Genome resources
Explore cultivated strawberries, wild relatives, pathogens and pangenome assemblies.
Cultivated strawberry
14 cultivarsFragaria × ananassa · octoploid genomes
| Cultivar | Genome record |
|---|---|
| Reikou | Genome assembly |
| Camarosa | Reference assembly |
| Seolhyang | Chromosome-level assembly |
| Yuexin | Haplotype-resolved assembly |
| Benihoppe | Gap-free phased assembly |
| Chulian | T2T (author-reported) · haplotype-resolved |
| EA78 | Phased · maternal component |
| Florida Brilliance | T2T (author-reported) · v1.0.a1 |
| Florida Medallion | Phased · haplotype 1 |
| FL15.89-25 | Phased assembly |
| Royal Royce | Primary · phased source |
| Yanli | Primary · phased source |
| FL17.68-110 | Haplotype-phased assembly |
| FL20.82-27 | Two parent haplotypes |
Wild strawberry
17 speciesFragaria diversity · diploid to octoploid
| Species | Ploidy |
|---|---|
| F. vesca | 2x |
| F. iinumae | 2x |
| F. nilgerrensis | 2x |
| F. nipponica | 2x |
| F. nubicola | 2x |
| F. viridis | 2x |
| F. daltoniana | 2x |
| F. mandshurica | 2x |
| F. pentaphylla | 2x |
| F. chinensis | 2x |
| F. bucharica | 2x |
| F. orientalis | 4x |
| F. corymbosa | 4x |
| F. moupinensis | 4x |
| F. moschata | 6x |
| F. chiloensis | 8x |
| F. virginiana | 8x |
Strawberry pathogens
7 pathogensDisease-associated fungi, oomycetes and bacteria
| Disease | Pathogen | Strain |
|---|---|---|
| Grey mould | Botrytis cinerea | B05.10 |
| Anthracnose | Colletotrichum fructicola | CGMCC3.17371 |
| Powdery mildew | Podosphaera aphanis | DRCT72020 |
| Phytophthora crown rot / leather rot | Phytophthora cactorum | 10300 |
| Red stele / red core root rot | Phytophthora fragariae | BC-16 |
| Verticillium wilt | Verticillium dahliae | 12008 |
| Bacterial angular leaf spot | Xanthomonas fragariae | PD885 |
Pangenome
7 genomesDiploid Fragaria · 6 graph genomes · 7 proteomes
| Species | Assembly |
|---|---|
| F. daltoniana | YNU v1.0 |
| F. iinumae | v1.0 |
| F. mandshurica | YNU v1.0 |
| F. nilgerrensis | YNU v1.0 |
| F. vesca | v4.0.a1 |
| F. viridis | YNU v1.0 |
| F. pentaphylla | YNU v1.0 |
Disease & stress resistance
-
Postharvest quasi-circadian immunity
Wang et al., Cell, 2026 -
Gray mold resistance
FaSnRK1αFaWRKY33.2Luo et al., Hortic Plant J, 2024 -
FaRCa1-associated anthracnose resistance
LRK10AHan et al., GigaScience, 2025Fxa6Bg1786910 -
Salt tolerance and Na+ homeostasis
FaWRKY40Yang et al., J Adv Res, 2025FxaYL_612g0113550FaWRKY70FxaYL_732g0836350
Fruit quality
-
Fruit skin and flesh coloration
Castillejo et al., Plant Cell, 2020 -
Mesifurane aroma
FaOMTZorrilla-Fontanesi et al., Plant Physiol, 2012GenBank: AF220491.2 -
Soluble sugar accumulation
FaDOF1.7FaDOF1.5FaSUS1FaSUS2FaCWINV1Tao et al., Plant J, 2026 -
γ-lactone aroma
FaECHFvECH-likePorter et al., New Phytol, 2026FvH4_7g09160
Growth & development
-
Flowering habit and everbearing
FaTFL1Koskela et al., Plant Biotechnol J, 2016 -
Flowering–runnering decision
Tenreira et al., Plant Cell, 2017 -
Branch crown versus stolon fate
FveBRC1Alonso et al., New Phytol, 2026FvH4_5g12710 -
Fertilization-induced fruit initiation
FveAGL62Guo et al., Nat Commun, 2022FvH4_2g03030FveAGL80FvH4_6g08460FveATHB29bFvH4_5g17830FveATHB30FvH4_6g48610FveYUC10FvH4_2g24750FveTAA1FvH4_4g25850
Ripening & postharvest
-
Ripening master regulation
FaRIF (FaNAC035)Martín-Pizarro et al., Plant Cell, 2021FxaC_10g22240 -
Fruit development and ripening
FaMADS9Seymour et al., J Exp Bot, 2011GenBank: AF484683.1 -
ABA–m6A ripening cascade
Tang et al., Nat Commun, 2024 -
ABA-dependent ripening
FaNCED1Jia et al., Plant Physiol, 2011GenBank: HQ290318.1 (partial CDS)FaCHLH / ABARGenBank: GQ201451.1 -
Fruit firmness and postharvest shelf life
FaPG1López-Casado et al., Hortic Res, 2023FxaC_21g15770
About the database
Overview, highlights, and news from Strawberry Data Hub.
Strawberry Data Hub (SDH) is an assembly-aware research platform integrating genomic, pangenomic and multi-omics resources for Fragaria and strawberry pathogens. It connects genes and sequences with comparative genomics, expression, epigenomic, metabolomic and trait-association evidence, while retaining the source species and genome version needed for reproducible analysis.
Current coverage spans 18 Fragaria taxon profiles, with 53 strawberry genome/annotation datasets and seven pathogen assemblies. Curated literature, gene-family and transcription-factor catalogs, sequence retrieval and breeding-oriented tools support candidate-gene discovery and experimental planning.
From assembly-specific genes to multi-omics evidence, SDH brings strawberry data, literature and analysis into one research workspace.
- Strawberry AI and a curated knowledge base. Chat explores evidence from 302 curated strawberry papers with clickable literature citations. Agent queries internal data, retrieves sequences and supports multi-gene investigation. Use the SDH trial or connect your own API.
- Assembly-resolved genome resources. 60 searchable genome/annotation datasets include 53 strawberry and seven pathogen entries. Annotation revisions and haplotype components are counted separately. Gene records retain their species and version, with annotation, protein/CDS retrieval, JBrowse and resource downloads.
- Comparative and regulatory genomics. Explore assembly-specific synteny comparisons, gene families, transcription factors and miRNAs. The pangenome connects SDH-derived orthogroups from seven diploid proteomes with a separate six-genome sequence-graph layer.
- Expression from tissues to cells. 28 transcriptome datasets cover cultivated and wild strawberry, with tissue profiles, eFP views and multi-gene heatmaps. The leaf single-cell atlas adds cell-type markers and infection-response results, distinguishing published findings from SDH reanalysis.
- Epigenomic evidence in context. The epigenomics catalog documents 38 public projects and two data gaps. Explore histone modifications, chromatin accessibility and available gene- or region-linked evidence while retaining project and assembly context.
- Metabolites and trait associations. Six metabolomics studies and 18 assays provide study-specific features, abundance data and statistical contrasts. GWAS covers disease resistance, fruit quality, firmness, yield and fruit size; associated loci and nearby genes remain distinct from experimentally validated functions.
- Tools for the next analysis. Use GO and KEGG enrichment with 51 assembly-specific annotation backgrounds. Continue with BLAST, batch FASTA retrieval, sequence processing, ORF finding and primer design.
- Connected analysis workspaces. The Tools collection includes GuideRNA, primer design, MICE, KNN and iCluster; breeding-oriented prediction workspaces include SCCG and flowering-gene prediction. These embedded external services complement SDH and are not automatically executed by Agent.
Data counts checked against the live catalogs on . Coverage varies by dataset and assembly.
Year summaries are retrospective, not first-release dates. Earlier GDS announcements retain their documented dates.
· SDH progress
Germplasm Resources moved to Breeding; the wild-genome directory now follows ploidy order.
Gene-family and transcription-factor catalogs extended to the new GDR genome components.
Seven-species single-copy maximum-likelihood phylogeny added to the diploid pangenome workspace.
Cultivated, wild and pathogen genome catalogs updated.
Primer Design, GuideRNA and multi-omics tools integrated.
Chloroplast genome downloads added.
Trait-linked functional genes curated with literature references.
Strawberry AI and visitor statistics introduced.
Transcriptome expression datasets loaded for tissue- and treatment-based gene queries.
· Retrospective summary
Germplasm and breeding-related information compiled.
Trait-associated variation resources curated.
Graph pangenome resources organized.
Synteny and orthogroup analyses integrated.
Gene family and transcription factor resources expanded.
· Retrospective summary
Metabolomic resources incorporated.
Epigenomic datasets organized.
Single-cell transcriptomic resources curated.
Gene expression profiles integrated.
Transcriptomic datasets organized by tissue and treatment.
· Retrospective summary
Sequence retrieval and processing tools added.
GO and KEGG annotation resources curated.
Genome and annotation downloads organized.
BLAST and JBrowse integrated.
Gene search and annotation browsing developed.
· Retrospective summary
Genome annotation and sequence datasets prepared.
Species and assembly information curated.
Strawberry genome resources collected and organized.
Strawberry database resource preparation.
Database history
GDS milestones retain the dates documented on the earlier website.
GDS version 2.0
The earlier GDS website recorded the release of version 2.0. That site remains available as a separate resource following the public-address exchange.
GDS version 1.0
The original site recorded its version 1.0 release, following the introduction of sequence-analysis, genome-browsing and gene-search services.
Gene-search data added to GDS
The historical announcement documented the addition of gene-search data, establishing a route from a gene identifier to information in the database.
BLAST and JBrowse introduced
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.
Earlier GDS project started
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.
SDH-owned content is free for non-commercial academic use. For commercial licensing, please contact us. Third-party resources retain their original licenses.