Abstract
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.
Highlights
Lettuce (Lactuca sativa), of the Asteraceae family, is a leafy vegetable with important economic value
In this study, based on the lettuce reference genome (Reyes-Chin-Wo et al, 2017), miRNAs in lettuce were systematically annotated by sRNA sequencing and the plant miRNA identification pipeline (Kuang et al, 2019) developed by our laboratory
The combination of these analyses provides a strong foundation for understanding and mining miRNA functions in lettuce
Summary
Lettuce (Lactuca sativa), of the Asteraceae family, is a leafy vegetable with important economic value. According to the Food and Agriculture Organization, the global production of lettuce, together with chicory, exceeded 29 million tons in 2019, ranking third of all leafy vegetables. In the United States alone, lettuce production in 2019 exceeded 3.6 million tons, with a market value of over 1.5 billion USD. With the availability of a reference genome (ReyesChin-Wo et al, 2017) and numerous transcriptomes (Zhang L. et al, 2017), lettuce has become a model for studying Asteraceae and related plants. Lettuce has numerous cultivars, including butterhead, crisphead, looseleaf, romaine, stem, and many mixed types, which are highly varied in morphology, and provide good material for studying the morphological development of plants (Seki et al, 2020; Yu et al, 2020). Lettuce has been used as a novel platform for biopharmaceutical production due to its numerous advantages, including low processing cost, consistent and scalable production, and the excellent biosafety profile of transgenic plants (Daniell et al, 2019; Zhang et al, 2019)
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