Full-Length Transcriptome and the Identification of lncRNAs Involved in Salicylic Acid-Induced Flowering in Duckweed (Lemna gibba)

Long noncoding RNAs (lncRNAs) are crucial components in regulating the flowering of plants. However, the regulatory mechanism of lncRNAs underlying salicylic acid (SA)-induced flowering remains unknown in duckweed (e.g., Lemna gibba L.), an aquatic model species with significant potential applications in agriculture and industry. In this work, L. gibba plants were collected at four crucial time points during SA-induced flowering and subjected to PacBio full-length sequencing and strand-specific RNA sequencing. A total of 474 lncRNAs were identified, of which 31 were differentially expressed and involved in SA-induced flowering. A trans-regulatory analysis found that these lncRNAs displayed temporal-specific expression trends and mainly participated in stress metabolism, photosynthesis, jasmonate metabolism, and transport under SA treatment. Five lncRNAs were determined to act as targets of miRNAs that played critical roles in regulating flowering. In addition, fifteen lncRNAs showed co-expression with flowering-related genes, and lncRNA03 and lncRNA25 were identified as key players involved in flowering via lncRNA-miRNA-mRNA interactions. Finally, twelve lncRNAs related to trans-regulation, miRNA targets, or co-expression with flowering-related genes were verified by qRT-PCR. These findings deepen our understanding of lncRNAs in SA-induced flowering in duckweed and provide valuable resources for in-depth functional analysis in the future.

Automated summary

This study investigated the regulatory mechanism of long noncoding RNAs (lncRNAs) in salicylic acid (SA)-induced flowering in duckweed. Through full-length sequencing and RNA sequencing, 31 differentially expressed lncRNAs were identified and found to be involved in stress metabolism, photosynthesis, jasmonate metabolism, and transport. Co-expression analysis revealed 15 lncRNAs that were co-expressed with flowering-related genes, and lncRNA03 and lncRNA25 were identified as key players in flowering through lncRNA-miRNA-mRNA interactions. qRT-PCR validation confirmed the expression of 12 lncRNAs involved in transcriptional regulation, miRNA targets, or co-expression with flowering-related genes. These findings provide valuable resources for future in-depth functional analysis of lncRNAs in SA-induced flowering in duckweed.