A comprehensive analysis of cotton VQ gene superfamily reveals their potential and extensive roles in regulating cotton abiotic stress

Abstract

<jats:title>Abstract</jats:title> <jats:p>Background Valine-glutamine (VQ) motif-containing proteins play important roles in plant growth, development and abiotic stress response. For many plant species, the <jats:italic>VQ</jats:italic> genes have been identified and their functions have been described. However, little is known about the origin, evolution, and functions (and underlying mechanisms) of the <jats:italic>VQ</jats:italic> family genes in cotton. Results In this study, we comprehensively analyzed the characteristics of 268 <jats:italic>VQ</jats:italic> genes from four <jats:italic>Gossypium</jats:italic> genomes and found that the <jats:italic>VQ</jats:italic> proteins evolved into ten clades, and each clade had a similar structural and conservative motif. The expansion of the <jats:italic>VQ</jats:italic> gene was mainly through segmental duplication, followed by dispersal. Expression analysis revealed that the <jats:italic>VQ</jats:italic> genes play important roles in response to salt and drought stress, especially <jats:italic>GhVQ18</jats:italic> and <jats:italic>GhVQ84</jats:italic> were significantly high expression in PEG stress and salt stress. Further analysis showed that <jats:italic>GhVQ</jats:italic> genes were co-expressed with <jats:italic>GhWRKY</jats:italic> transcription factors (TFs), and microRNAs (miRNAs) could hybridize to their cis-regulatory elements. Conclusions The results in this study broaden our understanding of the <jats:italic>VQ</jats:italic> gene family in plants, and the analysis of the structure, conserved elements, and expression patterns of the <jats:italic>VQ</jats:italic> genes provide a solid foundation for exploring their specific functions in the abiotic stress responses in cotton. Our study provides significant insight into the potential functions of <jats:italic>VQ</jats:italic> genes in cotton.</jats:p>