Genome-wide insights into the nomenclature, evolution and expression of tobacco TIFY/JAZ genes.

Main conclusion: A systematic nomenclature for tobacco TIFY/JAZ proteins was established via genome-wide analysis, and the gene transcription patterns and potential functions of these proteins were analyzed as well. Intensive studies focused on the plant-specific JAZ regulators of jasmonate (JA) signaling in tobacco due to their critical roles in regulating JA-mediated development, secondary metabolism, and stress responses. JAZs comprise a subfamily of the TIFY proteins, yet the reported TIFY/JAZ regulators of tobacco spp. are tangled in naming confusion, which resulted in nomenclature chaos. Here, we identified 32 TIFY/JAZ proteins via genome-wide analysis of tobacco cultivar TN90 and obtained their homologues in Nicotiana sylvestris and Nicotiana tomentosiformis. By bioinformatic analysis, these TIFY/JAZ regulators were classified into 4 subfamilies (i.e., 21 JAZs, 5 ZIM & ZMLs, 2 TIFY8s, and 4 PPDs) based on their phylogenetic relationship to establish a systematic nomenclature, which indicated gene loss or genomic rearrangement during the formation of common tobacco. Analysis of JA-induced expression revealed that these TIFY/JAZ genes displayed distinct expression patterns in the leaves and roots upon JA treatment. Further microarray and metabolomics assays observed that 5 TIFY/JAZ genes were differentially expressed in the plants with dysfunction of COI1, the receptor protein of JA hormone and that the abundance of a series of primary and secondary metabolites was altered as well. A predicted protein interaction network of tobacco TIFY/JAZ proteins was also constructed, and it indicated that 120 proteins may interact with these regulators. Findings of this work provide valuable information about TIFY/JAZ proteins in regulating JA responses and metabolic processes in tobacco and may contribute greatly to future studies on tobacco TIFY/JAZ proteins.