Gramene Oryza PanGenome 5.0 is released with 30 new synteny maps

Oryza PanGenome Release 5.0

Released: October 2022

Gramene's Oryza portal (https://oryza.gramene.org) is a pan-genome resource for rice. In its fifth release, the rice pan-genome includes 27 new synteny maps, using gene colinearity between the IRGSP1 Nipponbare assembly and all rice accessions (for example, see Nipponbare vs KitaakeX), as well as 3 new cross-species synteny maps between the Nipponbare assembly and each of Leersia, a perennial grass also known as rice cutgrass, sorghum, and maize (see the same region of Nipponbare compared to sorghum). In addition, DNA whole-genome alignments between Nipponbare, sorghum and maize are being provided (see example).

Usability of the site has also been improved through direct links from the Ensembl Browser Gene pages to the Oryza Search pages.

Nomenclature for naming of reference sequence assemblies was updated based on standard recommendations from the NSF-DBI (#2029854): CIBR-BBSRC: PanOryza: Globally coordinated genomes, proteomes and pathways for rice.

Core funding for the project was provided by the Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 8062-21000-041-00D) and NSF-DBI CIBR-BBSRC award #2029854.