State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Shaanxi, Yangling, China.
Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, China.
Mol Biol Evol. 2022 Jan 7;39(1). doi: 10.1093/molbev/msab299.
Epigenetic modifications play important roles in genome evolution and innovation. However, most analyses have focused on the evolutionary role of DNA modifications, and little is understood about the influence of posttranscriptional RNA modifications on genome evolution. To explore the evolutionary significance of RNA modifications, we generated transcriptome-wide profiles of N6-methyladenosine (m6A), the most prevalent internal modification of mRNA, for 13 representative plant species spanning over half a billion years of evolution. These data reveal the evolutionary conservation and divergence of m6A methylomes in plants, uncover the preference of m6A modifications on ancient orthologous genes, and demonstrate less m6A divergence between orthologous gene pairs with earlier evolutionary origins. Further investigation revealed that the evolutionary divergence of m6A modifications is related to sequence variation between homologs from whole-genome duplication and gene family expansion from local-genome duplication. Unexpectedly, a significant negative correlation was found between the retention ratio of m6A modifications and the number of family members. Moreover, the divergence of m6A modifications is accompanied by variation in the expression level and translation efficiency of duplicated genes from whole- and local-genome duplication. Our work reveals new insights into evolutionary patterns of m6A methylomes in plant species and their implications, and provides a resource of plant m6A profiles for further studies of m6A regulation and function in an evolutionary context.
表观遗传修饰在基因组进化和创新中发挥着重要作用。然而，大多数分析都集中在 DNA 修饰的进化作用上，对于转录后 RNA 修饰对基因组进化的影响知之甚少。为了探索 RNA 修饰的进化意义，我们针对跨越超过 5 亿年进化的 13 个代表性植物物种，生成了 N6-甲基腺苷（m6A）的转录组范围图谱，m6A 是 mRNA 中最普遍的内部修饰。这些数据揭示了植物中 m6A 甲基组的进化保守性和分化，揭示了 m6A 修饰对古老直系同源基因的偏好，并证明了进化起源更早的直系基因对之间的 m6A 分化较少。进一步的研究表明，m6A 修饰的进化分化与全基因组复制同源物之间的序列变异以及局部基因组复制基因家族扩张有关。出乎意料的是，m6A 修饰的保留率与家族成员数量之间存在显著的负相关。此外，m6A 修饰的分化伴随着全基因组和局部基因组复制中重复基因的表达水平和翻译效率的变化。我们的工作揭示了植物物种中 m6A 甲基组进化模式及其意义的新见解，并为进一步研究进化背景下 m6A 调节和功能提供了植物 m6A 图谱资源。
