Chaumier Timothée, Yang Feng, Manirakiza Eric, Ait-Mohamed Ouardia, Wu Yue, Chandola Udita, Jesus Bruno, Piganeau Gwenael, Groisillier Agnès, Tirichine Leila
Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France.
Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, Paris 75005, France.
ISME Commun. 2024 Jan 10;4(1):ycad008. doi: 10.1093/ismeco/ycad008. eCollection 2024 Jan.
Diatoms, a prominent group of phytoplankton, have a significant impact on both the oceanic food chain and carbon sequestration, thereby playing a crucial role in regulating the climate. These highly diverse organisms show a wide geographic distribution across various latitudes. In addition to their ecological significance, diatoms represent a vital source of bioactive compounds that are widely used in biotechnology applications. In the present study, we investigated the genetic and transcriptomic diversity of 17 accessions of the model diatom including those sampled a century ago as well as more recently collected accessions. The analysis of the data reveals a higher genetic diversity and the emergence of novel clades, indicating an increasing diversity within the population structure, compared to the previous study and a persistent long-term balancing selection of genes in old and newly sampled accessions. However, the study did not establish a clear link between the year of sampling and genetic diversity, thereby, rejecting the hypothesis of loss of heterozygoty in cultured strains. Transcript analysis identified novel transcript including noncoding RNA and other categories of small RNA such as PiwiRNAs. Additionally, transcripts analysis using differential expression as well as Weighted Gene Correlation Network Analysis has provided evidence that the suppression or downregulation of genes cannot be solely attributed to loss-of-function mutations. This implies that other contributing factors, such as epigenetic modifications, may play a crucial role in regulating gene expression. Our study provides novel genetic resources, which are now accessible through the platform PhaeoEpiview (https://PhaeoEpiView.univ-nantes.fr), that offer both ease of use and advanced tools to further investigate microalgae biology and ecology, consequently enriching our current understanding of these organisms.
硅藻是浮游植物中的一个重要类群，对海洋食物链和碳固存都有重大影响，因此在调节气候方面发挥着关键作用。这些高度多样化的生物在不同纬度地区广泛分布。除了具有生态意义外，硅藻还是生物活性化合物的重要来源，这些化合物在生物技术应用中被广泛使用。在本研究中，我们调查了17个模式硅藻品系的遗传和转录组多样性，其中包括一个世纪前采集的样本以及最近采集的样本。数据分析显示，与之前的研究相比，其遗传多样性更高，并且出现了新的进化枝，这表明种群结构内的多样性在增加，同时在旧样本和新样本中基因存在持续的长期平衡选择。然而，该研究并未在采样年份与遗传多样性之间建立明确的联系，因此否定了培养菌株中杂合性丧失的假设。转录分析鉴定出了包括非编码RNA和其他类别小RNA（如PiwiRNA）在内的新转录本。此外，使用差异表达以及加权基因共表达网络分析的转录本分析提供了证据，表明基因的抑制或下调不能仅仅归因于功能丧失突变。这意味着其他因素，如表观遗传修饰，可能在调节基因表达中起关键作用。我们的研究提供了新的遗传资源，现在可通过PhaeoEpiview平台（https://PhaeoEpiView.univ-nantes.fr）获取，该平台既易于使用又具备先进工具，可进一步研究微藻生物学和生态学，从而丰富我们目前对这些生物的理解。
