Comprehensive Identification and Expression Profiling of the VQ Motif-Containing Gene Family in Brassica juncea

SIMPLE SUMMARY: Plant valine-glutamine (VQ) motif-containing proteins are a type of plant-specific transcription factor (TF), which contain a short and conserved amino acid motif (FxxhVQxhTG). Recent studies showed that VQ proteins play key roles in various developmental processes and abiotic/biotic stresses in plants. In this study, we identified 120 VQ genes in mustard (Brassica juncea), and their phylogenetic relationship, sequence characteristics, conserved motif, gene structure, genome distribution, gene duplication, and cis-element in promoters were also determined. In addition, the organ expression profiles of the BjuVQ genes were analyzed based on RNA-seq data, and the expression profiles of the BjuVQ genes under cold stress were also examined. These results provide a basis for further elucidation of the biological function of BjuVQ genes in mustard. ABSTRACT: Valine-glutamine (VQ) motif-containing proteins are a class of highly conserved transcriptional regulators in plants and play key roles in plant growth, development, and response to various stresses. However, the VQ family genes in mustard have not yet been comprehensively identified and analyzed. In this study, a total of 120 VQ family genes (BjuVQ1 to BjuVQ120), which were unevenly distributed on 18 chromosomes (AA_Chr01 to BB_Chr08), were characterized in mustard. A phylogenetic tree analysis revealed that the BjuVQ proteins were clustered into nine distinct groups (groups I to IX), and members in the same group shared a highly conserved motif composition. A gene structure analysis suggested that most BjuVQ genes were intronless. A gene duplication analysis revealed that 254 pairs of BjuVQ genes were segmentally duplicated and one pair was tandemly duplicated. Expression profiles obtained from RNA-seq data demonstrated that most BjuVQ genes have different gene expression profiles in different organs, including leaf, stem, root, flower bud, pod, and seed. In addition, over half of the BjuVQ genes were differentially expressed at some time points under low temperature treatment. The qRT-PCR data revealed that BjuVQ23, BjuVQ55, BjuVQ57, BjuVQ67, BjuVQ100, and BjuVQ117 were upregulated in response to cold stress. Taken together, our study provides new insights into the roles of different BjuVQ genes in mustard and their possible roles in growth and development, as well as in response to cold stress.