植物 microRNA 百科全书 PmiREN3.0 发布，物种扩至 340 个并加入 AI 知识服务
PmiREN3.0: a multi-omics integrated and AI-assisted encyclopedia for plant microRNA research
植物 microRNA 百科全书 PmiREN3.0 发布，物种/亚种覆盖从 179 增至 340，新增 22 个目、51 个科、108 个属。沿用此前版本的标准流程与注释标准，从 5319 个小 RNA 测序（sRNA-seq）数据集中鉴定高置信度 miRNA，miRNA 位点从 39 751 增至 87 667，miRNA 家族从 7838 增至 18 389。旧版资源与工具做了大幅更新，并新增六个模块，分别覆盖初级转录本、DNA 甲基化、RNA 修饰、胁迫响应表达、代谢通路和核心基因调控网络。
来源：Nucleic Acids Research · doi.org
植物 miRNA 数据库大幅扩充物种与位点，并新增多组学模块和 AI 问答服务，做植物小 RNA 研究可据此判断是否迁移。
MicroRNAs (miRNAs) are key post-transcriptional regulators in gene regulatory networks (GRNs). Comprehensive research on miRNAs increasingly requires the integration of large and heterogeneous datasets, together with more efficient approaches to knowledge exploration. Here, we present PmiREN3.0, a major update of the Plant MicroRNA Encyclopedia. Compared with PmiREN2.0, species/subspecies coverage increased from 179 to 340, adding 22 orders, 51 families, and 108 genera. Using the same standardized workflow and annotation criteria as previous releases, high-confidence miRNAs were identified from 5319 small RNA sequencing (sRNA-seq) datasets, with miRNA loci increasing from 39 751 to 87 667 and miRNA families from 7838 to 18 389. Resources and tools from previous releases were extensively updated, while six new modules were added for primary transcripts, DNA methylation, RNA modifications, stress-responsive expression, metabolic pathways, and core GRNs. PmiREN3.0 also introduces miRai+, a knowledge service powered by artificial intelligence (AI) that combines a language model fine-tuned on miRNA knowledge with retrieval augmented generation. Evaluation yielded scores of 0.910 for answer relevance, 0.965 for faithfulness, and 0.906 for factual correctness. Together, PmiREN3.0 provides an expanded plant miRNA dataset and an integrated platform combining multi-omics data and AI-assisted knowledge services for plant miRNA research. PmiREN3.0 is available at https://pmiren.com/.