Subgenome-dominant expression and alternative splicing in response to pathogen stress in polyploid Brassica napus and progenitors

Polyploidy has played an extensive role in the evolution of flowering plants. Allopolyploids, with subgenomes containing duplicated gene pairs called homeologs, can show rapid transcriptome changes including novel alternative splicing (AS) patterns. The extent to which abiotic stress modulates AS of homeologs is a nascent topic in polyploidy research. We subjected both natural and resynthesized lines of polyploid Brassica napus, along with the progenitors B. rapa and B. oleracea, to infection with the fungal pathogen Sclerotinia sclerotiorum. RNA-seq analyses revealed widespread divergence between polyploid subgenomes in both gene expression and AS patterns. Resynthesized B. napus displayed significantly more A and C subgenome biased homeologs under pathogen infection than during uninfected growth. Differential AS (DAS) in response to infection was highest in natural B. napus (12,709 DAS events) and lower in resynthesized Brassica napus (8,863 DAS events). Natural B. napus had more up-regulated events and fewer down-regulated events. There was a global expression bias towards the B. oleracea-derived (C) subgenome in both resynthesized and natural B. napus, enhanced by widespread non-parental downregulation of the B. rapa-derived (A) homeolog. In the resynthesized B. napus specifically, this resulted a disproportionate C subgenome contribution to pathogen defense response, characterized by biases in both transcript expression levels and the proportion of induced genes. Our results elucidate the complex ways in which Sclerotinia infection affects expression and AS of homeologous genes in natural and resynthesized B. napus, and indicate that abiotic stress can influence the evolution of homeologous genes in polyploids. Comparative gene expression profiling and alternative splicing analyses in Sclerotinium sclerotiorum-infected and control mock-infected leaves of Brassica napus (natural and resynthesized polyploids) and progenitors Brassica rapa and Brassica oleracea.

多倍体化(Polyploidy)在显花植物(flowering plants)的演化进程中发挥了广泛作用。异源多倍体(allopolyploids)的亚基因组(subgenomes)包含被称为部分同源基因(homeologs)的重复基因对，可表现出快速的转录组(transcriptome)变化，包括新型可变剪接(alternative splicing, AS)模式。非生物胁迫对部分同源基因可变剪接的调控程度，是多倍体研究领域中的新兴议题。
我们将天然及人工合成的多倍体甘蓝型油菜(Brassica napus)品系，与其亲本芸薹(B. rapa)和甘蓝(B. oleracea)一同进行核盘菌(Sclerotinia sclerotiorum)侵染处理。RNA测序(RNA-seq)分析显示，多倍体亚基因组在基因表达与可变剪接模式上均存在广泛分化。人工合成甘蓝型油菜在病原菌侵染条件下，表现出的A、C亚基因组偏向性部分同源基因数量，显著高于未感染生长状态。
响应侵染的差异可变剪接(Differential AS, DAS)事件数量在天然甘蓝型油菜中最高（12,709个DAS事件），人工合成甘蓝型油菜中则为8,863个，数量较低。天然甘蓝型油菜的上调剪接事件更多，下调剪接事件更少。
在人工合成与天然甘蓝型油菜中，均存在全局表达偏向于甘蓝来源（C亚基因组）的现象，这一偏向因芸薹来源（A亚基因组）部分同源基因的广泛非亲本型下调而进一步加剧。
仅在人工合成甘蓝型油菜中，这一现象导致C亚基因组对病原菌防御响应的贡献不成比例地偏高，具体表现为转录表达水平与诱导基因占比均存在偏向性。
我们的研究结果阐明了核盘菌侵染如何通过复杂途径影响天然与人工合成甘蓝型油菜中部分同源基因的表达与可变剪接，并表明非生物胁迫可影响多倍体中部分同源基因的演化。
本数据集涵盖经核盘菌侵染与模拟侵染对照处理的甘蓝型油菜（天然及人工合成多倍体）及其亲本芸薹、甘蓝的叶片的比较基因表达谱分析与可变剪接分析数据。