https://researchdata.se/sv/catalogue Search results sv This repository contains files associated with the analysis performed during the Norway spruce and Scots pine genome assembly and annotation, associated epigenetic analyses, and population genetics in Norway spruce. The repository contains four folders that contain files relating to different sections in the associated publication: - Genome - Orthogroups - Epigenetics - Co-expression - Population genetics Further details are provided in Readme files within each folder. These files are referred to in the associated publication as “Data Availability” as a link to the Data Availability statement where details of this repository are provided. The two genomes were assembled using PacBio HiFi reads and Micro-C (Norway spruce) or Hi-C (Scots pine) chromatin contact data. The chromatin contact data was also used to perform analysis of global compartmentalisation of chromatin and to detect Topologically Associating Domains (TADs) and chromatin loops. The genomes were annotated using collections of RNA-Seq data and PacBio IsoSeq reads. A comparative co-expression network analysis was performed for data profiling wood formation in both species to identify conserved and diverged patterns of gene co-expression. This was linked to analysis of orthogroups to examine evidence for neo- and sub-functionalisation among paralogs. In Norway spruce and extensive set of individuals were re-sequenced using Illumina short read data. Subsets of those individuals were used to perform environmental GWAS, detect signals of selection and to identify geographically segregating gene presence/absence variants. The associated ENA Umbrella project is PRJEB88492. Thu, 30 Apr 2026 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-28737623 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-28737623 Umeå universitet Nathaniel Street Despite their importance, the pathways and enzymes associated with the biosynthesis of many specialized metabolites are yet to be characterized. The integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis. However, suitable multi-omics data resources for this approach are scarce. Here we present a data resource comprising Liquid Chromatography Mass Spectrometry (LC-MS) and mRNA-Sequencing data from European aspen (Populus tremula L.) including tissues sampled from different organs, and genotypes that produce contrasting sets of salicinoid phenolic glucosides (SPGs), that are specialized metabolites characteristic for Salicaceae. Tue, 25 Mar 2025 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-27336156 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-27336156 Umeå universitet Sara M. Rydman Kathryn Robinson Jenna Lihavainen Benedicte R. Albrectsen Stefan Jansson Nathaniel Street RNA-Seq data was generated from stages of somatic (SE) and zygotic embryogenesis (ZE). The developing zygotes (Zem) were isolated from the female megagametyophyte (FG) tissue at later stages. Differential expression analysis was performed for each dataset and the results were compared to identify common and contrasting expression changes. The somatic embryogenesis data was used to predict long intergenic RNAs and a co-expression network was generated. The network was used to assign putative functional annotation to the lincRNAs using a guilt-by-association approach. The normalised expression values, results of differential expression test, results of functional enrichment of gene sets and figures representing these are included. The sequences of identified lncRNAs are included as well as annotation information. The data is structured in three folders: SE = Somatic Embryogenesis ZE = Zygotic Embryogenesis SE_ZE = All files related to the comparison of differentially expressed genes between the two datasets. Some of the file names or figures can contain abbreviations different from the ones in the original publications. A conversion table is provided in the README file. More information on the folder and file content can be found in the manifest file. Tue, 01 Oct 2024 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25315867-v1 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25315867-v1 Umeå universitet Nathaniel Street Katja Stojkovič Ulrika Egertsdotter Kim-Cuong Le Nicolas Delhomme Camilla Canovi RNA-Seq data was generated from stages of somatic (SE) and zygotic embryogenesis (ZE). The developing zygotes (Zem) were isolated from the female megagametyophyte (FG) tissue at later stages. Differential expression analysis was performed for each dataset and the results were compared to identify common and contrasting expression changes. The somatic embryogenesis data was used to predict long intergenic RNAs and a co-expression network was generated. The network was used to assign putative functional annotation to the lincRNAs using a guilt-by-association approach. The normalised expression values, results of differential expression test, results of functional enrichment of gene sets and figures representing these are included. The sequences of identified lncRNAs are included as well as annotation information. The data is structured in three folders: SE = Somatic Embryogenesis ZE = Zygotic Embryogenesis SE_ZE = All files related to the comparison of differentially expressed genes between the two datasets. Some of the file names or figures can contain abbreviations different from the ones in the original publications. A conversion table is provided in the README file. More information on the folder and file content can be found in the manifest file. Tue, 01 Oct 2024 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25315867 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25315867 Umeå universitet Nathaniel Street Katja Stojkovič Ulrika Egertsdotter Kim-Cuong Le Nicolas Delhomme Camilla Canovi