Data from: An updated gene atlas for maize reveals organ-specific and stress-induced genes

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)