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Comprehensive Annotation and Functional Exploration of MicroRNAs in Lettuce

文献类型： 外文期刊

作者： Deng, Yang 1 ; Qin, Yajuan 1 ; Yang, Pan 1 ; Du, Jianjun 1 ; Kuang, Zheng 1 ; Zhao, Yongxin 1 ; Wang, Ying 4 ; Li, Dayong 1 ; Wei, Jianhua 1 ; Guo, Xinyu 1 ; Li, Lei 4 ; Yang, Xiaozeng 1 ;

作者机构： 1.Beijing Acad Agr & Forestry Sci, Beijing, Peoples R China

2.Beijing Agrobiotechnol Res Ctr, Beijing Key Lab Agr Genet Resources & Biotechnol, Beijing, Peoples R China

3.Fujian Agr & Forestry Univ, Coll Life Sci, Fuzhou, Peoples R China

4.Peking Univ, Peking Tsinghua Ctr Life Sci, Sch Adv Agr Sci, State Key Lab Prot & Plant Gene Res, Beijing, Peoples R China

5.Peking Univ, Sch Life Sci, Beijing, Peoples R China

6.Beijing Res Ctr Informat Technol Agr, Beijing Key Lab Digital Plant, Beijing, Peoples R China

7.Beijing Vegetable Res Ctr, Beijing Key Lab Vegetable Germplasm Improvement, Beijing, Peoples R China

关键词： lettuce; microRNA (miRNA); sRNA-Seq; expression correlation; regulatory network; miR408

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：6.627； 五年影响因子：7.255 ）

ISSN： 1664-462X

年卷期： 2021 年 12 卷

页码：

收录情况： SCI

摘要： MicroRNA (miRNA) is an important endogenous post-transcriptional regulator, while lettuce (Lactuca sativa) is a leafy vegetable of global economic significance. However, there are few studies on miRNAs in lettuce, and research on miRNA regulatory network in lettuce is absent. In this study, through deep sequencing of small RNAs in different tissues, together with a reference genome, 157 high-confidence miRNA loci in lettuce were comprehensively identified, and their expression patterns were determined. Using a combination of computational prediction and high-throughput experimental verification, a set of reliable lettuce miRNA targets were obtained. Furthermore, through RNA-Seq, the expression profiles of these targets and a comprehensive view of the negative regulatory relationship between miRNAs and their targets was acquired based on a correlation analysis. To further understand miRNA functions, a miRNA regulatory network was constructed, with miRNAs at the core and combining transcription factors and miRNA target genes. This regulatory network, mainly composed of feed forward loop motifs, greatly increases understanding of the potential functions of miRNAs, and many unknown potential regulatory links were discovered. Finally, considering its specific expression pattern, Lsa-MIR408 as a hub gene was employed to illustrate the function of the regulatory network, and genetic experiments revealed its ability to increase the fresh weight and achene size of lettuce. In short, this work lays a solid foundation for the study of miRNA functions and regulatory networks in lettuce.

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