Diploid Fragaria pangenome
Loading dataset scope…
Fvb1 structural-variation and TE evidence
Loading site evidence…
Genome context
F. vesca v4.0.a1 genes, panEDTA transposable elements and graph-site candidates.
Fvb1 evidence density
Select a genomic bin to filter the evidence table and open the same interval in JBrowse.
| Site ID | Fvb1 position | Length Δ | Path evidence | Reference overlap | Carrier evidence | TE context | Open details |
|---|---|---|---|---|---|---|---|
| Loading evidence… | |||||||
Graph-site detail
Carrier intervals
| Species path | Native interval | Coordinate status | Gene / CDS | TE overlap | TE family |
|---|
These are direct coordinate intersections for graph-review intervals. They do not by themselves establish TE presence/absence, orthology, allelism, functional disruption or biological gene absence.
Six-assembly path alignmentInspect strand and reference coverage for a 5–100 kb HAL intervalLoading graph…
Assembly path alignment
Fvb1–Fvb7 · reference-anchored HAL blocks
Protein-group occupancy
Loading composition…
Sampling diagnostics
Gene presence matrix
Loading matrix…
—
| Pan-gene | Type | Occupancy | Loading proteome columns… | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Loading presence matrix… | ||||||||||||
Selected gene-content profiles
Protein copy number across the seven published proteomes.
Orthogroup membership
Protein copy number and matched identifiers by proteome.
Protein membership across proteomes
Membership by proteome
| Species | Assembly | Proteins | Result |
|---|
Matched protein identifiers
| Species | Protein ID |
|---|
Seven-proteome phylogeny
Maximum-likelihood analysis of 5,437 single-copy orthologous proteins.
Analysis pending
The reproducible alignment and maximum-likelihood analysis is running. The tree will appear here only after its output and support values pass validation.
Compared proteomes
Loading…
| Species | Assembly | Analysis role | Graph | Proteins | In orthogroups | Unassigned | Evidence record |
|---|---|---|---|---|---|---|---|
| Loading proteomes… | |||||||
Methods
Protein groups were calculated with OrthoFinder 2.5.5 from seven published diploid Fragaria proteome annotations. Composition, matrices and addition curves therefore report annotation detection, not confirmed biological gene absence. The sequence graph contains six assemblies. Fvb1 records remain graph-site candidates; gene, CDS and TE labels report direct interval overlap and are not relabelled as validated structural variants. JBrowse uses the matching F. vesca Hawaii 4 v4.0.a1 coordinates.
Reference
- Qiao Q, Edger PP, Xue L, et al. Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.). Proceedings of the National Academy of Sciences. 2021;118(45):e2105431118. Article ↗ GDR dataset ↗