Whole transcriptome analysis and construction of a ceRNA regulatory network related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis).
Whole transcriptome analysis and construction of a ceRNA regulatory network related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis).
复制标题
DOI：
10.1186/s12864-023-09239-y
复制
发表时间：
2023-03-24
期刊：
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
--
作者：
叶片和叶柄的生长发育对光合作用有重要影响。了解叶片和叶柄发育的分子机制对于提高光合作用效率、培育光合作用效率高的品种和提高以叶片为粮食作物的产量是必要的。本研究旨在鉴定与大白菜(Brassica campestris L.SSP)叶片和叶柄发育相关的mRNAs、长非编码RNAs(LncRNAs)、微RNAs(MiRNAs)和环状RNAs(CircRNAs)。北京人)。这些数据被用来构建竞争内源RNA(CERNA)网络，以深入了解叶片和叶柄发育的机制。以大白菜‘PHL’自交系的叶片和叶柄为材料，进行了全转录组测序。在叶片和叶柄之间共鉴定出10,646个差异表达的mRNAs，303个DElncRNAs，7个DECircRNAs和195个DEmiRNAs。鉴定了在叶片和叶柄发育中起重要作用的转录因子和蛋白质，包括木葡聚糖内切葡糖苷酶/水解酶、膨胀蛋白及其前体、转录因子TCP15和bHLH、横向器官边界结构域蛋白、纤维素合酶、类似MOR1的蛋白以及与植物激素生物合成相关的蛋白。构建了与叶片和叶柄发育相关的CERNA调控网络，共鉴定出85对CERNA关系，其中DEmiRNA-DEmRNA 71对，DEmiRNA-DElncRNA 12对，DEmiRNA-DECircRNA 2对。从转录组数据中筛选出在叶片和叶柄中有显著差异表达的3个LSH基因(BrLSH1、BrLSH2和BrLSH3)，并通过亚细胞定位分析和转基因过表达验证来探讨它们的功能。BrLSH1、BrLSH2和BrLSH3为核蛋白，BrLSH2抑制拟南芥的生长发育。本研究鉴定了可能参与大白菜叶片和叶柄发育的mRNAs和非编码RNA，并建立了与叶片和叶柄发育相关的CERNA调控网络，为进一步研究大白菜叶片和叶柄发育的分子机制提供了宝贵的基因组资源。网上版载有补充材料，可在10.1186/s12864-023-09239-y查阅。
The growth and development of leaves and petioles have a significant effect on photosynthesis. Understanding the molecular mechanisms underlying leaf and petiole development is necessary for improving photosynthetic efficiency, cultivating varieties with high photosynthetic efficiency, and improving the yield of crops of which the leaves are foodstuffs. This study aimed to identify the mRNAs, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis). The data were used to construct a competitive endogenous RNA (ceRNA) network to obtain insights into the mechanisms underlying leaf and petiole development. The leaves and petioles of the ‘PHL’ inbred line of Chinese cabbage were used as research materials for whole transcriptome sequencing. A total of 10,646 differentially expressed (DE) mRNAs, 303 DElncRNAs, 7 DEcircRNAs, and 195 DEmiRNAs were identified between leaves and petioles. Transcription factors and proteins that play important roles in leaf and petiole development were identified, including xyloglucan endotransglucosylase/hydrolase, expansion proteins and their precursors, transcription factors TCP15 and bHLH, lateral organ boundary domain protein, cellulose synthase, MOR1-like protein, and proteins related to plant hormone biosynthesis. A ceRNA regulatory network related to leaf and petiole development was constructed, and 85 pairs of ceRNA relationships were identified, including 71 DEmiRNA–DEmRNA, 12 DEmiRNA–DElncRNA, and 2 DEmiRNA–DEcircRNA pairs. Three LSH genes (BrLSH1, BrLSH2 and BrLSH3) with significant differential expression between leaves and petioles were screened from transcriptome data, and their functions were explored through subcellular localization analysis and transgenic overexpression verification. BrLSH1, BrLSH2 and BrLSH3 were nuclear proteins, and BrLSH2 inhibited the growth and development of Arabidopsis thaliana. This study identifies mRNAs and non-coding RNAs that may be involved in the development of leaves and petioles in Chinese cabbage, and establishes a ceRNA regulatory network related to development of the leaves and petioles, providing valuable genomic resources for further research on the molecular mechanisms underlying leaf and petiole development in this crop species. The online version contains supplementary material available at 10.1186/s12864-023-09239-y.
登录
查看更多内容
影响因子：
14.9
作者：
Dai X;Zhao PX
通讯作者：
Zhao PX
芹菜叶片发育相关小 RNA 和解剖特征的高通量测序
影响因子：
4.6
作者：
Jia XL;Li MY;Jiang Q;Xu ZS;Wang F;Xiong AS
通讯作者：
Xiong AS
影响因子：
7.4
作者：
Ichihashi, Yasunori;Kawade, Kensuke;Tsukaya, Hirokazu
通讯作者：
Tsukaya, Hirokazu
景天酸代谢（CAM）光合作用途径中菠萝叶 lncRNA 的鉴定和表征
影响因子：
4.6
作者：
Bai, Youhuang;Dai, Xiaozhuan;Qin, Yuan
通讯作者：
Qin, Yuan
影响因子：
5.8
作者：
Bo, XC;Wang, SQ
通讯作者：
Wang, SQ