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

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. Environ Toxicol Chem 2015;34:2573–2582. © 2015 SETAC