You Chenjiang, Cui Jie, Wang Hui, Qi Xinping, Kuo Li-Yaung, Ma Hong, Gao Lei, Mo Beixin, Chen Xuemei
Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China.
Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China.
Genome Biol. 2017 Aug 23;18(1):158. doi: 10.1186/s13059-017-1291-2.
As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. However, both small RNAs themselves and small RNA pathways are not well characterized in other land plants such as lycophytes and ferns, preventing a comprehensive evolutionary perspective on small RNAs in land plants.
Using 25 representatives from major lineages of lycophytes and ferns, most of which lack sequenced genomes, we characterized small RNAs and small RNA pathways in these plants. We identified homologs of DICER-LIKE (DCL), ARGONAUTE (AGO), and other genes involved in small RNA pathways, predicted over 2600 conserved microRNA (miRNA) candidates, and performed phylogenetic analyses on small RNA pathways as well as miRNAs. Pathways underlying miRNA biogenesis, degradation, and activity were established in the common ancestor of land plants, but the 24-nucleotide siRNA pathway that guides DNA methylation is incomplete in sister species of seed plants, especially lycophytes. We show that the functional diversification of key gene families such as DCL and AGO as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered a conserved AGO subfamily absent in angiosperms.
Our phylogenetic analyses of miRNAs in bryophytes, lycophytes, ferns, and angiosperms refine the time-of-origin for conserved miRNA families as well as small RNA machinery in land plants.
作为真核生物基因表达的关键调节因子，小RNA已在许多种子植物中得到表征，其生物合成、降解及作用途径已在模式被子植物中得以明确。然而，小RNA本身及小RNA途径在其他陆生植物（如石松类植物和蕨类植物）中尚未得到充分表征，这妨碍了对陆生植物中小RNA的全面进化认识。
我们选取了来自石松类植物和蕨类植物主要谱系的25个代表物种，其中大多数缺乏已测序的基因组，对这些植物中的小RNA和小RNA途径进行了表征。我们鉴定了与小RNA途径相关的DICER-LIKE（DCL）、ARGONAUTE（AGO）及其他基因的同源物，预测了2600多个保守的微小RNA（miRNA）候选物，并对小RNA途径以及miRNA进行了系统发育分析。miRNA生物合成、降解及活性的途径在陆生植物的共同祖先中已经确立，但指导DNA甲基化的24核苷酸小干扰RNA（siRNA）途径在种子植物的姊妹物种中并不完整，尤其是在石松类植物中。我们表明，被子植物中观察到的DCL和AGO等关键基因家族的功能多样化在陆生植物早期就已发生，随后AGO家族在蕨类植物和被子植物中平行扩张。我们发现了一个被子植物中不存在的保守AGO亚家族。
我们对苔藓植物、石松类植物、蕨类植物和被子植物中miRNA的系统发育分析，完善了陆生植物中保守miRNA家族以及小RNA机制的起源时间。
