DataSheet_3_Gene Expression Changes During the Allo-/Deallopolyploidization Process of Brassica napus.xlsx

Gene expression changes due to allopolyploidization have been extensively studied in plants over the past few decades. Nearly all these studies focused on comparing the changes before and after genome merger. In this study, we used the uniquely restituted Brassica rapa (RBR, AeAe, 2n = 20) obtained from Brassica napus (AnAnCnCn, 2n = 38) to analyze the gene expression changes and its potential mechanism during the process of allo-/deallopolyploidization. RNA-seq-based transcriptome profiling identified a large number of differentially expressed genes (DEGs) between RBR and natural B. rapa (ArAr), suggesting potential effects of allopolyploidization/domestication of AA component of B. napus at the tetrapolyploid level. Meanwhile, it was revealed that up to 20% of gene expressions were immediately altered when compared with those in the An-subgenome. Interestingly, one fifth of these changes are in fact indicative of the recovery of antecedent gene expression alternations occurring since the origin of B. napus and showed association with homoeologous expression bias between An and Cn subgenomes. Enrichment of distinct gene ontology (GO) categories of the above sets of genes further indicated potential functional cooperation of the An and Cn subgenome of B. napus. Whole genome methylation analysis revealed a small number of DEGs were identified in the differentially methylated regions.

近几十年来，异源多倍化（allopolyploidization）引发的基因表达变化在植物领域得到了广泛研究。此类研究几乎均聚焦于基因组融合前后的基因表达差异对比。本研究利用从甘蓝型油菜（Brassica napus, AnAnCnCn, 2n=38）中获得的独特恢复型白菜型油菜（Brassica rapa, RBR, AeAe, 2n=20），分析异源多倍化/去多倍化过程中的基因表达变化及其潜在分子机制。基于RNA测序（RNA-seq）的转录组分析鉴定出RBR与天然白菜型油菜（ArAr）间存在大量差异表达基因（differentially expressed genes, DEGs），提示甘蓝型油菜AA组分在四倍体水平上的异源多倍化/驯化可能产生了相应影响。同时，研究发现相较于甘蓝型油菜的An亚基因组，高达20%的基因表达在RBR中发生了快速改变。有趣的是，其中五分之一的变化实则反映了自甘蓝型油菜起源以来便存在的先前基因表达差异的恢复，且这类变化与An与Cn亚基因组间的部分同源基因表达偏倚存在关联。对上述基因集合的基因本体（Gene Ontology, GO）类别富集分析进一步表明，甘蓝型油菜的An与Cn亚基因组可能存在功能协同作用。全基因组甲基化分析显示，在差异甲基化区域中仅鉴定出少量差异表达基因。