Gramene Maize PanGenome is released with 25 new NAM founder genomes

Maize PanGenome Release 2.0

Released: July, 2021

Gramene's Maize Pan-Genome (maize-pangenome.gramene.org) is a web portal for comparative plant genomics focused on maize (Zea mays) crop varieties built with open source components including the Ensembl genome browser, the Plant Reactome pathway portal, and the Expression Atlas data widget. The site provides access to a total of 35 assembled genomes, including the 25 maize NAM founders and an updated version 5 of the B73 reference described by Hufford et al (2021). For backward compatability, we also offer versions 3 and 4 of the B73 reference. For this first official release, the Gramene team contributed maize gene annotations constructed with a genome annotation workflow that uses Mikado, an approach to integrate transcript assemblies (Venturini et al, 2018), and BRAKER, an eukaryotic gene prediction pipeline (Hoff et al, 2019), and canonical transcripts selected for downstream analysis with a new tool that integrates gene expression data with length criteria (Olson and Ware, 2021). For more information see the NAM genomes Project and MaizeGDB's NAM Project pages.

The maize gene models, together with seven outgroups (Arabidopsis thaliana, Oryza sativa Japonica, Sorghum bicolor, Vitis vinifera ssp. vinifera PN40024 v3, Selaginella moellendorffii, Chlamydomonas reinhardtii, and Drosophila melanogaster) were used to build 31,412 protein-coding gene family trees. Data from 25 baseline gene expression studies from the Expression Atlas, and 269 orthology-based pathway projections from the Plant Reactome are also provided for B73 (APGv4).

The genome databases were built in direct collaboration with the Gramene and Ensembl Plants projects. Other data sets were facilitated via collaborations with the Expression Atlas, and the Plant Reactome databases. Core funding for the project was provided by the National Sciene Foundation (NSF IOS-1127112) and the Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 8062-21000-041-00D) to the Ware Lab at the Cold Spring Harbor Laboratory.

For aditional details, please see the release notes at the Gramene Maize Pan-Genome site.

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