Identification of MicroRNAs and their targets in Helianthus

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs about 20-24 nucleotides long, playing regulatory role. The conserved nature among the various organisms makes them a good source of new miRNAs discovery by comparative genomics approach using bioinformatic tools. A systematic search approach was used for inter-species homologs of miRNA precursors (pre-miRNAs), from known Helianthus expressed sequence tags (ESTs). The study resulted in 61 novel miRNAs belonging to 34 families from Helianthus ESTs. The 28 miRNA families; mir 159,160, 164, 170, 390, 393, 413, 415, 419, 426, 446, 530, 822, 842, 846, 1310, 1888, 2086, 2657, 2667, 2678, 2659, 2911, 2938, 3440, 3521, 3623, and 3630 are reporting for the first time in Helianthus. In the 61 new miRNAs, 20 are from H. tuberosus, 17 miRNAs belong to H. annus, 8 are from H. ciliaris, 5 to H. exilis, 4 is from H. argophyllous, H. petiolaris each and 3 are from H. paradoxus. All the pre-miRNAs form stable minimum free energy (mfe) stem-loop structure as their orthologues form and the mature miRNAs reside in the stem portion of the stem-loop structures. Their targets consist of growth and development related, transcription factors, signalling pathway kinases, stress resistant proteins and transport related proteins.

Identification of microRNAs in ecological model plant <i>Mimulus</i>

“…The Mimulus miRNAs characterization such as source miRNAs, pre-miRNAs length (PL), minimum free folding energies (MFE), mature miRNA sequences (MS), number of mismatches (NM),mature sequence length (ML), source ESTs (SE), mature sequence arm (MSA) and GC percentage are summarized in Table 1. These findings are similar to the reported works of various groups working on miRNAs [21,22,[33][34][35]. Sometimes the miRNAs are expressed in clusters.…”

Computational identification of miRNAs and their targets in Phaseolus vulgaris

“…The lengths of these identified mature miRNA sequences ranged from 19 to 24 nucleotides; however, most of the potential miRNAs (17 of 27 or 62.96%) were 21 nt in length (Table 1). This length was quite similar to other mature miRNAs already identified in other plants (Zhang et al, 2006a;Xie et al, 2010;Barozai et al, 2012;Neutelings et al, 2012). The A+U contents of these predicted P. vulgaris pre-miRNA sequences ranged from 30.34 to 68.37%, with an average of 57.95 ± 8.53% (Table 1), which closely matched the results of previous studies (Ambros et al, 2003;Neutelings et al, 2012).…”

“…The identified P. vulgaris pre-miRNAs were between 68 and 202 nt in length, with an average of 111.37 ± 34.17 nt; however, the majority of the pre-miRNAs (24 of 27 or 88.89%) were 60-150 nt in length (Table 1). These results matched the lengths of most previously predicted premiRNAs in plant species (Zhang et al, 2007;Unver and Budak, 2009;Barozai et al, 2012;Neutelings et al, 2012). Although the identified P. vulgaris miRNA precursors were of a wide range of lengths, they could be folded into the typical miRNA secondary structures (Figure 2).…”

The relationship between codon usage bias and salt resistant genes in Arabidopsis thaliana and Oryza sativa

“…Keywords: Arabidopsis thaliana; codon usage bias; housekeeping genes; rice; salt stress Bioinformatics' approaches are the well-known way of research for nucleic acid (DNA and RNA) sequence analyses to find new findings [7][8][9]. In this particular study, five salt stress tolerant genes Salt Overly sensitive (SOS1), basic lucien-Zipper Protein (bZIP), Calcinurin B like binding 10 (CBL10), Mitogen Activated Protein Kinase-3 (MPK3) and Histidine Kinase-1 (HK1) and three housekeeping genes (Actin, Tubulin and Ubiquitin) were selected from Arabidopsis thaliana and rice (Oryza sativa) and subjected to CUB analysis using bioinformatic's tools.…”