Lipopolysaccharide perception leads to dynamic alterations in the microtranscriptome of Arabidopsis thaliana cells and leaf tissues

BACKGROUND: MicroRNAs (miRNAs) are non-coding RNA molecules which have recently emerged as important gene regulators in plants and their gene expression analysis is becoming increasingly important. miRNAs regulate gene expression at the post-transcriptional level by translational repression or target degradation of specific mRNAs and gene silencing. In order to profile the microtranscriptome of Arabidopsis thaliana leaf and callus tissues in response to bacterial lipopolysaccharide (LPS), small RNA libraries were constructed at 0 and 3 h post induction with LPS and sequenced by Illumina sequencing technology. RESULTS: Differential regulation of subset of miRNAs in response to LPS treament was observed. Small RNA reads were mapped to the miRNA database and 358 miRNAs belonging to 49 miRNA families in the callus tissues and 272 miRNAs belonging to 40 miRNA families in the leaf tissues were identified. Moreover, target genes for all the identified miRNAs families in the leaf tissues and 44 of the 49 miRNAs families in the callus tissues were predicted. The sequencing analysis showed that in both callus and leaf tissues, various stress regulated-miRNAs were differentially expressed and real time PCR validated the expression profile of miR156, miR158, miR159, miR169, miR393, miR398, miR399 and miR408 along with their target genes. CONCLUSION: A. thaliana callus and leaf callus tissues respond to LPS as a microbe-associated molecular pattern molecule through dynamic changes to the microtranscriptome associated with differential transcriptional regulation in support of immunity and basal resistance. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-015-0465-x) contains supplementary material, which is available to authorized users.