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.<br> Using a precisely defined framework of highly conserved syntenic genes on hexaploid wheat chromosome 3DL and its progenitor 3L chromosome arm of diploid <i>Aegilops tauschii</i>, 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 <i>Ae. tauschii.</i>Approximately 30% of genes were differentially expressed, including several genes with elevated expression during the later stages of grain development in wheat compared to <i>Ae. tauschii</i>. 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 <i>Ae. tauschii</i> context. <br>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.

多倍体在植物演化与驯化过程中具有核心重要性，因其可引发基因组尺度的重大改变——例如基因表达模式的重塑，而这类改变被认为是新性状诞生的基础。尽管这类全基因组范围的基因表达模式改变在多倍体中普遍存在，但其背后的分子机制目前仍未被充分阐明。<br>本研究以六倍体小麦3DL染色体及其二倍体祖先种节节麦（*Aegilops tauschii*）3L染色体臂上的高度保守同线基因（syntenic genes）为精准界定的研究框架，发现70%的这类基因对呈现出比例性的基因表达下调：3DL基因在六倍体背景下的表达量约为二倍体节节麦中该基因表达水平的40%。约30%的基因呈现差异表达，其中包括若干在小麦籽粒发育后期表达量相较于节节麦显著上调的基因。基因序列与甲基化差异仅能解释约11%的基因表达差异。与之相反，超过80%的差异表达基因在六倍体染色体臂中呈现出染色质可及性模式的改变，相较于其二倍体祖先种。相较于二倍体节节麦背景，六倍体背景下基因调控区域的染色质可及性整体呈现下降趋势。<br>本项染色体臂分析表明，染色质可及性的差异或许是小麦3DL染色体臂与其二倍体祖先染色体臂之间基因表达差异的核心成因。