Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis).
Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis).
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全转录组测序揭示了大白菜（Brassica Campestris L. ssp. pekinensis）春化相关的 ceRNA 调控网络
DOI：
10.1186/s12864-021-08110-2
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发表时间：
2021-11-13
期刊：
影响因子：
4.4
通讯作者：
Liu Z
中科院分区：
文献类型：
--
作者：
Shi F;Xu H;Liu C;Tan C;Ren J;Ye X;Feng H;Liu Z
背景
从营养生长到生殖生长的转变涉及多种途径。春化是植物花器官形成和花期调控的重要过程，在植物育种中被广泛应用。本研究旨在鉴定与大白菜春化相关的mRNA、microRNA（miRNAs）、长链非编码RNA（lncRNAs）和环状RNA（circRNAs）的全局格局。然后，这些数据被用来构建一个竞争性的内源RNA（ceRNA）网络，提供有价值的信息，以更好地了解春化反应。
结果
在这项研究中，从经过或未经春化处理的大白菜双单倍体（DH）系“FT”中采集的种子进行全转录组测序。在春化处理的种子中共鉴定出2702个差异表达（DE）mRNA、151个DE lncRNA、16个DE circRNA和233个DE miRNAs。在春化过程中，WRKY、MYB、NAC、bHLH、MADS-box、锌指蛋白CONSTANS-like基因、B3结构域蛋白等转录因子和调控蛋白发挥重要作用。此外，我们构建了春化相关的ceRNA-miRNA-靶基因网络，获得了199对大白菜中的ceRNA关系，包括108对DEmiRNA-DEmRNA，67对DEmiRNA-DElncRNA和12对DEmiRNA-DEcircRNA相互作用。此外，还鉴定了几个重要的春化相关基因及其相互作用的lncRNA、circRNA和miRNAs，这些基因参与了开花时间、花器官形成、抽薹和开花的调控。
结论
本研究揭示了大白菜春化过程中可能涉及的mRNA和非编码RNA，为进一步研究大白菜春化的分子机制奠定了基础。
Background
The transition from vegetative growth to reproductive growth involves various pathways. Vernalization is a crucial process for floral organ formation and regulation of flowering time that is widely utilized in plant breeding. In this study, we aimed to identify the global landscape of mRNAs, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to vernalization in Chinese cabbage. These data were then used to construct a competitive endogenous RNA (ceRNA) network that provides valuable information to better understand the vernalization response.
Results
In this study, seeds sampled from the Chinese cabbage doubled haploid (DH) line ‘FT’ with or without vernalization treatment were used for whole-transcriptome sequencing. A total of 2702 differentially expressed (DE) mRNAs, 151 DE lncRNAs, 16 DE circRNAs, and 233 DE miRNAs were identified in the vernalization-treated seeds. Various transcription factors, such as WRKY, MYB, NAC, bHLH, MADS-box, zinc finger protein CONSTANS-like gene, and B3 domain protein, and regulatory proteins that play important roles in the vernalization pathway were identified. Additionally, we constructed a vernalization-related ceRNA–miRNA–target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA‒DEmRNA, 67 DEmiRNA‒DElncRNA, and 12 DEmiRNA‒DEcircRNA interactions, in Chinese cabbage. Furthermore, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs, which are involved in the regulation of flowering time, floral organ formation, bolting, and flowering, were identified.
Conclusions
Our results reveal the potential mRNA and non-coding RNAs involved in vernalization, providing a foundation for further studies on the molecular mechanisms underlying vernalization in Chinese cabbage.
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