Gramene Maize Release 4 is out with the Teosinte Til11 Genome and Expression Tracks from the MaizeCODE and NAM Projects!

The Gramene Maize Knowledgebase Team is pleased to announce its fourth data release with the following highlights:

• Comparative Genomics:

  • Addition of a new maize reference genome, Til11, to a total of 35 maize genomes.

  • Curated gene function with literature references for 357 maize genes.

  • Comparative genomics collection of 35,360 phylogenetic trees.

  • 143 pairwise synteny maps comparing all maize genomes with Zea mays B73 v5, Arabidopsis, rice, and sorghum.

• New Search Features:

  • New Sequences tab in gene search results provides quick access to gene, transcript and protein sequences for a gene model.

  • Expression tab now shows an eFP browser, an alternative visualization tool for researchers to explore which genes are expressed in which parts of the plant, and at what levels.

  • Papers tab now has a user entry form to suggest gene function given experimental evidence.

• New Gene Expression Data: 

  • Genome browser:

    • MaizeCODE data: New tracks with RNA (RNA-seq, RAMPAGE and shRNA-seq) and chIP-seq (H3K27ac, H3Kme3, H3K4me1) data for four genomes: Til11, B73, NC350 and W22, in immature ears, endosperm, root tips, coleoptilar tips and pollen; and TF ChIP-seq data (GT1, HDZIV6, TU1A) for B73 in immature ears.

    • NAM data: New RNAseq tracks across the 26 NAM maize genomes.

  • Gramene Search:

    • eFP browser: Gene expression from 12 studies displayed in the BAR eFP browser section of the Expression tab.

    • EBI Atlas widget: 7 newly curated studies to a total of 32 with baseline expression (and 57 with differential expression) available for the reference genome Z. mays B73 v5.

• New Pathways Data:

  • Additional orthology-based pathway projections to a total of 270 are available for the reference genome Z. mays B73 v5 via the Search functionality.

For more details, visit our Release Notes.