Integrated analysis of transcriptome and small RNAome reveals the regulatory network for rapid growth in Mikania micrantha [RNA-seq]

M. micrantha has caused huge ecological damage and economic losses worldwide due to its rapid growth and serious invasion. However, the underlying molecular mechanisms of its rapid growth and environmental adaption remain unclear. Here, we performed transcriptome and small RNA sequencing with five tissues of M. micrantha to dissect miRNA-mediated regulation in M. micrantha. WGCNA and GO enrichment analysis of transcriptome identified the gene association patterns and potential key regulatory genes for plant growth in each tissue. The genes highly correlated with leaf and stem tissues were mainly involved in the chlorophyll synthesis, response to auxin, the CAM pathway and other photosynthesis-related processes, which promoted the fast growth of M. micrantha. Importantly, we identified 350 conserved and 192 novel miRNAs, many of which displayed differential expression patterns among tissues. PsRNA target prediction analysis uncovered target genes of both conserved and novel miRNAs, including GRFs and TCPs, which were essential for plant growth and development. Further analysis revealed that miRNAs contributed to the regulation of tissue-specific gene expression in M. micrantha, such as mmi-miR396 and mmi-miR319. Taken together, our study uncovered the miRNA-mRNA regulatory networks and the potential vital roles of miRNAs in modulating the rapid growth of M. micrantha. Overall design: Integrated analysis of transcriptome and small RNAome for M. micrantha flower, leaf, shoot apex, stem, and root tissues

微甘菊（M. micrantha）凭借其快速的生长特性与极强的入侵能力，已在全球范围内造成了严重的生态破坏与经济损失。然而，其快速生长与环境适应背后的分子调控机制仍未明确。本研究对微甘菊的5种组织开展了转录组与小RNA测序，以解析miRNA（microRNA）介导的调控通路。
对转录组数据进行加权基因共表达网络分析（Weighted Gene Co-expression Network Analysis, WGCNA）与基因本体（Gene Ontology, GO）富集分析后，我们明确了各组织的基因关联模式，并筛选出与植物生长相关的潜在关键调控基因。与叶、茎组织高度相关的基因主要参与叶绿素合成、生长素响应、景天酸代谢（Crassulacean Acid Metabolism, CAM）通路及其他光合相关过程，这些过程共同推动了微甘菊的快速生长。
值得注意的是，本研究共鉴定出350个保守miRNA与192个新miRNA，其中多数在不同组织中呈现出差异表达模式。通过psRNA靶基因预测分析，我们发掘出保守miRNA与新miRNA的靶基因，包括对植物生长发育至关重要的生长调控因子（Growth Regulating Factors, GRFs）与TCP转录因子家族（TCP transcription factors, TCPs）。进一步分析显示，miRNA参与调控微甘菊的组织特异性基因表达，例如mmi-miR396与mmi-miR319。
综上，本研究揭示了微甘菊中miRNA-mRNA调控网络，以及miRNA在调控其快速生长过程中发挥的潜在关键作用。
整体实验设计：对微甘菊的花、叶、茎尖、茎以及根组织开展转录组与小RNA组整合分析。