LncRNA expression profile and ceRNA analysis in tomato during flowering

Area of Science:

• Plant Molecular Biology
• Genomics
• Transcriptomics

Background:

• Long non-coding RNAs (lncRNAs) are key regulators in plant development and stress responses.
• The specific functions of lncRNAs during tomato flowering remain largely unexplored.

Purpose of the Study:

• To investigate lncRNA profiles and functions during tomato flowering.
• To identify novel differentially expressed lncRNAs and their potential roles in flower development.

Main Methods:

• Strand-specific paired-end RNA sequencing of tomato leaves, flowers, and roots.
• Identification and differential expression analysis of lncRNAs.
• Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses for cis-target genes.
• Analysis of interactions between microRNAs (miRNAs), lncRNAs, and messenger RNAs (mRNAs).

Main Results:

• 10,919 lncRNAs identified, including 248 novel ones.
• 65 novel lncRNAs showed significant differential expression in flowers, leaves, and roots.
• lncRNAs are implicated in regulating flower tissue development, molecular binding, metabolic pathways, and apoptosis.
• Interactions involving 32 miRNAs, 78 lncRNAs, and 397 mRNAs were identified, suggesting a regulatory network.

Conclusions:

• lncRNAs play significant roles in tomato flowering, growth, development, and apoptosis.
• lncRNAs regulate gene expression via competitive endogenous RNA (ceRNA) mechanisms during flowering.
• These findings provide insights into the regulatory networks governing tomato reproductive development.