National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
BMC Evol Biol. 2019 Feb 14;19(1):55. doi: 10.1186/s12862-019-1382-7.
Micro RNAs (miRNAs), a class of small non-coding RNAs, have been implicated in various aspects of plant development. miR394 is required for shoot apical meristem organization, stem cell maintenance and abiotic stress responses in Arabidopsis, where it functions by negatively regulating the transcript level of target LEAF CURLING RESPONSIVENESS (LCR), which is an F-box protein-coding gene. The evolutionary conservation of stem cell regulatory miR394-LCR module among plants remains elusive.
Our study has identified 79 miR394 and 43 target sequences across 40 plant species using various homology based search tools and databases, and analysed their co-evolution pattern. We customised an annotation workflow which computationally validates 20 novel miR394s from 14 plant species. Independent phylogenetic trees were reconstructed with precursor MIR394s, mature miR394s, and their target sequences along with complementary miR394 binding sites. The phylogeny revealed that mature sequences of miR394s as well as their targets belonging to the F-box protein encoding gene families, were highly conserved. Though, miR394-3p were complementary to miR394s/miR394-5p, they clustered separately.
The existence and separate clustering of miR394-3p and miR394s/miR394-5p indicate their independent regulation. The phylogeny also suggests that miR394s had evolved at the beginning of gymnosperm-angiosperm divergence. Despite strong conservation, some level of sequence variation in miR394s and the complementary binding sites of their targets suggests possible functional diversification of miR394-LCR mediated stem cell regulation in plants.
微小 RNA（miRNA）是一类小的非编码 RNA，参与植物发育的各个方面。miR394 对拟南芥的茎尖分生组织组织、干细胞维持和非生物胁迫反应是必需的，它通过负调控靶标 LEAF CURLING RESPONSIVENESS（LCR）的转录水平起作用，LCR 是一个 F-box 蛋白编码基因。植物中干细胞调节 miR394-LCR 模块的进化保守性仍然难以捉摸。
我们使用各种基于同源性的搜索工具和数据库，在 40 种植物物种中鉴定了 79 个 miR394 和 43 个靶序列，并分析了它们的共同进化模式。我们定制了一个注释工作流程，该流程可以从 14 种植物物种中计算验证 20 个新的 miR394。根据前体 MIR394s、成熟 miR394s 及其靶序列以及互补 miR394 结合位点，独立重建了系统发育树。系统发育树表明，miR394s 的成熟序列以及属于 F-box 蛋白编码基因家族的靶序列高度保守。虽然 miR394-3p 与 miR394s/miR394-5p 互补，但它们分别聚类。
miR394-3p 的存在和单独聚类以及 miR394s/miR394-5p 表明它们的独立调节。系统发育树还表明，miR394s 在裸子植物-被子植物分化的早期就已经进化。尽管存在强烈的保守性，但 miR394s 及其靶标互补结合位点的一些序列变异表明，miR394-LCR 介导的干细胞调节在植物中的功能多样化。
