Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber (Cucumis sativus L.)

Abstract

Cucumber is an extremely perishable vegetable; however, under room conditions, the fruits become unfit for consumption 2–3 days after harvesting. One natural variant, DC-48 with an extended shelf-life was identified, fruits of which can be stored up to 10–15 days under room temperature. The genes involved in this economically important trait are regulated by non-coding RNAs. The study aims to identify the long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) by taking two contrasting genotypes, DC-48 and DC-83, at two different fruit developmental stages. The upper epidermis of the fruits was collected at 5 days and 10 days after pollination (DAP) for high throughput RNA sequencing. The differential expression analysis was performed to identify differentially expressed (DE) lncRNAs and circRNAs along with the network analysis of lncRNA, miRNA, circRNA, and mRNA interactions. A total of 97 DElncRNAs were identified where 18 were common under both the developmental stages (8 down regulated and 10 upregulated). Based on the back-spliced reads, 238 circRNAs were found to be distributed uniformly throughout the cucumber genomes with the highest numbers (71) in chromosome 4. The majority of the circRNAs (49%) were exonic in origin followed by inter-genic (47%) and intronic (4%) origin. The genes related to fruit firmness, namely, polygalacturonase, expansin, pectate lyase, and xyloglucan glycosyltransferase were present in the target sites and co-localized networks indicating the role of the lncRNA and circRNAs in their regulation. Genes related to fruit ripening, namely, trehalose-6-phosphate synthase, squamosa promoter binding protein, WRKY domain transcription factors, MADS box proteins, abscisic stress ripening inhibitors, and different classes of heat shock proteins (HSPs) were also found to be regulated by the identified lncRNA and circRNAs. Besides, ethylene biosynthesis and chlorophyll metabolisms were also found to be regulated by DElncRNAs and circRNAs. A total of 17 transcripts were also successfully validated through RT PCR data. These results would help the breeders to identify the complex molecular network and regulatory role of the lncRNAs and circRNAs in determining the shelf-life of cucumbers.

Underlying physiological mechanism and expression analysis of important genes associated with extended shelf-life in cucumber

“…The potential candidate genes associated with extended shelf-life are the genes encoding cell-wall degradation enzymes, biosynthesis of ethylene and key upstream transcription factors. Cell walls, tissue turgors, and cuticles are reported to be critical players in cell wall stability and the retention of fruit rmness (Dey et al, 2022). The retention of green colour in the genotype, DC-48 was mainly due to the slower degradation of chlorophyll after harvest.…”

“…Cucumber fruits are often consumed in their unripe green form, as the ripe yellow form is bitter and acidic. However, the storage of fresh cucumber fruits is a complex process that requires cost-intensive storage facilities to keep them marketable for an extended period (Friedman 2020; Dey et al 2022). Moreover, cucumber fruits are not well-suited for storage at low temperatures due to chilling damage, which rules out the use of cooling, a common method to prolong the shelf life of fresh items (Paul et al 2012).…”

Identification, characterization and transcriptional analysis of the long non-coding RNA landscape in the familyCucurbitaceae

“…Recent studies have revealed the potential importance of lncRNAs as modulators of the development (22, 23) or the response to biotic (24–26) or abiotic (27, 28) stress conditions in diverse Cucurbitaceae family members. However, detailed information about lncRNAs in cucurbits is limited, and only a list of unclassified and barely characterized lncRNAs in cucumber, melon and watermelon are currently available in GreeNC (29), PLncDB V2.0 (30) or CANTATAdb 2.0 (31), the most relevant databases containing plant lncRNAs.…”

Genome-wide identification and characterization of tissue-specific non-coding RNAs in black pepper (Piper nigrum L.)

“…HOTAIR (Hox Antisense Intergenic RNA) is a trans-acting lncRNA in humans that transports itself to other locations on different chromosomes and regulates the gene expression ( Chen and Carmichael, 2010 ; Song et al., 2016 ). Apart from the extensive studies done in humans and other mammals, various plant lncRNAs have also been identified including Arabidopsis thaliana ( Lu et al., 2017 ), wheat ( Lu et al., 2020 ), rice ( Wang et al., 2018 ; Zhou et al, 2021 ), maize ( Li et al., 2014 ), tomato ( Yang et al., 2019 ), cucumber ( He et al., 2020 ; Dey et al., 2022 ), pearl millet ( Kumar et al., 2022 ), and watermelon ( Sun et al., 2020 ). LDMAR (Long Day Specific Male-sterility-associated RNA) which is a 1236 bp long lncRNA can regulate the male sterility sensitive to photoperiod in rice.…”