Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Litchi

Authors

  • Muhammad Waseem School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, Hainan, China Author https://orcid.org/0000-0001-7947-7722
  • Sana Basharat School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, Hainan, China Author
  • Iffat Shaheen College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China Author
  • Pingwu Liu School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, Hainan, China Author

DOI:

https://doi.org/10.66835/psh.2026.e0005

Keywords:

Litchi, lncRNA, Transcriptome, Target mimics, Regulation

Abstract

Long non-coding RNAs (lncRNAs) play key regulatory roles in different developmental processes and responses to stress. However, the bioinformatic identification of lncRNAs in litchi are largely unknown. To explore the lncRNA profiles and functions in litchi different tissues, we performed RNA sequencing of litchi leaves, pericarp, seeds, flowers fruitlet, and carpopodium, with varying biological replicates for each. We identified 2229 lncRNAs including average 293 lncRNAs were significantly differentially expressed (DE) in all the tissues used in this study. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out to identify the cis target gene of DE lncRNAs. The results showed that the lncRNAs might play an important role in the immune response, response to abiotic stress, and metabolic processes related to fatty acids and glucose. Moreover, we identified lncRNAs associated with miRNAs, including lncRNAs acting as precursors for miR156, miR171, miR172, miR319, miR393, miR396, and miR482, as well as lncRNAs targeted by these miRNAs. The results suggest that the lncRNAs can regulate the expression of mRNA during litchi growth and development by forming competitive endogenous RNA, and further regulate various biological metabolism pathways in litchi.

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Published

2026-06-01

Data Availability Statement

The data supporting the findings of this study are publicly available as supplementary files. All relevant information is included within the manuscript.

Issue

Vol. 1 No. 1 (2026)

Section

Research Articles

License

Copyright (c) 2026 Muhammad Waseem, Sana Basharat, Iffat Shaheen, Pingwu Liu (Author)

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

How to Cite

[1]
M. Waseem, S. Basharat, I. Shaheen, and P. Liu, Trans., “Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Litchi”, Plant Sci. Horiz., vol. 1, no. 1, pp. 12–21, Jun. 2026, doi: 10.66835/psh.2026.e0005.

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