PDF(Pubmed)
Abstract：
The molecular underpinnings and consequences of cycles of whole-genome duplication (WGD) and subsequent gene loss through subgenome fractionation remain largely elusive. Endogenous drivers, such as transposable elements (TEs), have been postulated to shape genome-wide dominance and biased fractionation, leading to a conserved least-fractionated (LF) subgenome and a degenerated most-fractionated (MF) subgenome. In contrast, the role of exogenous factors, such as those induced by environmental stresses, has been overlooked. In this study, a chromosome-scale assembly of the alpine buckler mustard (Biscutella laevigata; Brassicaceae) that underwent a WGD event about 11 million years ago is coupled with transcriptional responses to heat, cold, drought, and herbivory to assess how gene expression is associated with differential gene retention across the MF and LF subgenomes. Counteracting the impact of TEs in reducing the expression and retention of nearby genes across the MF subgenome, dosage balance is highlighted as a main endogenous promoter of the retention of duplicated gene products under purifying selection. Consistent with the \"turn a hobby into a job\" model, about one-third of environment-responsive duplicates exhibit novel expression patterns, with one copy typically remaining conditionally expressed, whereas the other copy has evolved constitutive expression, highlighting exogenous factors as a major driver of gene retention. Showing uneven patterns of fractionation, with regions remaining unbiased, but with others showing high bias and significant enrichment in environment-responsive genes, this mesopolyploid genome presents evolutionary signatures consistent with an interplay of endogenous and exogenous factors having driven gene content following WGD-fractionation cycles.
摘要：
全基因组复制（WGD）循环的分子基础和后果以及随后通过亚基因组分级分离的基因丢失在很大程度上仍然难以捉摸。内生驱动因素，如转座因子，已被假定为塑造全基因组优势和偏倚分级分离，从而导致保守的最小分级分离（LF）和退化的最大分级分离（MF）亚基因组。相比之下,外源性因素的作用，例如由环境压力引起的，被忽视了。大约1100万年前经历了WGD事件的高山巴克勒芥末（Biscutellalaevigata；十字花科）的染色体规模组装与对热的转录反应相结合，冷,干旱和食草动物来评估基因表达如何与MF和LF亚基因组中的差异基因保留相关。抵消转座因子在减少MF亚基因组中附近基因的表达和保留方面的影响，剂量平衡被强调为在纯化选择下保留重复基因产物的主要内源性启动子。与“把爱好变成工作”模式一致，大约三分之一的环境响应重复显示新的表达模式，一个拷贝通常保持有条件表达，而另一个拷贝已经进化了组成型表达，强调外源因素是基因保留的主要驱动因素。显示不均匀的分馏模式，区域保持不偏不倚，而其他区域则显示出高偏倚和环境响应基因的显着富集，这个中多倍体基因组呈现的进化特征与内源性和外源性因素的相互作用相一致,这些因素在WGD分级分离周期后具有驱动的基因含量.
