Small RNA sequencing and identification of papaya (Carica papaya L.) miRNAs with potential cross-kingdom human gene targets

Abstract

Several studies have demonstrated potential role of plant-derived miRNAs in cross-kingdom species relationships by transferring into non-plant host cells to regulate certain host cellular functions. How nutrient-rich plants regulate host cellular functions, which in turn alleviate physiological and disease conditions in the host remains to be explored in detail. This computational study explores the potential targets, putative role, and functional implications of miRNAs derived from Carica papaya L., one of the most cultivated tropical crops in the world and a rich source of phytochemicals and enzymes, in human diet. Using the next-generation sequencing, -Illumina HiSeq2500, ~ 30 million small RNA sequence reads were generated from C. papaya young leaves, resulting in the identification of a total of 1798 known and 49 novel miRNAs. Selected novel C. papaya miRNAs were predicted to regulate certain human targets, and subsequent annotation of gene functions indicated a probable role in various biological processes and pathways, such as MAPK, WNT, and GPCR signaling pathways, and platelet activation. These presumptive target gene in humans were predominantly linked to various diseases, including cancer, diabetes, mental illness, and platelet disorder. The computational finding of this study provides insights into how C. papaya-derived miRNAs may regulate certain conditions of human disease and provide a new perspective on human health. However, the therapeutic potential of C. papaya miRNA can be further explored through experimental studies.

Keywords: Carica papaya; Cross-kingdom; Next-generation sequencing; miRNA.

Fig. 1

Reads and member distribution of identified known miRNAs. MiR156 and miR166 shows the highest family members and miR157 shows the lowest

Fig. 2

Phylogenetic tree of C. papaya shows the relationship between novel miRNA and reported miRNA of C. papaya miRNA family. Purple diamond indicates the identified novel miRNA

Fig. 3

The representative bar graphs illustrate the functional annotation analysis of C. papaya regulated human target genes. A Gene ontology for known miRNAs performed at level 2 for three main categories (cellular component, molecular function, and biological process). B Gene ontology for novel miRNAs performed at level 2 for three main categories (cellular component, molecular function, and biological process)

Fig. 4

Gene network analysis showing association between significantly modulated genes. Top ten genes marked with red color have been detected from bottleneck method

Fig. 5

A Four novel miRNA and their human targets are depicted by circos diagram, and their connection is shown by respective color links. B Novel miRNAs and their targeted genes involved in platelet disorders