An approach to identify the novel miRNA encoded from H. Annuus EST sequences

Abstract

MicroRNAs are a newly discovered class of non-protein small RNAs with 22–24 nucleotides. They play multiple roles in biological processes including development, cell proliferation, apoptosis, stress responses and many other cell functions. In this research, several approaches were combined to make a computational prediction of potential miRNAs and their targets in Helianthus annuus (H. annuus). The already available information of the plant miRNAs present in miRBase v21 was used against expressed sequence tags (ESTs). A total of three miRNAs were detected from which one potential novel miRNA was identified following a range of strict filtering criteria. The target prediction was carried out for these three miRNAs having various targets. These targets were functionally annotated and GO terms were assigned. To study the conserved nature of the miRNAs, predicted phylogenetic analysis was carried out. These findings will significantly provide the broader picture for understanding the functions in H. annuus.

Whole Aegilops tauschii Transcriptome Investigation Revealed Nine Novel miRNAs Involved in Stress Response

“…Briefly, an identified structure was considered as a predicted stem-loop miRNA only if the following six criteria were met: (1) the sequence could fold into an appropriate stem-loop hairpin structure (2) at least one mature miRNA matched to the one arm of the stem-loop; (3) no loop between mature miRNA and its opposite sequence (4) miRNA having less than six mismatches with its opposite sequence; (5) stem-loop with higher minimal folding free energy (MFE) minimal folding free energy index (MFEI); ( 6) and the MFEI ranged around 0.6-0.9; 15,16,22 . MFE was estimated using miReap and MFEI was calculated using the following equation:…”

“…Significant roles of miRNAs made researchers to look up intensively for novel miRNAs. To this end, expressed sequence tags have been used widely [13][14][15][16] . Pani and Mahapatra have predicted two new miRNAs in a medicinal plant C. roseus.…”

“…Furthermore, computational prediction has been also used to detect potential miRNAs in H. annuus. This prediction led to identify three potential miRNAs that could regulate various target genes 16 .…”

Whole Aegilops tauschii transcriptome investigation revealed nine novel miRNAs involved in stress response

“…Briefly, an identified structure was considered as a predicted stem-loop miRNA only if the following six criteria were met: (1) the sequence could fold into an appropriate stem-loop hairpin structure (2) at least one mature miRNA matched to the one arm of the stem-loop; (3) no loop between mature miRNA and its opposite sequence (4) miRNA having less than six mismatches with its opposite sequence; (5) stem-loop with higher minimal folding free energy (MFE) minimal folding free energy index (MFEI); (6) and the MFEI ranged around 0.6-0.9; 15,16,22 . MFE was estimated using miReap and MFEI was calculated using (6) Range of central mismatch leading to translational inhibition = between 9 and 11 nt 23 .…”

Identification and expression analysis of a microRNA cluster derived from pre-ribosomal RNA in Papaver somniferum L. and Papaver bracteatum L.

“…EST sequences have been analyzed for identification and prediction of miRNAs in Brassica napus L. [ 24 ], Glycine max L. [ 7 ], P . somniferum L. [ 22 ], Helianthus annuus L. [ 25 ]. Recently, computational prediction and deep sequencing technology, are the main approaches in order to detection of given miRNA [ 26 ].…”