Global Identification and Analysis of Long Noncoding RNAs Involved in Banana Fruit Ripening

In the life cycle of fruit, ripening is a crucial period for the formation of fruit quality. During this phase, a series of physiological and biochemical changes occur, leading to alterations in color and texture, softening, and the production of aroma volatiles. Relevant studies have demonstrated that ethylene-induced fruit ripening is a complex regulatory network involving numerous transcription factors, ethylene receptor protein families, signal transduction pathways, and downstream maturation-related genes. In this study, we conducted a genome-scale identification and characterization of long noncoding RNAs (lncRNAs) from the predominant AAA triploid banana cultivar, ‘Tianbaojiao’, using rich RNA-sequencing (RNA-seq) datasets from fruit tissues treated with ethylene and untreated controls. This represents one of the first comprehensive investigations into banana lncRNAs associated with ripening. A total of 11,268 banana fruit lncRNAs were identified and found to be distributed across all banana chromosomes; ∼76.1% of these lncRNAs were transcribed from intergenic regions. Banana fruit lncRNAs are relatively short, with 91.32% ranging from 100 to 1000 nucleotides in length. Most contain one or two exons, contrasting with protein-coding genes, which can have one to ≥10 exons. Compared with naturally ripened bananas, many lncRNAs exhibited significant differential expression in ethylene-treated banana fruits. Furthermore, downregulating the expression of lncRNA TCONS00507247 in the peel markedly inhibited the yellowing process. These findings suggest that lncRNAs play a vital role in regulating banana fruit ripening and offer new insights into fruit ripening research.