When multiple maps are displayed with thousands of connectors linking shared features, it can be difficult to trace which regions correspond to a specific interval. The new version of Persephone introduces connector filtering, allowing you to hide all links except...
If you haven’t noticed, we’ve added a new view of the synteny matrix that arranges all maps from both genomes in two parallel rows. In many cases, this layout highlights structural variations—such as inter‑chromosomal translocations—more clearly than the traditional matrix. When...
We are excited to announce a new, separate portal, specifically for barley pangenome data: https://barley.persephonesoft.com. It hosts 76 Hordeum vulgare assemblies described in the paper by Jayakodi, M., Lu, Q., Pidon, H., et al. Structural variation in the pangenome of...
The Human Pangenome Reference Consortium is building a pangenome reference resource. As you probably know, the de facto reference genome, GRCh38, is derived from the sequences of over 20 individuals. The new collection of assemblies represents validated, telomere-to-telomere genomic sequences...
To facilitate the quick export of gene information, including exon/intron structure, we added a new tab to the gene properties form. It displays text in GFF format that "spells out" exon and CDS coordinates. Now, you can copy the gene...
The tomato pangenome described in the paper Shi, C., Chen, S., Wang, J. et al. A tomato telomere-to-telomere super-pangenome empowers stress resilience breeding. Nat Genet (2026). https://doi.org/10.1038/s41588-026-02508-y, is now a part of the Persephone pangenome collection. This super-pangenome has 20...
The latest addition to Persephone’s toolset is an interactive interface for editing gene models. When you encounter an issue in an existing gene model, you can now create your own corrected version of the gene structure and save it so...
With the help of 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...
We have added two barley (Hordeum vulgare) genomes: morexV3 and 10TJ18_BPGv2. Both assemblies are available with gene annotation. The ortholog pairs link syntenic maps with wheat and oat chromosomes: Chromosomes from four genomes are aligned: morexV3, 10TJ18_BPGv2, wheat, and oat. The full...
We have added two large genomes for Allium cepa (onion) and Allium sativum (garlic). Both assemblies contain exceptionally long chromosomes, some exceeding 2 Gbp in length. We also located a genetic map for onion on Figshare that includes marker coordinates anchored...