Structural and functional based identification of the bean (Phaseolus) microRNAs and their targets from expressed sequence tags

  • Muhammad Younas Khan BarozaiEmail author
  • Muhammad Din
  • Iftikhar Ahmed Baloch


MicroRNAs (miRNAs) are small, 18–26 nucleotides long, non-coding RNAs that play role in post-transcriptional gene regulation. Many of these are evolutionarily conserved. This suggests a powerful approach to predict new miRNAs in other species. In this research, structural and functional approaches were combined to make computational prediction of potential miRNAs and their targets in Bean (Phaseolus). Total 55 novel miRNAs were detected from 38 miRNAs families in Bean (Phaseolus). These families are; miR156, 160, 164, 168, 170, 171, 172, 319, 393, 396, 397, 398, 408, 414, 438, 444, 535, 1310, 1424, 1426, 1848, 1860, 1863, 2055, 2091, 2093, 2094, 2102, 2103, 2105, 2864, 2866, 2925, 2926, 4221, 4245, 4246 and 4250. In the 55 putative miRNAs; 28 miRNAs belong to Phaseolus acutifolius, 23 to Phaseolus vulgaris, 4 to Phaseolus coccineus. All the mature miRNAs reside in the stem portion of the hairpin structures. Total 146 potential protein targets were predicted for these miRNAs.


Phaseolus MicroRNAs Expressed sequence tags (ESTs) 



Arabidopsis lyrata


Arabidopsis thaliana


Basic local Alignment Search Tool


Core Hairpin Ratio


Expressed Sequence Tags


Messenger RNA




Minimum Free Energy


Precursor microRNAs


National Center for Biotechnology Information


Oryza sativa


Phaseolus acutifolius


Phaseolus coccineus


Phaseolus vulgaris


Populus trichocarpa


Primary Transcripts of Mature miRNAs


Ricinus communis


RNA Induced Silencing Complex

Pol II

RNA Polymerase II Enzyme


Theobroma cacao


Untranslated Regions


Vitis vinifera

Supplementary material

10969_2013_9152_MOESM1_ESM.doc (360 kb)
The novel Phaseolus miRNAs secondary structures. The Phaseolus pre-miRNAs secondary structures were developed through Mfold algorithm. These structures clearly showing the mature miRNAs in stem portion of the stem-loop structures, highlighted in green (DOC 360 kb)
10969_2013_9152_MOESM2_ESM.doc (242 kb)
The Phaseolus miRNAs targets. The Phaseolus miRNA families and their putative targets, predicted with the help of Blastn and RNA-hybrid tools are represented. The targeted proteins name, Genbank Acc., RNA-Hybrid results and functions are also provided (DOC 241 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Muhammad Younas Khan Barozai
    • 1
    Email author
  • Muhammad Din
    • 1
  • Iftikhar Ahmed Baloch
    • 1
  1. 1.Department of BotanyUniversity of BalochistanQuettaPakistan

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