Data from: Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower

Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant - having both retained more genes and being more highly expressed - a phenomenon termed subgenome dominance. The genomic features that determine how quickly and which subgenome dominates within a newly formed polyploid remain poorly understood. To investigate the rate of subgenome dominance emergence, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural, less than 140 year old allopolyploid (Mimulus peregrinus), a resynthesized inter-species triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and diploid progenitors (M. guttatus and M. luteus). We show that subgenome expression dominance occurs instantly following the hybridization of two divergent genomes and significantly increases over generations. Additionally, CHH methylation levels are significantly reduced in regions near genes and within TEs in the first generation hybrid, intermediate in the resynthesized allopolyploid, and are repatterned differently between the dominant and recessive subgenomes in the natural allopolyploid. In addition, subgenome differences in levels of TE methylation mirror the increase in expression bias observed over the generations following hybridization. These findings provide important insights into genomic and epigenomic shock that occurs following hybridization and polyploid events.

过往研究表明，古多倍体（ancient polyploids）的亲本亚基因组中通常存在一个更具主导性的亚基因组——该亚基因组不仅保留了更多基因，且表达水平也更高——这一现象被称为亚基因组优势（subgenome dominance）。目前学界对于新形成多倍体中，亚基因组主导的发生速率以及决定哪一个亚基因组占据主导的基因组特征仍知之甚少。为探究亚基因组优势的出现速率，本研究对天然异源多倍体（诞生不足140年的Mimulus peregrinus）、人工合成种间三倍体杂种（M. robertsii）、人工合成异源多倍体（M. peregrinus）以及二倍体亲本（M. guttatus与M. luteus）的基因表达、基因甲基化及转座因子（transposable element, TE）甲基化水平进行了检测。本研究发现，两个分化基因组杂交后，亚基因组表达优势会即刻显现，并随世代推移显著增强。此外，第一代杂种的基因附近区域及转座因子内的CHH甲基化水平显著降低，人工合成异源多倍体的该甲基化水平处于中间状态，而天然异源多倍体中显性与隐性亚基因组的甲基化模式重塑存在显著差异。不仅如此，转座因子甲基化水平的亚基因组差异，与杂交后世代间表达偏倚的增强趋势相一致。本研究结果为杂交与多倍化事件引发的基因组及表观基因组震荡提供了重要见解。