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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 #402103

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

Location: Plant, Soil and Nutrition Research

Title: Gramene 2023: An online resource for plant reference genomes, pan-genomes and plant reactome pathways

item OLSON, ANDREW - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item OLSON, AUDRA - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item ZHANG, LIFANG - Cold Spring Harbor Laboratory
item Ware, Doreen
item ELSER, JUSTIN - Oregon State University
item GUPTA, PARUL - Oregon State University
item NAITHANI, SUSHMA - Oregon State University
item GEORGE, NANCY - Embl-Ebi
item NAAMATI, GUY - Embl-Ebi
item FERRERO-SERRANO, ANGEL - Pennsylvania State University
item D'EUSTACHIO, PETER - Nyu Langone Health
item ASSMAN, SARAH - Pennsylvania State University
item DYER, SARAH - Embl-Ebi
item PAPTHEIODOROU, IRENE - Oregon State University
item JAISWAL, PANKAJ - Oregon State University

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/13/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The Gramene resource is an integrated comparative genomics platform that has been extended to include multiple pan-genome sites focused on rice, maize, sorghum, and grapevine. Researchers focused on a particular crop now have access to genome browsers for multiple assembled genomes, protein coding gene trees, and pairwise genome alignments and synteny maps. Each of the sites includes a community reference genome from rice, maize, sorghum and grapevine as well as from outgroups; poplar, arabidopsis, selaginella and chlamydomonas. These community reference genomes provide functional annotation that can be projected via orthology to the crop species of interest. In total, Gramene hosts 125 plant reference genomes, pan- genomes from 28 rice, 26 maize, 28 sorghum, and 18 grapevine genomes, nearly 1000 gene expression datasets from EBI Expression Atlas, and Plant Reactome pathways from 120 species. Pathway Browsers allow users to upload, analyze, and visualize their own omics data. The CLIMtools portal provides interactive views of environment x genome associations, RiboSNitch predictions, and correlations between the environment and curated phenotypes for Arabidopsis. Gramene supports open access and reproducible science, based on the FAIR data principles, and encourages researchers to contact them for data hosting and sharing. Funded by USDA-ARS (8062-21000-044-00D).