Resource updates and database development.
Resource descriptions below reflect the catalog checked on . They describe current availability, not separate first-release dates.
The current SDH portal is available at sci.hainanu.edu.cn/strawberry/. The earlier GDS website remains accessible at /strawberry1/. Researchers preparing manuscripts, bookmarks or teaching materials can use the new address for the current portal. The two websites retain distinct interfaces and data services.
The searchable genome catalog contains 60 species–assembly/annotation entries: 53 strawberry entries and seven pathogen entries. Cultivars, annotation revisions and haplotype components remain distinct. Gene searches retain the species and reference version so that similarly named models are not silently treated as the same gene. The species pages connect reference descriptions with available sequence and analysis resources.
The download catalog brings genome FASTA, annotation, CDS and protein resources together by assembly. Seventeen chloroplast sequence accessions are listed separately from nuclear genomes. Files are served through the controlled download catalog, with filenames and sizes available before retrieval. Assembly components are not combined merely because they share a cultivar name, and alternative files may remain hidden from the main download table.
The expression module contains 28 datasets spanning cultivated and wild strawberry. Tissue atlases, fruit-development series and treatment experiments can be explored through gene profiles and multi-gene views. The matrices contain 465 sample or condition columns in total. Some columns represent condition means or combined runs, so this number is not presented as a count of independent biological samples. Dataset descriptions retain the reference assembly, expression unit and processing context.
The single-cell module connects the woodland strawberry leaf study CRA004848 with cell-type markers and infection-response results. Mock, 6-hour and 12-hour infection samples support exploration across the response to Botrytis cinerea. Published analyses are distinguished from the SDH STARsolo reanalysis. The reanalysis contains 50,702 cells, while the publication reports 50,327; these are separate processing results, not interchangeable totals.
The epigenomics catalog documents 38 public projects and two data gaps. Chromatin accessibility, histone modification and other regulatory data are organized with project and reference information. Archived run metadata, verified files and gene-linked evidence are recorded separately. A project appearing in the catalog does not imply that all its raw sequencing files or every downstream analysis are available locally.
The metabolomics module covers six studies and 18 assays. Users can investigate assay-specific features, deposited abundance measurements, available spectra and statistical contrasts. Positive- and negative-ion assays remain separate because they can reuse biological samples and detect different features. Canonical metabolite entries retain their identification status; provisional records are not described as fully structure-confirmed compounds.
The GWAS module provides yield and fruit-size results for the University of Florida breeding population, with 5,895 markers in its marker catalog and Royal Royce as the reference assembly. Trait-specific associations can be examined alongside nearby genes. Statistical association, genomic proximity and experimentally demonstrated gene function remain different kinds of evidence. Phenotyped sample counts are also distinguished from the fitted sample size for an individual marker.
The synteny workspace contains 276 pairwise comparisons across 24 assemblies. These comparisons help researchers follow corresponding genomic regions and candidate genes between references. The pangenome workspace uses seven diploid proteomes for SDH-derived orthogroup analysis, with six corresponding genomes included in the sequence-graph layer. Protein grouping and graph membership are reported separately, and the current graph-site evidence is limited to Fvb1.
GO and KEGG enrichment use 45 assembly-specific backgrounds. The featured-family catalog includes 28 classes, while the transcription factor catalog includes 58 classes. Assembly-level analysis states are retained, including entries that require review or are excluded. Family assignment is a prediction-based classification and does not, by itself, establish an experimentally validated function.
The homepage's Genetics&Breeding genes section organizes literature-linked genes under disease and stress resistance, fruit quality, growth and development, and ripening and postharvest biology. Internal gene links are supplied where assembly-specific IDs have been matched. Germplasm resources provide a complementary route through taxonomic and material records. A linked external accession is a resource reference, not a claim that SDH physically maintains that accession.
The knowledge base contains 300 indexed strawberry articles, with full text indexed for 278 records. Strawberry AI supports literature questions and read-only exploration of SDH data. Literature citations, source records and assembly context help users trace answers to supporting evidence. Article counts are kept distinct from extracted evidence records and text fragments. Generated interpretations still require scientific review.
The tools collection connects primer design, sequence processing, ORF finding, batch sequence retrieval and existing genome-analysis services. GuideRNA, MICE, KNN and iCluster are available through linked or embedded workspaces. External tools operate under their own service conditions, and data submitted to those workspaces are handled by the external provider. These integrations extend the analysis workflow without implying that SDH has independently generated every external result.
Earlier GDS milestones below reproduce the dates recorded on the retained GDS website. They are distinguished from the current SDH resource inventory.
The earlier GDS website recorded the release of version 2.0. That site remains available as a separate resource following the public-address exchange.
The original site recorded its version 1.0 release, following the introduction of sequence-analysis, genome-browsing and gene-search services.
The historical announcement documented the addition of gene-search data, establishing a route from a gene identifier to information in the database.
The earlier GDS site recorded the implementation of sequence similarity search and genome browsing. These remain important research workflows in the broader strawberry database resource.
The retained GDS announcement dates the start of its strawberry omics database to September 2020. This historical date refers to GDS and is not a first-release date for the current SDH portal.
Historical source: retained GDS website. Dates are not interpolated for years without a documented announcement.
We welcome corrections, suggestions and data contributions. Please include the relevant publication, dataset accession and reference assembly when sharing a resource with the database team.