Oat Pangenome at https://oat.persephonesoft.com
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 assemblies from the oat pangenome to the barley pangenome, which was loaded earlier. The reference genome for the oat pangenome is Pepsico OT3098. We have two copies of this genome. One is published on our main website: https://web.persephonesoft.com/?data=genomes/OT3098, and the other is part of the pangenome available at https://oat.persephonesoft.com/?data=genomes/Oat_Asativa_OT3098. On the barley side, the reference is the Morex cultivar https://oat.persephonesoft.com/?data=genomes/Morex.
We streamlined the pangenome loading procedure, which PersephoneShell greatly facilitates by building individual instruction files from a template file. This time, we applied this mechanism to load the oat pangenome. As with other pangenomes, our routine produced gene orthologs that we can study using Persephone’s multiple alignment module.
The synteny matrices visualize the full genome alignment. The hexaploid set of chromosomes in oats sometimes complicates the picture. Use the parallel layout of the synteny matrix and its filtering feature to show synteny for selected chromosomes only.
Here is the full list of oat genomes with URLs to open in Persephone:
Oat Abyssinica Oat Ainsularis_BYU209 Oat Alongiglumis_CN58138 Oat Amagalon Oat Asativa_GMI423 Oat Asativa_OT3098 Oat Asativa_Sang Oat Aslak Oat Atlantica_CC7277 Oat Avena_sterilis_TN1 Oat Avena_sterilis_TN4 Oat Bannister Oat Barbata (PI388828) Oat Bilby Oat Bingo Oat Byzantina Oat Clintland60 Oat Delfin Oat Eriantha_BYU132 Oat Fatua_CN25955 Oat FM13 Oat Gehl Oat GS7 Oat Hatives_des_Alpes Oat HiFi Oat Leggett Oat Lion Oat Morgan Oat Nicolas Oat OT380 Oat Park Oat PI182478 Oat Rhapsody Oat Victoria Oat Williams