DOI: 10.5061/dryad.r73c5
title: Data from: Insights into the maize pan-genome and pan-transcriptome

description: 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.
description: Fragments per kilo base
 of exon model perl million fragments mapped (FPKM) values for 503 diverse
 maize inbred lines.This file is a tab
 delimited file with a header line. The columns in the file are gene name,
 chromosome, gene start, and gene stop followed by the expression data for
 the 503 inbred lines.maize_503genotypes_raw_expression_values_FPKM.txtSingle Nucleotide Polymorphisms (SNPs) for 503 diverse maize inbred lines.This is a tab delimited file with a header line that contains raw SNP data for 485,179 SNPs across 503 diverse maize inbred lines. The file contains a column for chromosome, position, the reference B73 v2 allele, number of missing data points, and observed alleles across the 503 inbred lines, followed by the data for the 503 inbred lines.maize_503genotypes_485179SNPs_working_SNP_set.txtTranscript assemblies for representative transcripts generated in individual assemblies for 366 diverse maize inbred lines.The assemblies were generated from reads that could not be mapped to the maize v2 reference sequence. Only the representative transcript assembly for each locus, defined as the longest transcript within the locus, is presented in the file.individual_assembly_747977_RTAs.fastaTranscript assemblies for representative transcripts generated in a joint assembly across 503 diverse maize inbred lines.The assembly was generated from reads that could not be mapped to the maize v2 reference sequence. Only the representative transcript assembly for each locus, defined as the longest transcript within the locus, is presented in the file.joint_assembly_8681_RTAs.fastaGenome wide association study (GWAS) results for growing degree days to pollen shed, growing degree days to silk, and last leaf with juvenile wax.The file is a tab delimated file with a header that contains GWAS results presented as p-values for ~438K SNPs. The columns in the file are SNP, chromosome, position, growing degree days to pollen shed p- values, growing degree days to silk p-values, and last leaf with juvenile wax p-values.438K_Imputed_GWASresults_withRTA.txtImputed Genotype Scores 438K Single Nucleotide Polymorphisms across 503 diverse maize inbred linesThe file is a CSV file with a header that contains genotype scores imputed using GAPIT.GAPIT.RNAseq.hmp_438K_imputed2.csv