from the Solanum tuberosum Phureja DM reference genome alongside RNA-seq reads to provide high-quality gene and transcript annotations. Additionally, we provide a genome-wide DNA methylation profile using Oxford Nanopore reads, enabling insights into potato epigenetics. The assembled genome, annotations, methylation and expression data are visualised in a publicly accessible genome browser (https://desiree.nib.si), providing a valuable resource for the potato research community.
Ključne besede: cultivar Désirée, potato, functional genomics, genome assembly, annotation pipeline, DNA methylation, epigenetics
Objavljeno v DiRROS: 28.01.2025; Ogledov: 254; Prenosov: 132
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