A comprehensive review by the team of Xinhua Zhang at Shandong University of Technology on the significant roles and regulatory mechanisms of lncRNAs in fruit and vegetables

With the development of genome sequencing technologies, many long non-coding RNAs (lncRNAs) have been identified in fruit and vegetables. Extensive research on lncRNAs has revealed their roles in regulating the expression of protein-coding genes at both transcriptional and post-transcriptional levels, thereby playing crucial roles in the growth, development, and stress responses in fruit and vegetables.

This review provides a comprehensive summary of the current understanding of the formation, functional characteristics, and regulatory mechanisms of lncRNAs in fruits and vegetables. Based on their transcription direction and position relative to protein-coding genes, lncRNAs are classified into four types: intergenic lncRNAs (lincRNAs), long non-coding antisense transcripts (lncNATs), sense lncRNAs, and intronic lncRNAs (incRNAs). In this paper, the formation, and the basic characteristics of lncRNAs in fruit and vegetables are described from three aspects: abundance and size, structure and localization, decay and evolution. The roles of lncRNAs in fruit and vegetables have been comprehensively summarized and discussed through recent research reports, covering various aspects including pigment accumulation, reproductive organ development, fruit ripening, as well as responses to nutrient deficiency, salt, drought, temperature, and pathogenic bacteria (Fig. 1).

In addition, we elucidated the regulatory mechanisms of lncRNAs in gene transcriptional regulation and alternative splicing, as well as the interactions between lncRNAs and plant hormones, transcription factors, and miRNAs (Fig. 2).

The development of high-throughput sequencing technology has greatly improved the ability to discover, predict, and identify lncRNAs. However, there remains a scarcity of comprehensive lncRNA analysis data in plant databases pertaining to lncRNAs in fruits and vegetables, hindering the characterization of lncRNA expression and localization. Moreover, the cost associated with subcellular localization experiments of lncRNAs, such as FISH, poses a limitation on lncRNA studies, highlighting the urgent need for the development of more affordable methods for lncRNAs research. The exploration of the function and mechanism of lncRNAs in fruit and vegetables crops is still in its early stages, and the rapid development of technology will bring new opportunities and breakthroughs for lncRNA research in fruit and vegetables.

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References

DOI

10.1093/hr/uhae046

Original Source URL

https://doi.org/10.1093/hr/uhae046

Authors

Xiuming Zhao, Fujun Li, Maratab Ali, Xiaoan Li, Xiaodong Fu, Xinhua Zhang

Affiliations

College of Agricultural Engineering and Food Science, Shandong University of Technology

About Xinhua Zhang

Xinhua Zhang, Professor and Ph.D. supervisor at Shandong University of Technology. Dr. Zhang obtained her Ph.D. from the College of Food Science and Nutritional Engineering at China Agricultural University. Over the years, she has been primarily engaged in research on postharvest biology of fruits and vegetables and storage technologies. Using tomatoes as a model fruit, she has conducted in-depth research on the molecular networks of fruit ripening and senescence, quality control, as well as the molecular mechanisms of endogenous signal substances inducing postharvest low temperature and pathogen resistance in fruit and vegetables. She has undertaken in nearly 30 research projects, including the National Natural Science Foundation of China, the National Modern Agricultural Industry System Project, key projects of Shandong Province Natural Science Foundation, and collaborative projects with enterprises. Dr. Zhang has published over 70 SCI/EI papers. Under her guidance, graduate students have won seven awards for outstanding master's theses and research innovation achievements. Dr. Zhang has been honored with titles such as "Outstanding Graduate Supervisor in Shandong Province".