biostudies-literatureUnknown2025Bakhtari BPlant-specific transcription factors known as WUSCHEL-related homeobox (WOX) proteins are crucial for regulating plant development and responses to stress. This study represents the first thorough characterization of the WOX gene family in quinoa (Chenopodium quinoa, CqWOXs). In total, we identified 13 probable CqWOX genes, which were categorized into three main subgroups (ancient subgroup, intermediate subgroup, and WUS subgroup) based on phylogenetic analysis. Synteny analysis revealed 12 CqWOX genes as orthologs of WOX genes in Beta vulgaris, Amaranthus hypochondriacus, and Spinacia oleracea, while 10 orthologs were found in Arabidopsis thaliana. Five segmentally duplicated WOX gene pairs were identified in the quinoa genome, all of which have undergone purifying selection, as indicated by their Ka/Ks values being less than one. Additionally, the 2.0 kb promoter regions of CqWOXs were found to harbor various cis-acting elements related to hormone-responsiveness, stress-responsiveness, growth and development, and light-responsiveness elements. The protein-protein interaction network established included 6 Arabidopsis WOX proteins and 10 other notable proteins that showed strong interactions with WOX proteins, comprising 16 nodes in total. Transcriptome analysis demonstrated that CqWOX genes in quinoa exhibit both tissue-specific and salt-responsive expressions. Several genes were repressed in salt bladders, while others showed increased expression, suggesting their potential roles in stress adaptation. Expression profiles differed in leaf and root tissues under salt stress conditions. This study suggested that CqWOX genes exhibit unique characteristics that may facilitate further investigation in future research.International journal of genomics7924847https://www.ebi.ac.uk/biostudies/studies/S-EPMC12434705biostudies-literatureWUSCHEL-Related Homeobox (WOX) Gene Family in Quinoa (Chenopodium quinoa): Genome-Wide Identification and In Silico Characterization.PMC12434705Bakhtari BZamani EfalseWUSCHEL-Related Homeobox (WOX) Gene Family in Quinoa (Chenopodium quinoa): Genome-Wide Identification and In Silico Characterization.Plant-specific transcription factors known as WUSCHEL-related homeobox (WOX) proteins are crucial for regulating plant development and responses to stress. This study represents the first thorough characterization of the WOX gene family in quinoa (Chenopodium quinoa, CqWOXs). In total, we identified 13 probable CqWOX genes, which were categorized into three main subgroups (ancient subgroup, intermediate subgroup, and WUS subgroup) based on phylogenetic analysis. Synteny analysis revealed 12 CqWOX genes as orthologs of WOX genes in Beta vulgaris, Amaranthus hypochondriacus, and Spinacia oleracea, while 10 orthologs were found in Arabidopsis thaliana. Five segmentally duplicated WOX gene pairs were identified in the quinoa genome, all of which have undergone purifying selection, as indicated by their Ka/Ks values being less than one. Additionally, the 2.0 kb promoter regions of CqWOXs were found to harbor various cis-acting elements related to hormone-responsiveness, stress-responsiveness, growth and development, and light-responsiveness elements. The protein-protein interaction network established included 6 Arabidopsis WOX proteins and 10 other notable proteins that showed strong interactions with WOX proteins, comprising 16 nodes in total. Transcriptome analysis demonstrated that CqWOX genes in quinoa exhibit both tissue-specific and salt-responsive expressions. Several genes were repressed in salt bladders, while others showed increased expression, suggesting their potential roles in stress adaptation. Expression profiles differed in leaf and root tissues under salt stress conditions. This study suggested that CqWOX genes exhibit unique characteristics that may facilitate further investigation in future research.2025-01-01T00:00:00Z20252026-06-30T03:26:02.009Z2026-06-30T03:20:49.327ZS-EPMC124347054103121810.1155/ijog/7924847