Genomic Characterization and Expression Analysis of the SnRK Family Genes in Dendrobium officinale Kimura et Migo (Orchidaceae)

Genomic signatures of SnRKs highlighted conserved evolution within orchids and stress responses through ABA signaling in the Cymbidium ensifolium

Sucrose non-fermenting 1-related protein kinases (SnRKs) are crucial for modulating plant responses to abiotic stresses, linking metabolism with stress signaling pathways. Investigating the roles and stress responses of SnRKs in plants paves the way for developing stress-tolerant strategies in orchid species. Here, 362 SnRK members were identified from nine current orchid genomes, highlighting the conservation of these genes in evolution. Among these, 33 CeSnRKs were found across 20 chromosomes of C. ensifolium genome. Multiple duplication events increased the complexity of CeSnRKs during independent evolution. Moreover, distinct functional domains beyond the kinase domain differentiated the subfamilies. These multi-copy members existed tissue specific expressions falling into 6 main trends, especially CeSnRK1, CeCIPK9, CeCIPK23 displayed a strict floral expression. ABA-related elements were enriched in the promoters of CeSnRKs, and stress-related miRNA binding sites were identified on partial CeSnRKs. Consequently, most CeSnRKs exhibited up-regulated expression during ABA treatment. Several genes, such as CeSnRK2.1 and CeCIPK28 involved growth and development at different times and various tissues. The up-regulation of SnRK2.1, along with high expression of SnRK1 and CIPK27 under drought stress, and the differential expression patterns of CeSnRKs under cold stress, underscore the involvement of CeSnRK genes in different stress responses. Additionally, the diverse interactions of CeSnRKs with proteins highlighted a multifaceted functional network.These findings offer valuable insights for the future functional characterization formation of CeSnRKs and the adaptive evolution of genes in orchids.

Genome-Wide Analysis of the WOX Transcription Factor Genes in Dendrobium catenatum Lindl

The WUSCHEL-related homeobox (WOX) proteins are a class of transcription factors exclusive to plants. They can promote cell division or inhibit stem cell differentiation to regulate plant growth and development. However, the WOX transcription factor genes in the monocotyledon Dendrobium catenatum Lindl. remain relatively uncharacterized. Specifically, the effects of phytohormones on their expression levels are unclear. In this study, we identified and analyzed 10 candidate DcaWOX transcription factor genes in D. catenatum. The DcaWOX family was divided into the modern/WUS, intermediate, and ancient clades. The subcellular localization analysis detected DcaWOX-GFP fusion proteins in the tobacco epidermal leaf cell nucleus. In DcaWOX, members of the WUS clade with the WUS-box motif can significantly activate the expression of TPL in vivo, while members of the intermediate and ancient clades cannot. The expression of the DcaWOX genes varied among the examined tissues. Moreover, the DcaWOX expression patterns were differentially affected by the phytohormone treatments, with differences detected even between homologs of the same gene. Furthermore, the gene expression patterns were consistent with the predicted cis-acting elements in the promoters. The above results suggest that DcaWOX may have an important role in its growth and development and resistance to stress. The results of this comprehensive investigation of the DcaWOX gene family provide the basis for future studies on the roles of WOX genes in D. catenatum.