Identification of long non-coding RNAs, lncRNA-derived miRNAs, and their target genes associated with jelly seed malady and fruit ripening in mango (Mangifera indica L.)

Abstract:

The mango (Mangifera indica L.) is one of the major fruit crops in tropical and sub-tropical regions of the world, especially in Asia. In North India, thousands of farmers depend on the commercial mango cultivar ‘Dashehari’; however, the fruit quality is severely impacted by a mesocarp-specific malady called Jelly Seed. Long non-coding RNA (lncRNA) and microRNAs (miRNAs) are naturally occurring, endogenous, non-coding RNA molecules that play a crucial role in post-transcriptional gene regulation either by directing mRNAs for cleavage or translational repression. Raw reads from Jelly seed transcriptome data were used for lncRNA identification and the sequences of identified lncRNA were used to mine miRNA encoded by lncRNA. A total of 11 putative miRNAs from 5 different families were identi?ed. psRNA Target tool and BLAST2GO analysis were used to identify and annotate targets. The predicted targets of miRNAs revealed a wide range of gene targets for both translational and cleavage-type inhibition, conforming the hypothesis that a single miRNA might target genes engaged in several metabolic pathways and physiological functions. Predicted miRNA target genes, transcription factors (Glutathione peroxidase, Phytoene synthase, ACS, CNR8, TIFY, MYBetc) and structural genes (Histone) associated with different functional pathways. This work has led to the discovery of conserved putative miRNAs encoded by putative lncRNA, targeting the regulation of lncRNA, enzymatic and TFs genes. The findings of this study will help to study the functions and regulatory mechanisms of miRNAs in jelly seed malady and fruit ripening.

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