Table_12_Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization.XLSX

The formation of interspecific hybrids results in the coexistence of two diverged genomes within the same nucleus. It has been hypothesized that negative epistatic interactions and regulatory interferences between the two sub-genomes may elicit a so-called genomic shock involving, among other alterations, broad transcriptional changes. To assess the magnitude of this shock in hybrid yeasts, we investigated the transcriptomic differences between a newly formed Saccharomyces cerevisiae × Saccharomyces uvarum diploid hybrid and its diploid parentals, which diverged ∼20 mya. RNA sequencing (RNA-Seq) based allele-specific expression (ASE) analysis indicated that gene expression changes in the hybrid genome are limited, with only ∼1–2% of genes significantly altering their expression with respect to a non-hybrid context. In comparison, a thermal shock altered six times more genes. Furthermore, differences in the expression between orthologous genes in the two parental species tended to be diminished for the corresponding homeologous genes in the hybrid. Finally, and consistent with the RNA-Seq results, we show a limited impact of hybridization on chromatin accessibility patterns, as assessed with assay for transposase-accessible chromatin using sequencing (ATAC-Seq). Overall, our results suggest a limited genomic shock in a newly formed yeast hybrid, which may explain the high frequency of successful hybridization in these organisms.

种间杂种的形成会导致两个已发生分化的基因组共存于同一细胞核内。已有假说认为，两个亚基因组间的负上位性相互作用与调控干扰可能引发所谓的基因组冲击（genomic shock），除其他改变外，该冲击还涉及广泛的转录组变化。为评估该基因组冲击在杂种酵母中的强度，我们对新形成的酿酒酵母（Saccharomyces cerevisiae）×乌瓦酵母（Saccharomyces uvarum）二倍体杂种与其二倍体亲本间的转录组差异展开了研究，二者的分化时间约为2000万年前。基于RNA测序（RNA-Seq）的等位基因特异性表达（ASE）分析结果显示，杂种基因组中的基因表达变化幅度有限：仅约1%~2%的基因相较于非杂种背景发生了显著表达改变。相较而言，热冲击诱导的基因表达改变量是其六倍。此外，两个亲本物种间直系同源基因的表达差异，在杂种中对应的部分同源基因上呈现出减弱趋势。最后，与RNA-Seq结果一致，通过转座酶可及性测序（assay for transposase-accessible chromatin using sequencing, ATAC-Seq）评估的结果显示，杂交对染色质可及性模式的影响同样有限。总体而言，本研究结果表明新形成的酵母杂种仅存在有限的基因组冲击，这或许可以解释此类物种中成功杂交事件发生频率较高的原因。