Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
Zarinshahr, Isfahan, Iran.
BMC Plant Biol. 2023 Jan 2;23(1):3. doi: 10.1186/s12870-022-04031-8.
Lettuce (Lactuca sativa L.) is considered the most important vegetable in the leafy vegetable group. However, bolting affects quality, gives it a bitter taste, and as a result makes it inedible. Bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although bolting/flowering responsive genes have been identified in most sensitive and non-sensitive species, non-coding RNA molecules like long non-coding RNAs (lncRNAs) have not been investigated in lettuce. Hence, in this study, potential long non-coding RNAs that regulate flowering /bolting were investigated in two lettuce strains S24 (resistant strain) and S39 (susceptible strain) in different flowering times to better understand the regulation of lettuce bolting mechanism. For this purpose, we used two RNA-seq datasets to discover the lncRNA transcriptome profile during the transition from vegetative to reproductive phase.
For identifying unannotated transcripts in these datasets, a 7-step pipeline was employed to filter out these transcripts and terminate with 293 novel lncRNAs predicted by PLncPRO and CREMA. These transcripts were then utilized to predict cis and trans flowering-associated targets and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Computational predictions of target gene function showed the involvement of putative flowering-related genes and enrichment of the floral regulators FLC, CO, FT, and SOC1 in both datasets. Finally, 17 and 18 lncRNAs were proposed as competing endogenous target mimics (eTMs) for novel and known lncRNA miRNAs, respectively.
Overall, this study provides new insights into lncRNAs that control the flowering time of plants known for bolting, such as lettuce, and opens new windows for further study.
生菜（Lactuca sativa L.）被认为是叶菜类蔬菜中最重要的蔬菜。然而，抽薹会影响品质，使其产生苦味，从而变得不可食用。抽薹是由各种环境因素和内源性遗传成分协同作用引起的事件。尽管在大多数敏感和非敏感物种中已经鉴定出了开花/抽薹响应基因，但尚未在生菜中研究非编码 RNA 分子，如长非编码 RNA（lncRNA）。因此，在这项研究中，我们在两个生菜品系 S24（抗性品系）和 S39（敏感品系）中研究了在不同开花时间调节开花/抽薹的潜在长非编码 RNA，以更好地理解生菜抽薹机制的调控。为此，我们使用了两个 RNA-seq 数据集来发现从营养生长到生殖阶段过渡过程中的 lncRNA 转录组谱。
为了在这些数据集中鉴定未注释的转录本，我们采用了一个 7 步流程来过滤这些转录本，并以通过 PLncPRO 和 CREMA 预测的 293 个新的 lncRNA 结束。然后，我们利用这些转录本预测顺式和反式开花相关靶标以及基因本体论（GO）和京都基因与基因组百科全书（KEGG）途径富集分析。靶基因功能的计算预测表明，这些基因参与了假定的开花相关基因的富集，并在两个数据集中富集了花调节因子 FLC、CO、FT 和 SOC1。最后，分别提出了 17 个和 18 个 lncRNA 作为新型和已知 lncRNA miRNA 的竞争性内源靶标模拟物（eTMs）。
总的来说，这项研究为控制生菜等抽薹植物开花时间的 lncRNA 提供了新的见解，并为进一步研究开辟了新的窗口。
