We are excited to announce a major feature improvement: use Persephone to view data by connecting to the NCBI Datasets API. So, now you can engage the fast graphical engine of Persephone to visualize the vast collection of NCBI's genomes...
The new version of the Arabidopsis thaliana genome, TAIR12, is now in Persephone. The corresponding Genetics paper on TAIR12 describes "the community-driven reannotation of the A. thaliana Col-0 reference genome, which integrates new long-read assemblies, updated structural annotations, and expert manual...
The 35 genomes published in the paper Avni, R., Kamal, N., Bitz, L. et al. A pangenome and pantranscriptome of hexaploid oat. Nature 649, 131–139 (2026) https://doi.org/10.1038/s41586-025-09676-7 have been loaded to Persephone's new dedicated website at https://oat.persephonesoft.com. We cross-linked the annotated...
First, we improved rendering performance for quantitative tracks. In our tests, Persephone shows 10 tracks, each containing 10 subtracks combined via Multi-trace mode without a noticeable delay! In addition, we’ve expanded the controls available for rendering quantitative tracks (typically bedGraph or...
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...