Virgen Andres Lopez, Yadav Narendra Singh, Byeon Boseon, Ilnytskyy Yaroslav, Kovalchuk Igor
Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada.
Biomedical and Health Informatics, Computer Science Department, State University of New York, 2 S Clinton St, Syracuse, NY 13202, USA.
Life (Basel). 2025 Mar 20;15(3):502. doi: 10.3390/life15030502.
Continuous exposure to stress contributes to species diversity and drives microevolutionary processes. It is still unclear, however, whether epigenetic changes, in the form of epimutations such as, for example, differential DNA methylation, are the pre-requisite to speciation events. We hypothesized that continuous stress exposure would increase epigenetic diversity to a higher extent than genetic diversity. In this work, we have analyzed the effect of 25 consecutive generations of UV-C-stress exposure on the genome and epigenome. We found no evidence of increased tolerance to UV-C in the progeny of UV-C-stressed plants (F25UV) as compared to the progeny of control plants (F25C). Genetic analysis showed an increased number of single nucleotide polymorphisms (SNPs) and deletions in F25UV plants. Most common SNPs were mutations in cytosines, C to T, C to A, and C to G. Analysis of cytosine methylation showed a significant increase in the percentage of methylated cytosines at CG context in F25UV as compared to F25C or F2C (parental control). The most significant differences between F25UV and either control group were observed in CHG and CHH contexts; the number of hypomethylated cytosines at CHH contexts was over 10 times higher in the F25UC group. F25UV plants clustered separately from other groups in both genomic and epigenomic analyses. GO term analysis of differentially methylated genes revealed enrichments in "DNA or RNA metabolism", "response to stress", "response to biotic and abiotic stimulus", and "signal transduction". Our work thus demonstrates that continuous exposure to UV-C increases genomic and epigenomic diversity in the progeny, with epigenetic changes occurring in many stress-responsive pathways.
持续暴露于压力下有助于物种多样性并推动微观进化过程。然而，表观遗传变化，如差异DNA甲基化等表观突变形式，是否是物种形成事件的先决条件仍不清楚。我们假设持续的压力暴露会比遗传多样性更大程度地增加表观遗传多样性。在这项工作中，我们分析了连续25代暴露于UV-C压力对基因组和表观基因组的影响。我们发现，与对照植物的后代（F25C）相比，UV-C胁迫植物的后代（F25UV）对UV-C的耐受性没有增加的证据。遗传分析表明，F25UV植物中单核苷酸多态性（SNP）和缺失的数量增加。最常见的SNP是胞嘧啶的突变，C突变为T、C突变为A和C突变为G。胞嘧啶甲基化分析表明，与F25C或F2C（亲本对照）相比，F25UV中CG背景下甲基化胞嘧啶的百分比显著增加。在CHG和CHH背景下观察到F25UV与任一对照组之间最显著的差异；F25UC组中CHH背景下低甲基化胞嘧啶的数量比其他组高10倍以上。在基因组和表观基因组分析中，F25UV植物与其他组分别聚类。对差异甲基化基因的GO术语分析揭示了在“DNA或RNA代谢”、“对压力的反应”、“对生物和非生物刺激的反应”以及“信号转导”方面的富集。因此，我们的工作表明，持续暴露于UV-C会增加后代的基因组和表观基因组多样性，且表观遗传变化发生在许多应激反应途径中。
