Check our Gramene Oryza poster at the 19th International Symposium on Rice Functional Genomics (ISRFG 2022)

Twenty years ago, Oryza sativa became the first rice genome to be sequenced (Goff et al, 2002; Yu et al, 2002), and like so, the foundation of the Gramene database (https://www.gramene.org), a comparative genome mapping database for grasses and a community resource for rice (Ware et al, 2002). Since then, new genomes representing a wider variety to explore agriculturally important traits (e.g., disease, flooding and drought resistance, as well as increased nutritional value) have been sequenced, prompting the creation of the first Pan-Genome site: Gramene Oryza (https://oryza.gramene.org).

The Gramene Project is honored to present a virtual poster describing Gramene Oryza, a dedicated pan-genome resource to map rice diversity, at the 19th International Symposium on Rice Functional Genomics (ISRFG 2022) to be held in Phuket, Thailand on November 4-7, 2022.  If you are attending the ISRFG meeting,stop by to find out more about this resource. In its fifth release (October 2022), the Oryza Pangenome will feature 28 Oryza genomes, including domesticated African rice, 16 MAGIC16 collection, short life cycle KitaakeX, and heirloom US Carolina Gold Rice. It uses the International Rice Genome Sequencing Project (IRGSP) genome as the reference for gene expression and pathway information, and 27 cross-rice synteny maps. In addition, over 38K gene trees were built with the Oryza proteomes and 8 outgroups (Leersia, Arabidopsis, sorghum, maize, grape, Chlamydomonas, Selaginella, Drosophila), enabling phylogenetic inference of orthologs and paralogs, insights of allelic genes within and across species, as well as lineage specific expansion and contraction, gene function projection, and synteny maps. Also provided whole-genome alignments between Nipponbare, sorghum and maize, updated nomenclature for naming of reference sequence assemblies according to the standard recommendations from the NSF-DBI (#2029854): CIBR-BBSRC: PanOryza: Globally coordinated genomes, proteomes and pathways for rice; and improved usability through direct links from the Ensembl Browser Gene pages to the Oryza Search pages. Various views exist to interrogate the gene tree data, including the novel neighborhood view in the search component of the site. In addition, the site includes BLAST and text-based searches.

Goff, S.A., et al. (2002). A draft sequence of the rice genome. Science, 296: 92-100. PMID: 11935018.

Yu, J., et al. (2002). A draft sequence of the rice genome. Science, 296: 79-92. PMID: 11935017.

Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD, McCouch SR (2002). Gramene, a tool for grass genomics. Plant Physiology 130: 1606-1613. PMID: 12481044, doi:10.1104/pp.015248, Free PDF.