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Identification of microRNAs from transcriptome data in gurmar (Gymnema sylvestre)

Kalariya, Kuldeepsingh A., Meena, Ram Prasnna, Saran, Parmeshwar Lal, Manivel, Ponnuchamy
Horticulture, environment and biotechnology 2019 v.60 no.3 pp. 383-397
Gibbs free energy, Gymnema sylvestre, adenine, auxins, cytosine, flowers, fruits, gene expression regulation, genomics, guanine, leaves, medicinal plants, messenger RNA, microRNA, phytoene synthase, polyproteins, prediction, tissues, transcriptome, transcriptomics, unigenes, uracil
MicroRNAs (miRNAs) are single-stranded, non-coding, small (~ 22 nt) RNAs that regulate mRNA targets in plants and animals. Gymnema sylvestre (Retz.) is an important medicinal plant that lacks genomic as well as transcriptomic information. Here, to identify homologous miRNAs, we screened 6028 unique known plant miRNAs against 272,161 unigenes of G. sylvestre (Retz.) generated by paired-end deep transcriptome sequencing. We utilized 76 aligned unigenes for extracting the precursor sequences in G. sylvestre (Retz.) and identified 16 potential candidate miRNAs belonging to 12 miRNA families. The mean minimal folding free energy index (MFEI) value of these 16 predicted miRNAs was − 0.966, ranging from − 0.653 to − 2.37, while the G + C% content varied between 27.3 and 61.9%. Nucleotide composition analysis revealed that cytosine was the dominant nucleotide in mature miRNAs (26.3%), while uracil was the next most prevalent nucleotide (25.7%), followed by guanine (24.3%) and adenine (23.7%). In most cases (81%), the first position of the 5′ end was occupied by uracil in the identified mature G. sylvestre (Retz.) miRNAs. Differential expression of target unigenes revealed that, as compared to leaf tissue, a total 16 and 12 target unigenes were differentially expressed in flower and fruit tissues, respectively. Among the differentially expressed target unigenes were Auxin Response Factors 17-like, Copia-type polyprotein Phytoene synthase 2, as well as several encoding unnamed, predicted, uncharacterized, and/or hypothetical proteins. After detailed prediction of miRNAs and their corresponding target unigenes, we report for the first time a total of 13 miRNA and 213 corresponding target unigenes in G. sylvestre (Retz.).