Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France.
Corteva Agriscience, The V Ascendas, Atria Block, 12th Floor, Madhapur, Hyderabad, 500081, India.
Sci Rep. 2021 Feb 3;11(1):2954. doi: 10.1038/s41598-021-82529-1.
Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diatom Fragilariopsis cylindrus in association with adaptation to external cues, as well as in Fistulifera solaris in the context of natural hybridization. However, the role of aASE and its extent in diatoms remain elusive. In this study, we investigate allele-specific expression in the model diatom Phaeodactylum tricornutum by the re-analysis of previously published whole genome RNA sequencing data and polymorphism calling. We found that 22% of P. tricornutum genes show moderate bias in allelic expression while 1% show nearly complete monoallelic expression. Biallelic expression associates with genes encoding components of protein metabolism while moderately biased genes associate with functions in catabolism and protein transport. We validated candidate genes by pyrosequencing and found that moderate biases in allelic expression were less stable than monoallelically expressed genes that showed consistent bias upon experimental validations at the population level and in subcloning experiments. Our approach provides the basis for the analysis of aASE in P. tricornutum and could be routinely implemented to test for variations in allele expression under different environmental conditions.
新一代测序技术的最新进展使得人们能够发现哺乳动物和植物中广泛存在的常染色体等位基因特异性表达（aASE），其具有潜在的表型效应。在与适应外部线索相关的硅藻脆杆藻以及在自然杂交背景下的 Fistulifera solaris 中，已经描述了大量具有等位基因特异性表达的基因。然而，aASE 的作用及其在硅藻中的程度仍然难以捉摸。在这项研究中，我们通过重新分析先前发表的全基因组 RNA 测序数据和多态性调用，研究了模式硅藻三角褐指藻中的等位基因特异性表达。我们发现，22%的三角褐指藻基因表现出中等程度的等位基因表达偏倚，而 1%的基因表现出几乎完全的单等位基因表达。双等位基因表达与编码蛋白质代谢成分的基因相关，而中度偏倚的基因与分解代谢和蛋白质转运的功能相关。我们通过焦磷酸测序验证了候选基因，发现等位基因表达的中度偏倚不如单等位基因表达的基因稳定，单等位基因表达的基因在群体水平和亚克隆实验的实验验证中表现出一致的偏倚。我们的方法为三角褐指藻中 aASE 的分析提供了基础，并可以常规实施，以测试不同环境条件下等位基因表达的变化。
