Abstract
As emerging essential regulators in plant development, long non-coding RNAs (lncRNAs) have been extensively investigated in multiple horticultural crops, as well as in different tissues of plants. Tomato fruits are an indispensable part of people’s diet and are consumed as fruits and vegetables. Meanwhile, tomato is widely used as a model to study the ripening mechanism in fleshy fruit. Although increasing evidence shows that lncRNAs are involved in lots of biological processes in tomato plants, the comprehensive identification of lncRNAs in tomato fruit during its expansion and ripening and their functions are partially known. Here, we performed strand-specific paired-end RNA sequencing (ssRNA-seq) of tomato Heinz1706 fruits at five different developmental stages, as well as flowers and leaves. We identified 17,674 putative lncRNAs by referencing the recently released SL4.0 and annotation ITAG4.0 in tomato plants. Many lncRNAs show different expression patterns in fleshy fruit at different developmental stages compared with leaves or flowers. Our results indicate that lncRNAs play an important role in the regulation of tomato fruit expansion and ripening, providing informative lncRNA candidates for further studies in tomato fruits. In addition, we also summarize the recent advanced progress in lncRNAs mediated regulation on horticultural fruits. Hence, our study updates the understanding of lncRNAs in horticultural plants and provides resources for future studies relating to the expansion and ripening of tomato fruits.
Highlights
To isolate the long non-coding RNAs (lncRNAs) candidates that may be essential in regulating the fruit exTo isolate the lncRNA candidates that may be essential in regulating the fruit expanpansion and ripening, we found 18 lncRNAs sion and ripening, we found 18 lncRNAs whose whose expression levels were consistently increased (Figure 5A) and 14 lncRNAs (names expression levels were consistently increased (Figure 5A) and 14 lncRNAs were consistently decreased (Figure 5B) during the whole lncRNAs marked with blue) were consistently decreased (Figure 5B) during the whole developmental cycle of fruits
By Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, we found that multiple pathways were enriched in the co-expressed genes (Figure 6A,C,E) and co-localized genes (Figure 6B,D,F) of the lncRNAs that were varied at different tomato fruit developmental stages
It beenknown knownthat thatlncRNAs lncRNAs play essential in diverse biological processes plants
Summary
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. A total of 10,919 lncRNAs, including 248 novel lncRNAs, were identified, of which 65 novel lncRNAs were significantly differentially expressed in the flowers, leaves, and roots [51] These studies indicate that the emerging lncRNAs play essential regulatory roles in various developmental processes and stress responses in tomato plants and fruits. This concept could be further supported by the fact that lncRNAs have been widely studied in multiple horticultural crops, including strawberry, mango, walnut, kiwifruit, orange, pepper, gnetum luofuense, apple, sweet cherry, grapevine, pineapple, sea buckthorn, eucommia ulmoides, mulberry, and Cucumis melo (Table 2)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
