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...
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...
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 loaded 23 genomes of the genus Solanum from the project described at Solgenomics.net. The set includes species such as bitter tomato, African eggplant, melon-pear, and others. They can be opened in Persephone by following these direct links: Solanum abutiloides...
It was a pleasure collaborating with scientists from KAUST, INRAE, and other institutions on our recent publication in Nature, titled "Genome assembly of a diversity panel of Chenopodium quinoa." As part of this collaboration, we uploaded nine quinoa genomes to...
A small addition to the coffee pangenome data set: Coffea arabica var. Geisha. Chromosomes of C.arabica Geisha and Cara_1.0 are aligned using minimap2 Here is the direct link to this screen in Persephone: https://web.persephonesoft.com/?bookmark=B71E475989EAFC13B9D9E68A8FE6ACC9 The genome of Geisha variety was downloaded from Phytozome....
Happy New Year, All! We are going to the Plant and Animal Genome conference in San Diego. There, we will present our latest version of Persephone. It includes new features that make navigating pangenomes easier.We are introducing the redesigned Synteny matrix,...
In addition to the popular versions of the Human genome, such as GRCh38 or CHM13v2, we now host full assemblies for 96 individuals from the Human pangenome. The sequences were downloaded from NCBI. Unlike the well-annotated data sets, the sequences...
In collaboration with our colleagues from KAUST, we have added 21 reference-quality rice genome assemblies to our web portal and to the demo Windows version. Os GJ-temp: IRGSP-1.0 (Nipponbare)Os GJ-subtrp: CHAO MEOOs GJ-trop1: AzucenaOs GJ-trop2: KETAN NANGKAOs cB: ARC 10497Os...
We have expanded our collection of public data sets by adding several reference genomes of soybean: Glycine max (soybean) and Glycine soja (wild soybean):G. max Wm82.a2.v1G. max Wm82.a4.v1G. max Zhonghuang 13G. max Zhonghuang 13 NCBI version (sequence only)G. max Lee...