Cucumber Pangenome with 37 Assemblies Loaded
With help from Dr. Zhangjun Fei (Cornell University, cucumberdb.com), we uploaded the dataset containing 37 annotated cucumber (Cucumis sativus) assemblies described in the paper Graph-based pangenome reveals structural variation dynamics during cucumber breeding | Nature Genetics.
All 37 genomes have been interlinked via orthologous gene pairs, enabling users to align the maps and entire genomes.
The Synteny matrix in parallel layout visualizes the alignment for all chromosomes of two genomes:
In Persephone’s Multimap mode, you can quickly find and align syntenic maps. The interface draws ribbon connectors between matching regions to present a simplified, easy‑to‑inspect view.
We also uploaded 2.3 billion SNPs for 446 genotypes. You can navigate to the variants via Variant Explorer or open the map set WI7633 and add the variation track from the context menu. Here is an example of the Variants track with 50 samples sorted by distance from the reference:
The full list of assemblies:
| Organism | Map set with Persephone URL | #Maps |
| Cucumis sativus var. hardwickii (cucumber) | Cucumber PI 179678 | 8 |
| Cucumis sativus var. hardwickii (cucumber) | Cucumber PI 215589 | 8 |
| Cucumis sativus var. hardwickii (cucumber) | Cucumber PI 214155 | 8 |
| Cucumis sativus var. hardwickii (cucumber) | Cucumber PI 462369 | 8 |
| Cucumis sativus var. hardwickii (cucumber) | Cucumber PI 531313A | 8 |
| Cucumis sativus var. hardwickii (cucumber) | Cucumber PI 183967 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber 9110gt | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber Chinese Long 9930 v4 | 152 |
| Cucumis sativus var. sativus (cucumber) | Cucumber WI2757 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber WI7012 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber WI7037 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber True Lemon | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber WI7150 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber WI7204 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber Poinsett 76 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber Marketmore 76 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber PI 197088 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber PI 249561 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber PI 330628 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber WI5551 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber PI 109483 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber WI7439 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber WI7724 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber WI7646 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber WI7633 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber WI7773 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber PI 618917 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber CG6663 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber PI 221440 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber PI 500361 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber PI 175120 | 8 |
| Cucumis sativus var. sativus (cucumber) | Cucumber Cu2 | 8 |
| Cucumis sativus var. xishuangbannanesis (cucumber) | Cucumber WI7167 | 8 |
| Cucumis sativus var. xishuangbannanesis (cucumber) | Cucumber WI7180 | 8 |
| Cucumis sativus var. xishuangbannanesis (cucumber) | Cucumber WI7651 | 8 |
| Cucumis sativus var. xishuangbannanesis (cucumber) | Cucumber WI7698 | 8 |
| Cucumis sativus var. xishuangbannanesis (cucumber) | Cucumber CG9192 | 8 |