Supporting data for "Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat"

Polyploidy is centrally important in the evolution and domestication of plants as it leads to major genomic-scale changes, such as altered patterns of gene expression, which are thought to underlie the emergence of new traits. Despite the common occurrence of these globally altered patterns of gene expression in polyploids, the mechanisms involved are currently not well understood.
Using a precisely defined framework of highly conserved syntenic genes on hexaploid wheat chromosome 3DL and its progenitor 3L chromosome arm of diploid Aegilops tauschii, we show that 70% of these gene pairs exhibited proportionately reduced gene expression, in which expression in the hexaploid context of the 3DL genes was approximately 40% of the levels observed in diploid Ae. tauschii.. Approximately 30% of genes were differentially expressed, including several genes with elevated expression during the later stages of grain development in wheat compared to Ae. tauschii. Gene sequence and methylation differences accounted for approximately 11% of the differences in gene expression. In contrast, over 80% of genes with differential expression exhibited altered patterns of chromatin accessibility of genes in the hexaploid chromosome arm compared to its diploid progenitor. An overall reduction in chromatin accessibility across regulatory regions of genes was observed in the hexaploid context compared to the diploid Ae. tauschii context.
These chromosome arm analyses show that differential chromatin accessibility may underlie differences in gene expression in hexaploid chromosome arm of wheat compared to its diploid progenitor chromosome arm.