Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico.
Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Department, Texas Tech University, Lubbock, TX, 79409, USA.
Sci Rep. 2021 Aug 3;11(1):15725. doi: 10.1038/s41598-021-95054-y.
The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide DNA methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in small plant genomes with reduced noncoding regions. Because of the small length of intergenic regions in the compact genome of the carnivorous plant Utricularia gibba, we investigated its repertoire of noncoding RNA and DNA methylation landscape. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of small RNAs and reduced global DNA methylation levels. DNA methylation was determined using a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, some key genes involved in the RdDM pathway may not represented by compensatory paralogs or comprise truncated proteins, for example, U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs, has lost key domains required for complete function. Our results unveil that a truncated DCL3 correlates with a decreased proportion of 24-nt small-interfering RNAs, low DNA methylation levels, and developmental abnormalities during female gametogenesis in U. gibba. Alterations in female gametogenesis are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of RdDM pathway in compact genomes.
植物中研究最多的 DNA 甲基化途径是 RNA 指导的 DNA 甲基化 (RdDM)，这是一种保守的机制，涉及非编码 RNA 的作用，以控制非编码基因组的扩展。全基因组 DNA 甲基化水平与基因组大小相关。然而，对于非编码区减少的小型植物基因组中的非编码 RNA 目录及其对 DNA 甲基化的影响知之甚少。由于肉食性植物狸藻 (Utricularia gibba) 紧凑基因组中的基因间区长度较小，我们研究了其非编码 RNA 目录和 DNA 甲基化景观。在这里，我们报告与其他被子植物相比，U. gibba 的小 RNA 分布异常，整体 DNA 甲基化水平降低。使用基于 Pacific Bioscience 平台的长读 DNA 测序的新策略确定 DNA 甲基化，并通过全基因组亚硫酸氢盐测序进行验证。此外，RdDM 途径中的一些关键基因可能没有由补偿性旁系同源物或截短蛋白代表，例如，U. gibba DICER-LIKE 3 (DCL3)，编码一种 DICER 内切酶，可产生 24-nt 小干扰 RNA，已失去完成功能所需的关键结构域。我们的研究结果揭示，截短的 DCL3 与 24-nt 小干扰 RNA 的比例降低、DNA 甲基化水平降低以及 U. gibba 雌性配子发生期间的发育异常相关。雌性配子发生的改变类似于拟南芥 RdDM 突变体的表型。进一步研究 DCL3 截短在 U. gibba 中的生物学意义将很有趣，因为它可能代表紧凑基因组中 RdDM 途径进化的初始步骤。
