Data from: Insights into the maize pan-genome and pan-transcriptome

Genomes at the species level are dynamic, with genes present in every
individual (core) and genes in a subset of individuals (dispensable) that
collectively constitute the pan-genome. Using transcriptome sequencing of
seedling RNA from 503 maize (Zea mays) inbred lines to characterize the
maize pan-genome, we identified 8681 representative transcript assemblies
(RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of
the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of
the RTAs with at least one single nucleotide polymorphism (SNP) could be
mapped to a single genetic position, distributed primarily throughout the
nonpericentromeric portion of the genome. Stepwise iterative clustering of
RTAs suggests, within the context of the genotypes used in this study,
that the maize genome is restricted and further sampling of seedling RNA
within this germplasm base will result in minimal discovery. Genome-wide
association studies based on SNPs and transcript abundance in the
pan-genome revealed loci associated with the timing of the
juvenile-to-adult vegetative and vegetative-to-reproductive developmental
transitions, two traits important for fitness and adaptation. This study
revealed the dynamic nature of the maize pan-genome and demonstrated that
a substantial portion of variation may lie outside the single reference
genome for a species.