Identification and expression profiling of selected MADS-box family genes in Dendrobium officinale

Whole-Transcriptome Sequencing Reveals the Global Molecular Responses and NAC Transcription Factors Involved in Drought Stress in Dendrobium catenatum

Dendrobium catenatum is a highly drought-tolerant herb, which usually grows on cliffs or in the branches of trees, yet the underlying molecular mechanisms for its tolerance remain poorly understood. We conducted a comprehensive study utilizing whole-transcriptome sequencing approaches to investigate the molecular response to extreme drought stress in D. catenatum. A large number of differentially expressed mRNAs, lncRNAs, and circRNAs have been identified, and the NAC transcription factor family was highly enriched. Meanwhile, 46 genes were significantly up-regulated in the ABA-activated signaling pathway. In addition to the 89 NAC family members accurately identified in this study, 32 members were found to have different expressions between the CK and extreme drought treatment. They may regulate drought stress through both ABA-dependent and ABA-independent pathways. Moreover, the 32 analyzed differentially expressed DcNACs were found to be predominantly expressed in the floral organs and roots. The ceRNA regulatory network showed that DcNAC87 is at the core of the ceRNA network and is regulated by miR169, miR393, and four lncRNAs. These investigations provided valuable information on the role of NAC transcription factors in D. catenatum's response to drought stress.

Genome-Wide Characterization and Expression Analysis of HD-ZIP Gene Family in Dendrobium officinale

The homeodomain-leucine zipper (HD-ZIP) gene family, as one of the plant-specific transcription factor families, plays an important role in regulating plant growth and development as well as in response to diverse stresses. Although it has been extensively characterized in many plants, the HD-ZIP family is not well-studied in Dendrobium officinale, a valuable ornamental and traditional Chinese medicinal herb. In this study, 37 HD-ZIP genes were identified in Dendrobium officinale (Dohdzs) through the in silico genome search method, and they were classified into four subfamilies based on phylogenetic analysis. Exon–intron structure and conserved protein domain analyses further supported the prediction with the same group sharing similar gene and protein structures. Furthermore, their expression patterns were investigated in nine various tissues and under cold stress based on RNA-seq datasets to obtain the tissue-specific and cold-responsive candidates. Finally, Dohdz5, Dohdz9, and Dohdz12 were selected to validate their expression through qRT-PCR analysis, and they displayed significantly differential expression under sudden chilling stress, suggesting they might be the key candidates underlying cold stress response. These findings will contribute to better understanding of the regulatory roles of the HD-ZIP family playing in cold stress and also will provide the vital targets for further functional studies of HD-ZIP genes in D. officinale.

Genomic Characterization and Expression Analysis of Basic Helix-Loop-Helix (bHLH) Family Genes in Traditional Chinese Herb Dendrobium officinale

Dendrobium officinale Kimura et Migo is of great importance as a traditional Chinese herb due to its abundant metabolites. The family of basic helix-loop-helix (bHLH) transcription factors widely exists in plants and plays an essential role in plant growth and development, secondary metabolism as well as responses to environmental changes. However, there is limited information on bHLH genes in D. officinale. In the present study, a total of 98 putative DobHLH genes were identified at the genomic level, which could be classified into 18 clades. Gene structures and conserved motifs in DobHLH genes showed high conservation during their evolution. The conserved amino acids and DNA bindings of DobHLH proteins were predicted, both of which are pivotal for their function. Furthermore, gene expression from eight tissues showed that some DobHLH genes were ubiquitously expressed while other DobHLH genes were expressed in the specific tissues. Expressional changes of DobHLH genes under MeJA and ABA treatments were detected by qRT-PCR. The protein-protein interactions between DobHLHs were predicted and several interactions were confirmed by yeast two hybrid. Therefore, our results here contribute to the understanding of bHLH genes in D. officinale and lay a foundation for the further functional study of its biological processes.

RNA Splicing of FLC Modulates the Transition to Flowering

Flowering is a critical stage of plant development and is closely correlated with seed production and crop yield. Flowering transition is regulated by complex genetic networks in response to endogenous and environmental signals. FLOWERING LOCUS C (FLC) is a central repressor in the flowering transition of Arabidopsis thaliana. The regulation of FLC expression is well studied at transcriptional and post-transcriptional levels. A subset of antisense transcripts from FLC locus, collectively termed cold-induced long antisense intragenic RNAs (COOLAIR), repress FLC expression under cold exposure. Recent studies have provided important insights into the alternative splicing of COOLAIR and FLC sense transcripts in response to developmental and environmental cues. Herein, at the 20th anniversary of FLC functional identification, we summarise new research advances in the alternative splicing of FLC sense and antisense transcripts that regulates flowering.