DOI: 10.5061/dryad.5p58q34
title: Data from: An updated gene atlas for maize reveals organ-specific and stress-induced genes

description: Maize(Zea mays L.), a model species for genetic studies, is one of the two
 most important crop species worldwide.The genome sequence of the reference
 genotype, B73, representative of the stiff stalk heterotic group was
 recently updated (AGPv4) using long‐read sequencing and optical mapping
 technology. To facilitate the use of AGPv4 and to enable functional
 genomic studies and association of genotype with phenotype, we determined
 expression abundances for replicated mRNA‐sequencing datasets from 79
 tissues and five abiotic/biotic stress treatments revealing 36,207
 expressed genes. Characterization of the B73 transcriptome across six
 organs revealed 4,154 organ‐specific and 7,704 differentially expressed
 genes following stress treatment. Gene co‐expression network analyses
 revealed 12 modules associated with distinct biological processes
 containing 13,590 genes providing a resource for further association of
 gene function based on co‐expression patterns. Presence/absence variants
 (PAVs) previously identified using whole genome resequencing data from 61
 additional inbred lines were enriched in organ‐specific and stress‐induced
 differentially expressed genes, suggesting PAVs may function in
 phenological variation and adaptation to environment. Relative to core
 genes conserved across the 62 profiled inbreds, PAVs have lower expression
 abundances which are correlated with their frequency of dispersion across
 inbreds and on average, have significantly fewer co‐expression network
 connections suggesting that a subset of PAVs may be on an evolutionary
 path to pseudogenization. To facilitate use by the community, we developed
 the Maize Genomics Resource website(maize.plantbiology.msu.edu) for
 viewing and data‐mining these resources and deployed two new views on the
 Maize electronic Fluorescent Pictograph Browser (bar.utoronto.
 ca/efp_maize)
description: Zea_mays.MSU.gene.info.txtMSU functional gene annotation and information for AGPv4 maize genes, including representative transcript informationZea_mays.MSU.InterPro.hits.txtInterPro (v67.0) matches to AGPv4 maize transcriptsZea_mays.MSU.PFAM.hits.txtPFAM (v31.0) matches to AGPv4 maize transcriptsZea_mays.MSU.GO.terms.transcr.txtGene Ontology term assignments for AGPv4 transcripts identified from the InterPro hitsZea_mays.MSU.GO.terms.gene.txtGene Ontology term assignments for AGPv4 genes identified from InterPro hitsZea_mays.OrthoFinder.by.orthogroup.csvOrthologous and paralogous groups identified by OrthoFinder listed by OrthoGroup IDZea_mays.OrthoFinder.by.Zm.txtOrthologous and paralogous groups identified by OrthoFinder listed by AGPv4 maize geneZea_mays.OrthoFinder.Statistics.Overall.csvTable summary of the OrthoFinder overall resultsZea_mays.OrthoFinder.Statistics.PerSpecies.csvTable summary of the OrthoFinder results per speciesZea_mays.OrthoFiner.SpeciesTree.nxsRooted species tree outputted by OrthoFinderZea_mays.OrthoFinder.SpeciesTree.node.labels.txtSpecies node labels for the rooted species treeZea_mays.OrthoFinder.gene.trees.tar.gzZipped folder containing the trees for each orthologous and paralogous groupsZea_mays.RNA-seq.libraries.xlsxList of RNA-seq libraries analyzedZea_mays.MSU.FKPM.matrix.txtFPKM matrix for AGPv4 genesZea_mays.MSU.FKPM.matrix.log2.flt1.txtLog-2 transformed FPKM matrix of genes which had an FPKM &gt; 1 in at least one sampleZea_mays.PAV.by.Inbred.txtPAV matrix where an AGPv4 gene considered a PAV is listed by inbred; data comes from Brohammer et al. (2018) (https://doi.org/10.1111/tpj.13765)Zea_mays.PAV.freq.txtFrequency of inbreds missing the AGPv4 gene; data comes from Brohammer et al. (2018) (https://doi.org/10.1111/tpj.13765)Zea_mays.WGCNA.gene.list.zipZipped folder containing list of genes in each moduleZea_mays.WGCNA.FPKM.matrix.zipZipped folder containing log-2 transformed FPKM values for the genes in each moduleZea_mays.WGCNA.Z_score.matrix.zipZipped folder containing Z score expression values for the genes in each moduleZea_mays.WGCNA.Z_score.graph.zipZipped folder containing Z score expression values plotted by library sampleZea_mays.WGCNA.network.edges.txtTable of WGNCA network connectionsZea_mays.WGCNA.network.nodes.txtTable of WGCNA network nodesZea_mays.WGCNA.Cytoscape.Network.cysCytoscape file for the WGCNA networkREADME.txtREADME.txt