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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #402302

Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: Gramene Oryza: a dedicated pan-genome resource to map rice diversity

item WEI, SHARON - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item CONTRERAS-MOREIRA, BRUNO - European Bioinformatics Institute
item DYER, SARAH - European Bioinformatics Institute
item Gladman, Nicholas
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item NAAMATI, GUY - European Bioinformatics Institute
item Ware, Doreen
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item ZHOU, YONG - King Abdullah University Of Science And Technology
item WING, ROD - King Abdullah University Of Science And Technology

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 11/4/2022
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Rice feeds more than half of the world’s population, and is a model system for plant genetics, genomics, and breeding due to its small size (~400Mb). The first rice genome, sequenced 20 years ago, was the foundation of the Gramene database ( at the time, for providing a comparative genome mapping resource for grasses. Since then, new genomes representing a wider variety to explore agriculturally important traits, have been sequenced, prompting the creation of the first Pan-Genome site: Gramene Oryza ( The current release 5 (Oct. 2022) features 28 Oryza genomes, including domesticated African rice, 16 MAGIC16 collection, short life cycle KitaakeX, and heirloom US Carolina Gold Rice. The International Rice Genome Sequencing Project (IRGSP) genome is the reference for gene expression and pathway information, and was used to build 27 cross-rice synteny maps. Gene trees are foundational for pan-genomes, supporting traversal and within-species analyses. 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. We provide various views 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. We work with the community to coordinate data stewardship, training and feedback. Gramene Oryza is funded by USDA-ARS-8062-21000-044-00D.