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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 #402115
Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: Gramene: comparative plant genome resource

Author
item Ware, Doreen
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item Gladman, Nicholas
item OLSON, AUDRA - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item ELSER, JUSTIN - Oregon State University
item GUPTA, PAUL - Oregon State University
item NAITHANI, SUSHMA - Oregon State University
item GEORGE, NANCY - Embl-Ebi
item NAAMATI, GUY - Embl-Ebi
item D'EUSTACHIO, PETER - Nyu Langone Health
item DYER, SARAH - Embl-Ebi
item PAPATHEODOROU, IRENE - Embl-Ebi
item JAISWAL, PANKAJ - Oregon State University

Submitted to: Maize Genetics Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 3/16/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The Gramene knowledgebase (www.gramene.org), established in 2002, was the first comparative plant genome database. Twenty one years later, the project has grown from hosting one crop genome to 128 plant genomes. Scaling the data has required collaborations, development of standards, dedication to FAIR principles. Gramene is built on public data available in archival resources and established standards, including software and workflows to provide added value and ease of data access. The current release 66 (December 2023) features 128 reference genomes, population data from 15 species, as well as expression data for 28 species. The genomes are inputs to the added value workflows, including whole-genome DNA alignments, and protein-based gene trees. The over 152K gene family trees provide insights on evolution and adaptation between eukaryotes, fly, yeast and worm, and expansion of the plant species from moss to flowering plants. We provide views to interrogate gene tree data, including amino acid alignments and gene neighborhood conservation, and have worked with different communities to curate the protein alignments to infer mis-annotations of gene structures. Expression information is available for multiple tissues and conditions and links to EBI-Atlas for more detailed information on each experiment. Where genetic variation data is available, SNPs are easily viewed and filtered based on their predicted functional effect (missense, stop-gained, etc.), impact (SIFT), and downloadable as images and tables. Genes can be queried via text-based searches and sequence-based BLAST. B73 accession serves as the maize reference assembly, and can be used to traverse to orthologs and paralogs for other species, enabling phylogenetic inference, insights of allelic genes within and across species, variation data, as well as lineage specific expansion and contraction, and synteny maps. We work with the community to coordinate data stewardship, training and feedback. Gramene is funded by USDA-ARS-8062-21000-044-00D.