Genome‐wide identification of chromium stress‐responsive micro RNAs and their target genes in tobacco (Nicotiana tabacum) roots

Abstract

Tobacco easily accumulates certain heavy metals in leaves and thus poses a potential threat to human health. To systematically dissect Cr-responsive microRNAs (miRNAs) and their targets at the global level, 4 small RNA libraries were constructed from the roots of Cr-treated (Cr) and Cr-free (control) for 2 contrasting tobacco genotypes,Yunyan2 (Cr-sensitive) and Guiyan1 (Cr-tolerant). Using high-throughput-sequencing-technology, the authors identified 53 conserved and 29 novel miRNA families. Comparative genomic analysis of 41 conserved Cr-responsive miRNA families revealed that 11 miRNA families showed up-regulation in Guiyan1 but unaltered in Yunyan2, and 17 miRNA families were up-regulated only in Yunyan2 under Cr stress. Only 1 family, miR6149, was down-regulated in Yunyan2 but remained unchanged in Guiyan1. Of the 29 novel miRNA families, 14 expressed differently in the 2 genotypes under Cr stress. Based on a high-throughput degradome sequencing homology search, potential targets were predicted for the 41 conserved and 14 novel Cr-responsive miRNA families. Clusters of Orthologous Groups functional category analysis revealed that some of these predicted target transcripts of miRNAs are responsive to biotic and abiotic stresses. Furthermore, the expression patterns of many Cr-responsive miRNAs were validated by stem-loop real-time transcription polymerase chain reaction. The results of the present study provide valuable information and a framework for understanding the function of miRNAs in Cr tolerance.

Emerging techniques to decipher microRNAs (miRNAs) and their regulatory role in conferring abiotic stress tolerance of plants

“…A differential expression pattern was observed only for the miR6149 family, whose expression remained unchanged in Guiyan1, but was suppressed in Yunyan2. Differential regulation of 14 novel miRNA families was also reported in the two genotypes under Cr toxicity (Bukhari et al 2015). This validates the important functions played by miRNAs in regulating heavy metal stress tolerance in plants.…”

“…In the same plant, the targets for miR156, miR159, miR833a, and miR396 were depicted to be SPL, TCP, RAX2, and GRF, respectively . Cr stress Bukhari et al (2015) recently identified 53 conserved and 29 miRNA families from the four sRNA libraries constructed from Cr-treated and Cr-free (control) roots of two contrasting tobacco genotypes, Yunyan2 (Cr-sensitive) and Guiyan1 (Cr-tolerant). The authors observed that 11 conserved miRNA families were up-regulated in Guiyan1; however, their expression pattern exhibited no significant changes in Yunyan2.…”

Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

“…Using GenBank (http://www.ncbi.nlm.nih.gov/) and Rfam 10.1 (http://rfam.sanger.ac.uk) databases comparison, non-coding RNAs such as ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), snoRNA, and signal recognition particle RNA (srpRNA) were identified and removed. The remaining sRNAs were subjected to a Basic Local Alignment Search Tool (BLASTn) search with no more than two mismatches against miRBase 18.0 database (http://www.mirbase.org/) to identify known miRNA in the samples [44, 45]. sRNA annotation followed a priority rule for classification to avoid redundancy: non-coding RNA (in which GenBank > Rfam) > known miRNA > repeat [46].…”

Traversing the Links between Heavy Metal Stress and Plant Signaling

“…Cotton seedlings treated with Pb showed downregulation of miR156, miR398, miR399 and upregulation of miR162, miR167, miR169, miR395, miR396, and miR397 (He et al, 2014 ). Chromium showed upregulation of miR156, miR167, miR169, miR171, and downregulation of miR166 (Bukhari et al, 2015 ) (Figure 3 ). Among the heavy metal responsive miRNAs, miR156, miR159, miR166, and miR398 were shown to be differentially regulated.…”

“…It has been shown that various conserved miRNAs are differentially regulated during the normal and stress conditions (Figure 3 ). Differential expression of miRNAs in heavy metal stress indicates the possible involvement of miRNAs in heavy metal stress detoxification and tolerance (Ding et al, 2011 ; Liu and Zhang, 2012 ; Zhou et al, 2012 ; Bukhari et al, 2015 ; Noman and Aqeel, 2017 ). Here, we have focused on studies showing differential expression of conserved miRNA in metal stress and regulation of signaling pathway by miRNAs or vice versa in response to heavy metals.…”