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

Yiting Chen,Ruilian Lai,Rujian Wu,Wenguang Chen,Xin Feng,Chunzhen Cheng,Minxia Gao

doi:10.1038/s41598-021-81155-1

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.

Highlights

Kiwifruit has gained increasing attention for its unique flavor and high vitamin C content
Starch degradation is generally considered to be the first sign of kiwifruit postharvest ripening, which contributes to the increase in total soluble solid (TSS)
The ascorbic acid (AsA) content dropped from 430.62 μg/g in the CK group to 322.19 μg/g in the room temperature (RT) group, while in the abscisic acid (ABA) group, it decreased to 138.28 μg/g

Summary

Introduction

Kiwifruit has gained increasing attention for its unique flavor and high vitamin C content. The RNAi transgene of ACO gene in kiwifruit significantly inhibited ethylene production and fruit s oftening[3]. Next-generation sequencing is a powerful tool for analyzing gene expression changes during certain processes or under certain treatments, which is widely used to elucidate the mechanism of fruit ripening and s oftening[18,19]. Given the importance of ABA in fruit softening and the limited knowledge of lncRNAs involved in kiwifruit ripening, genome-wide expression analysis of genes and lncRNAs was necessary. The integrated analysis of lncRNA and mRNA expression profiles might help understand the ripening mechanism of kiwifruit and provide clues for further elucidation of the role of ABA and lncRNAs in fruit ripening and softening

Objectives

Methods

Results

Conclusion