A genome-wide perspective of miRNAome in response to high temperature, salinity and drought stresses in Brassica juncea (Czern) L

PLoS One. 2014 Mar 26;9(3):e92456. doi: 10.1371/journal.pone.0092456. eCollection 2014.

Abstract

Micro RNAs (miRNAs) are involved in diverse biological processes including adaptive response towards abiotic stresses. To unravel small RNAs and more specifically miRNAs that can potentially regulate determinants of abiotic stress tolerance, next generation sequencing of B. juncea seedlings subjected to high temperature, high salt and drought conditions was carried out. With the help of UEA sRNA workbench software package, 51 conserved miRNAs belonging to 30 miRNA families were identified. As there was limited genomic information available for B. juncea, we generated and assembled its genome sequence at a low coverage. Using the generated sequence and other publically available Brassica genomic/transcriptomic resources as mapping reference, 126 novel (not reported in any plant species) were discovered for the first time in B. juncea. Further analysis also revealed existence of 32 and 37 star sequences for conserved and novel miRNAs, respectively. The expression of selected conserved and novel miRNAs under conditions of different abiotic stresses was revalidated through universal TaqMan based real time PCR. Putative targets of identified conserved and novel miRNAs were predicted in B. rapa to gain insights into functional roles manifested by B. juncea miRNAs. Furthermore, SPL2-like, ARF17-like and a NAC domain containing protein were experimentally validated as targets of miR156, miR160 and miR164 respectively. Investigation of gene ontologies linked with targets of known and novel miRNAs forecasted their involvement in various biological functions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Brassica / genetics*
  • Conserved Sequence
  • Droughts*
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Gene Ontology
  • Genome, Plant*
  • High-Throughput Nucleotide Sequencing
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism
  • Molecular Sequence Data
  • RNA, Plant / genetics
  • Reproducibility of Results
  • Salinity*
  • Stress, Physiological / genetics*
  • Temperature*

Substances

  • MicroRNAs
  • RNA, Plant

Grants and funding

The work was financially supported by grant from the Department of Biotechnology (DBT), Delhi, India (grant No. BT/PR628/AGR/36/674/2011). The support from University of Delhi, Delhi, India is also duly acknowledged. ARB, GJ and BK are supported by DBT, India. RP is thankful for research fellowship from Council of Scientific and Industrial research (CSIR), India and DBT, India. Deep sequencing was carried out by DBT-funded High-Throughput Sequencing Facility at University of Delhi South Campus, University of Delhi, New Delhi, India. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.