Computational Identification of miRNAs and Temperature-Responsive lncRNAs From Mango (Mangifera indica L.)

Abstract

Mango is a major tropical fruit in the world and is known as the king of fruits because of its flavor, aroma, taste, and nutritional values. Although various regulatory roles of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been investigated in many plants, there is yet an absence of such study in mango. This is the first study to provide information on non-coding RNAs (ncRNAs) of mango with the aims of identifying miRNAs and lncRNAs and discovering their potential functions by interaction prediction of the miRNAs, lncRNAs, and their target genes. In this analysis, about a hundred miRNAs and over 7,000 temperature-responsive lncRNAs were identified and the target genes of these ncRNAs were characterized. According to these results, the newly identified mango ncRNAs, like other plant ncRNAs, have a potential role in biological and metabolic pathways including plant growth and developmental process, pathogen defense mechanism, and stress-responsive process. Moreover, mango lncRNAs can target miRNAs to reduce the stability of lncRNAs and can function as molecular decoys or sponges of miRNAs. This paper would provide information about miRNAs and lncRNAs of mango and would help for further investigation of the specific functions of mango ncRNAs through wet lab experiments.

Emerging roles and mechanisms of lncRNAs in fruit and vegetables

“…In mango, a total of 7610 lncRNAs were identified in response to temperature changes. Notably, lnc26299 was found to have the capability to interact with related cDNA 12B (RC12B), a protein that exhibited significant upregulation in response to cold stress [ 80 ]. Additionally, Lai et al .…”

Coordinating Diverse Functions of miRNA and lncRNA in Fleshy Fruit

“…Ptr-miR396b was determined to target 1-aminocyclopropane-1carboxylic acid oxidase ( ACO ) in response to cold stress in orange ( Poncirus trifoliata ) [ 119 ]. In mango, bioinformatic analysis reveals that MmiR78769 and MmiR101928 target phospholipase A and phospholipase D, respectively, both of which are associated with plant temperature stress-responsive process [ 120 ]. Moreover, degradome-wide analyses have revealed that miR393- TIR1 / AFB displays a cold stress-specific response and miR156- SPL -mediated heat stress response in banana [ 121 ].…”

“…LncRNAs involved in the response of chilling injury in tomato fruit have been systematically identified, providing a new perspective on lncRNA roles in chilling tolerance in fruits [ 123 ]. In mango, the cold-responsive lncRNA CRlnc26299 can interact with RC12B , which is the low-temperature and salt-responsive protein [ 120 ]. A novel lncRNA, COLD INDUCED lncRNA 1 ( CIL1 ), is a positive regulator in plant response to cold stress by regulating the expression of endogenous reactive oxygen species ( ROS ) in Arabidopsis [ 124 ].…”

Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content

“…Transcriptome analysis facilitated the identification of 18 eIF genes (eukaryotic elongation factor) that were expressed under salinity, osmotic and low temperature (2 °C) stress [ 49 ]. Computational analysis using EST and RNA sequence databases in mango established non-coding RNAs such as miRNAs and lncRNAs to be involved in growth and development, ripening, transcription regulation and stress responses [ 96 , 99 ] ( Table 2 ). Furthermore, bHLH TF genes and WD40 protein family members regulating abiotic stress responses in mango, citrus and papaya can provide the knowledge for understanding the responses during salt, drought, alkaline and cold stress conditions [ 50 , 51 , 71 ].…”