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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 #402118

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

Location: Plant, Soil and Nutrition Research

Title: Gramene PanMaize: One-stop pan-genome browser for exploring the rich genetic diversity in maize

item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item GEORGE, NANCY - Embl-Ebi
item Ware, Doreen

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 project has developed pan-genome subsites, as a natural extension of the Gramene and Ensembl infrastructures. Each pan-genome site is dedicated to the study of individual crop groups (e.g., maize, rice, sorghum, and grape). The Gramene project ( was a key player in sequencing the first maize reference B73, more recently the 25 NAM founders, and continues to be engaged with the community. The maize pansite (, established in 2021, hosts reference assemblies for 26 maize accessions. Each maize accession is hosted in a separate genome browser, providing access to gene-based views with entry points via text-based searches or through BLAST. The B73 V5 genome serves as the reference assembly for anchoring expression, population and pathway views; transcript abundance across a gene model at different tissues and stages of development and views of paralog expression support decision making on candidate gene selection. Phylogenetic analyses are based on maize-specific gene trees built from the assigned canonical protein for each gene locus. The protein-based trees allow users to rapidly traverse between the different maize accessions, where alleles are considered orthologs in the trees, as well as other species; copy-number variations within maize can also be evaluated alongside lineage-specific gene expansions. Protein homology is viewable as amino acid alignments and as gene neighborhood conservation. We adapted these views to deploy community curation tools–from the homology tab–for users to flag potential structural annotation issues. More recent work has used these gene trees to build a pan-gene index used as the inputs to improve and extend the previous gene structural annotation workflow. Release 3 will include updated annotations and access to the teosinte reference genome, expression, and Maize ENCODE (NSF-IOS-1445025) related studies. Funded by USDA-ARS-8062-21000-044-00D.