| Summary: | Protein palmitoylation, the most common and the only reversible post-translational lipid modification following protein translation, plays a pivotal role in the biochemical and physiological processes of both animals and plants. DHHC proteins, enriched with DHHC (Asp-His-His-Cys) domains, serve as catalyst for protein palmitoylation. However, research on DHHC in cotton remains scarce. This study conducted a systematic characterization and bioinformatics analysis on <i>G. arboreum</i>, <i>G. raimondii</i>, <i>G. hirsutum</i>, and <i>G. barbadense</i>, detecting 38, 37, 74, and 74 DHHC genes, respectively. Phylogenetic analysis categorized the DHHC gene family into six subgroups, consistent with previous evolutionary studies in <i>Arabidopsis</i> and rice. A further examination of protein structure revealed a correlation between genetic relatedness, structural similarity, and functional identity. Cis-element analysis identified elements predominantly associated with light response, stress, growth and development, and plant hormones. The integration of cotton seed development transcriptome, tissue expression pattern analysis, and population transcriptome data collectively suggests that <i>Ghir_A05G027650</i> and <i>Ghir_D05G027670</i> are promising candidate genes influencing seed development in upland cotton. Conversely, <i>Gbar_A04G010750</i> and <i>Gbar_A12G020520</i> emerge as potential candidates affecting both seed and fiber development in sea island cotton. These findings lay down a theoretical foundation for delving into the functional diversity of DHHC genes in cotton, thereby paving the way for the development of new breeding strategies and the optimization of cotton seed and fiber production, ultimately contributing to improved crop yield and quality.
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