Integrated analysis of lncRNA and mRNA transcriptomes reveals the potential regulatory role of lncRNA in kiwifruit ripening and softening

Abstract

Kiwifruit has gained increasing attention worldwide for its unique flavor and high nutritional value. Rapid softening after harvest greatly shortens its shelf-life and reduces the commercial value. Therefore, it is imperative and urgent to identify and clarify its softening mechanism. This study aimed to analyze and compare the long noncoding RNA (lncRNA) and mRNA expression patterns in ABA-treated (ABA) and room temperature (RT)-stored fruits with those in freshly harvested fruits (CK) as control. A total of 697 differentially expressed genes (DEGs) and 81 differentially expressed lncRNAs (DELs) were identified while comparing ABA with CK, and 458 DEGs and 143 DELs were detected while comparing RT with CK. The Kyoto Encyclopedia of Genes and Genomes analysis of the identified DEGs and the target genes of DELs revealed that genes involved in starch and sucrose metabolism, brassinosteroid biosynthesis, plant hormone signal transduction, and flavonoid biosynthesis accounted for a large part. The co-localization networks, including 38 DEGs and 31 DELs in ABA vs. CK, and 25 DEGs and 25 DELs in RT vs. CK, were also performed. Genes related to fruit ripening, such as genes encoding β-galactosidase, mannan endo-1,4-β-mannosidase, pectinesterase/pectinesterase inhibitor, and NAC transcription factor, were present in the co-localization network, suggesting that lncRNAs were involved in regulating kiwifruit ripening. Notably, several ethylene biosynthesis- and signaling-related genes, including one 1-aminocyclopropane-1-carboxylic acid oxidase gene and three ethylene response factor genes, were found in the co-localization network of ABA vs. CK, suggesting that the promoting effect of ABA on ethylene biosynthesis and fruit softening might be embodied by increasing the expression of these lncRNAs. These results may help understand the regulatory mechanism of lncRNAs in ripening and ABA-induced fruit softening of kiwifruit.

Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.)

“…Distinct characterizations between lncRNAs and mRNAs have been found in the majority of plant and animal species. We found that blueberry lncRNAs had shorter transcript lengths, shorter ORF sizes, fewer exons, and lower expression levels than protein-coding RNAs, which is consistent with previous studies in other fruit species ( Zhang et al., 2017 ; Chen et al., 2021 ). Our research also found that blueberry lncRNAs have fewer isoforms, which indicates that alternative splicing (AS) of lncRNAs occurs at a lower frequency than that of mRNAs.…”

“…MdLNC499 is an apple lncRNA that functions in light-induced fruit coloration by inducing MdERF109 expression ( Ma et al., 2021 ). Using next-generation sequencing techniques, a large number of lncRNAs that participate in the fruit developmental process have been identified in several fruit species, including strawberry ( Kang and Liu, 2015 ), tomato ( Zhu et al., 2015 ; Wang et al., 2018 ), kiwifruit ( Tang et al., 2016 ; Chen et al., 2021 ), sea buckthorn ( Zhang et al., 2017 ), Cucumis melo ( Tian et al., 2019 ), and apple ( Yang et al., 2019 ). However, the presence of lncRNAs in blueberries has not been studied.…”

Nanopore-Based Comparative Transcriptome Analysis Reveals the Potential Mechanism of High-Temperature Tolerance in Cotton (Gossypium hirsutum L.)

“…LncRNAs have long been known to participate in development and stress resistance for plants [47]. For instance, lncRNAs may be involved in ripening and softening in kiwifruit via regulating the expression of genes involved in starch and sucrose metabolism, brassinosteroid biosynthesis, and plant hormone signal transduction [48]. A recent study showed that lncRNAs regulate expression of target genes to enhance high-temperature tolerance in poplar [49].…”

Advances in Non-Coding RNA Sequencing

“…A particular focus has been laid on the role of ncRNAs in plant immunity, development and stress response (e.g., abiotic factors) [ 192 , 193 ]. Sequencing has also facilitated the study of plants not commonly used in research, such as pistachio [ 194 ], sugar beet [ 195 ], and kiwifruit [ 196 ]. Even in a well studied plant such as Arabidopsis thaliana, sequencing has allowed to uncover a large number of previously undescribed lncRNAs and in particular highlighted the role of cold-induced lncRNA MAS in preventing precocious flowering [ 197 ].…”