Gramene Maize PanGenome 3.0 is out with 8 new genomes, MaizeCODE data, and NAM pan-gene annotations & structural variants

Submitted by marcela.karey on Sat, 04/01/2023 - 02:00

Maize PanGenome Release 3.0

Released: March 2023

The Gramene's Maize portal (https://maize-pangenome.gramene.org) is a pan-genome resource for maize. In its third release, find eight new maize genomes consisting of four European flint maize genomes (DK105, EP1, F7 and PE0075 (Haberer et al, 2020), plus Mo17 (Yang et al, 2017), W22 (Springer et al, 2018), PH207 (Hirsch et al, 2016), and A188 (Lin et al, 2021). This adds to a total of 36,021 GeneTree families that were constructed comprising 1,626,507 individual genes from 42 plant genomes with 1,668,034 input proteins.

In addition, we now offer updated pan-gene annotations and structural variation tracks for the NAM parent genomes, maize variation data from Gramene/Ensembl Plants, and manually curated gene models.

  • Eight new maize reference genomes:
  • 36,021 protein-coding gene family trees from 1,668,034 protein sequences
  • Gene expression and orthology-based pathway projections for the reference genome Zea mays B73 v4 and v5
  • Genetic variation from Gramene/Ensembl Plants (HapMap2 and Panzea 2.7 GBS SNPs)
  • Structural variation tracks for the NAM genomes
  • Manually curated gene models track
  • Gene curation user interface

Core funding for the project was provided by the Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 8062-21000-041-00D).