Please welcome: barley.persephonesoft.com
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 wild and domesticated barley. Nature 636, 654–662 (2024). https://doi.org/10.1038/s41586-024-08187-1
Each assembly has a gene annotation track. We calculated orthologs for all genes in the dataset. This means that each gene can potentially be linked to its counterpart in other genomes, bringing the number of orthologs per gene to nearly 75. Altogether, the total number of ortholog pairs for this pangenome is considerable: about 120 million.
When displaying two or more syntenic maps, the existence of orthologs allows linking related gene models. The connector lines between orthologs reveal syntenic regions, which can be further studied with the real-time sequence comparison in Persephone.
If you are interested in analyzing the regions that have low gene density, you can use another type of tracks – sequence tags. They are extracted at regular intervals from the main reference genome Morex v3 and mapped onto other genomes.
The recently introduced connector clustering, which replaces collinear line connectors with synteny ribbons, will help identify inversions that are difficult to spot at this resolution. In addition to adjusting the clustering granularity and size, the new feature allows specifying colors separately for direct and inverted synteny ribbons.
With this diversity and the number of barley varieties, you can build nice protein sequence profiles by running multiple alignments of orthologs. Open the gene properties form and go to its Orthologs tab. The multiple alignment is done on the fly by pushing the corresponding button.
We are always open to suggestions. If you are an expert in barley genomics, you might want to see other data related to this pangenome. Please let us know. We appreciate your feedback!
Here is the full list of the barley pangenome:
10TJ18 Foma Bowman FT11 Chikurin Ibaraki Barke Bonus Aizu6 Akashinriki Golden Promise Golden Melon FT628 HID101 FT67 FT880 HID055 FT286 FT333 HID249 HOR 10096 HOR 13594 Hockett HOR 12541 HOR 10350 HOR 1168 HOR 10892 HOR 12184 HID357 HID380 FT144 FT262 HOR 1702 HOR 18321 HOR 19184 HOR 14121 HOR 14273 HOR 13942 HOR 14061 HOR 21595 HOR 21322 HOR 21256 HOR 13663 HOR 13821 HOR 3081 HOR 3365 HOR 6220 HOR 4224 HOR 3474 HOR 2830 HOR 2779 HOR 495 HOR 2180 HOR 21599 Morex HOR 8148 HOR 9043 Igri HOR 7552 HOR 8117 HOR 9972 Maximus HOR 7385 HOR 7172 WBDC_237 WBDC_207 WBDC_199 WBDC_103 WBDC_078 WBDC_184 WBDC_133 RGT Planet OUN333 WBDC_348 WBDC_349 ZDM01467 ZDM02064