Genomic Identification and Characterization of the Cotton YABBY Gene Family

<b>Background</b>: <i>YABBY</i> transcription factors play important roles in plant growth and development. Although this gene family has been characterized in many plant species, a comprehensive analysis in cotton remains unavailable. <b>Methods</b>: In this study, we investigated the YABBY gene family in cotton by integrating multiple bioinformatics methods. <b>Results</b>: <i>YABBY</i> genes were identified in the genomes of four cotton species (<i>Gossypium hirsutum</i>, <i>Gossypium barbadense</i>, <i>Gossypium arboretum</i> and <i>Gossypium raimondii</i>) and these identified genes were further classified into six groups. Following this classification, the expansion of the cotton <i>YABBY</i> gene family was examined, and we found that the family exhibits diverse expansion patterns during evolution, with segmental duplication acting as the primary driving force. In contrast, the notably larger repertoire of <i>YABBY</i> genes in <i>G. raimondii</i> is likely attributable to transposon activity. Regarding their evolutionary trajectory, Ka/Ks analysis showed that the <i>YABBY</i> gene family has undergone purifying selection. Beyond evolution, expression and cis-element analyses further demonstrated that YABBY genes possess diverse functions. In addition, we identified <i>YABBY</i> genes involved in different developmental stages of cotton fibers. <b>Conclusions</b>: We clarify the function and evolution of the cotton <i>YABBY</i> gene family in this work, and these results will provide a critical resource for further research on YABBY genes.