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许景垚, 单春苗, 单婷玉, 赵历强, 马克龙, 吴家文. 基于小RNA测序的风轮菜microRNA及其靶基因分析[J]. 植物科学学报, 2022, 40(2): 216-228. DOI: 10.11913/PSJ.2095-0837.2022.20216
引用本文: 许景垚, 单春苗, 单婷玉, 赵历强, 马克龙, 吴家文. 基于小RNA测序的风轮菜microRNA及其靶基因分析[J]. 植物科学学报, 2022, 40(2): 216-228. DOI: 10.11913/PSJ.2095-0837.2022.20216
Xu Jing-Yao, Shan Chun-Miao, Shan Ting-Yu, Zhao Li-Qiang, Ma Ke-Long, Wu Jia-Wen. Analysis of microRNAs and their target genes in Clinopodium chinense (Benth.) O. Kuntze using small RNA sequencing[J]. Plant Science Journal, 2022, 40(2): 216-228. DOI: 10.11913/PSJ.2095-0837.2022.20216
Citation: Xu Jing-Yao, Shan Chun-Miao, Shan Ting-Yu, Zhao Li-Qiang, Ma Ke-Long, Wu Jia-Wen. Analysis of microRNAs and their target genes in Clinopodium chinense (Benth.) O. Kuntze using small RNA sequencing[J]. Plant Science Journal, 2022, 40(2): 216-228. DOI: 10.11913/PSJ.2095-0837.2022.20216

基于小RNA测序的风轮菜microRNA及其靶基因分析

Analysis of microRNAs and their target genes in Clinopodium chinense (Benth.) O. Kuntze using small RNA sequencing

  • 摘要: 本研究以风轮菜(Clinopodium chinense(Benth.) O.Kuntze)为材料,采用BGISEQ-500测序平台对风轮菜根、茎和叶的小RNA进行转录组测序,并对其黄酮类物质合成途径中参与调控的microRNA (miRNA)及其靶基因进行了分析。结果显示,鉴定出的保守miRNA有86个,属于26个家族,新发现miRNA 8个,筛选出风轮菜黄酮类物质合成途径中调控3个关键酶的候选miRNA (novel_mir3、miR167d-5p、miR396h)。通过对靶基因编码的关键酶4-香豆酸辅酶A连接酶进行序列分析和同源建模,发现其具有高度保守的底物结合区域、催化结构域及两个保守的肽基序。

     

    Abstract: To analyze the flavonoid biosynthesis pathway in Clinopodium chinense (Benth.) O. Kuntze and to explore the role of microRNAs (miRNAs) in target gene regulation, transcriptome sequencing of small RNAs (sRNAs) in the roots, stems, and leaves of C. chinense was carried out using the BGISEQ-500 platform. In total, 86 conserved miRNAs were identified, divided into 26 families, and eight novel miRNAs were predicted. Three candidate miRNAs (novel_mir3, miR167d-5p, and miR396h) and their target genes involved in the flavonoid biosynthesis pathway were screened out. Sequence analysis and homologous modeling of 4-coumarate-CoA ligase, a key enzyme encoded by a target gene, showed that it had two conserved peptide motifs and a highly conserved substrate binding groove and catalytic domain. This research lays a foundation for functional genomics study of C. chinense and understanding the regulation mechanism of flavonoid biosynthesis.

     

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