Genome-wide identification and characterization of DUF789 genes in cotton: implications for fibre development

Proteins containing domains of unknown function (DUFs) play a crucial role in plant growth, development and stress adaptation, but many of them are still uncharacterized. The DUF789 family is one of the least studied of these, especially in economically significant crops like cotton (Gossypium spp.), whose possible function in fibre production and abiotic stress response is yet unknown.

In a comprehensive genome-wide analysis, a total of 91 DUF789 genes were identified in four Gossypium species: G. arboreum, G. barbadense, G. raimondii and G. hirsutum. Evolutionary and phylogenetic analyses placed the GhDUF789 proteins into different clades, with purifying selection identified as the major evolutionary force. Analyses of gene structure and conserved motifs revealed considerable structural diversity, with closely related genes showing similar exon-intron patterns and motif compositions. Synteny and duplication analyses showed that segmental and tandem duplications contributed to the DUF789 family expansion in cotton. Analysis of cis-regulatory elements revealed that the GhDUF789 promoters are enriched in motifs responsive to hormonal, developmental, light-induced and abiotic stresses. GO enrichment analyses, prediction of protein-protein interaction and secondary and tertiary structure modelling, indicated that GhDUF789 proteins are involved in clathrin-mediated vesicle trafficking and membrane trafficking. The miRNA target prediction revealed regulatory interactions with conserved miRNAs from cotton, in particular ghr-miR414 and ghr-miR396. Expression profiling based on transcriptome analysis, supported by validation using qRT-PCR, revealed that several GhDUF789 genes are differentially expressed during fibre development and respond strongly to drought, heat, salinity and cold stress, especially in drought-tolerant genotypes.

This study provides the first comprehensive characterization of the DUF789 gene family in cotton and offers new insights into its evolutionary dynamics, structural features and potential role in fibre development and adaptation to abiotic stress. The results provide a solid foundation for future functional studies and identify candidate GhDUF789 genes for targeted genetic improvement of stress resistance and fibre quality in cotton.