Skip to main content
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 #397005

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

Location: Plant, Soil and Nutrition Research

Title: Gramene 2022: an online resource for plant reference genomes, pan-genomes and plant reactome pathways

item ZHANG, LIFANG - Cold Spring Harbor Laboratory
item Ware, Doreen

Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 6/2/2022
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Continued advances in genome sequencing, assembly, and annotation are generating an abundance of high-quality reference and pan-genomes for crops and other plant species, besides extending the genome-based genotype and phenotype studies. To help researchers conduct knowledge discovery and hypothesis building using a diversity of data and data sources, Gramene ( provides an integrated comparative genomics resource for plant genomics. It hosts 118 plant reference genomes, pangenomes from 28 rice, 26 maize, 18 sorghum, and 18 grapevine genomes, ~900 gene expression datasets from EBI Expression Atlas, and Plant Reactome pathway networks from 120 species. In addition, almost 6 million genes from 89 genomes are clustered and classified into 124K gene family trees, 320 pairwise genome alignments, and 80 synteny graphs to compare macro and micro-level genetic colinearity views. The gene trees provide evolutionary insights on gene duplications, gains and losses, help predict the putative function of orthologs, and allow users to compare gene structures and functional annotations through conservation between species. Gramene’s Genome Browser and Pathway Browser both allow uploading, analysis, and visualization of user-defined omics data. The new Pangenome sites for maize, rice, grapevine and sorghum are now accessible from Gramene’s homepage. The pansites allow users to compare multiple genomes from the same clade by aligning against the annotated genome representative. Another new feature includes the CLIMtools portal, which provides interactive web-based views of environment x genome associations, RiboSNitch prediction, and correlations between the growth environment and curated phenotypes. Currently CLIMtools hosts data for Arabidopsis pan-genomes. Researchers are encouraged to contact us for hosting and sharing their data via Gramene. We support open access and reproducible science, based on the FAIR data principles. Funding support for Gramene is provided by NSF (IOS-1127112) and USDA-ARS (8062-21000-041-00D), and for CLIMtools by NSF (IOS-2122357).