Abstract
Dendrobium catenatum is an important traditional Chinese medicine and naturally grows on tree trunks and cliffs, where it can encounter diverse environmental stimuli. MYB transcription factors are widely involved in response to abiotic stresses. However, the MYB gene family has not yet been systematically cataloged in D. catenatum. In this study, a total of 133 MYB proteins were identified in D. catenatum, including 32 MYB-related, 99 R2R3-MYB, 1 3R-MYB, and 1 4R-MYB proteins. Phylogenetic relationships, conserved motifs, gene structures, and expression profiles in response to abiotic stresses were then analyzed. Phylogenetic analysis revealed MYB proteins in D. catenatum could be divided into 14 subgroups, which was supported by the conserved motif compositions and gene structures. Differential DcMYB gene expression and specific responses were analyzed under drought, heat, cold, and salt stresses using RNA-seq and validated by qRT-PCR. Forty-two MYB genes were differentially screened following exposure to abiotic stresses. Five, 12, 11, and 14 genes were specifically expressed in response to drought, heat, cold, and salt stress, respectively. This study identified candidate MYB genes with possible roles in abiotic tolerance and established a theoretical foundation for molecular breeding of D. catenatum.
Highlights
Transcription factors (TFs), commonly called trans-acting factors, bind to cisacting elements of promoter regions in eukaryotic genes and activate or inhibit target gene expression (Riechmann et al, 2000)
To identify MYB proteins in D. catenatum, the genomic sequence was downloaded from NCBI.9
After searching through the Biolinux system using PF00249 as a seed sequence to perform HMMER alignment and removing redundant proteins and incomplete sequences, 133 candidate MYB genes were identified and designated DcMYB1 to DcMYB133 (Supplementary Table 1). These MYB TFs were classified into four distinct groups: MYB-related family (32 proteins, 24.06%), R2R3-MYB family (99 proteins, 74.44%), 3R-MYB (1 protein, 0.75%), and 4RMYB families (1 protein, 0.75%), where the R2R3-MYB family contained the most D. catenatum MYB (DcMYB) genes (Supplementary Table 3)
Summary
Transcription factors (TFs), commonly called trans-acting factors, bind to cisacting elements of promoter regions in eukaryotic genes and activate or inhibit target gene expression (Riechmann et al, 2000). TFs usually consist of four functional regions: a DNA-binding domain, transcriptional regulatory region, oligomerization site, and nuclear localization signal (De Vos et al, 2006). MYB TFs, which are part of one of the largest families of TFs in eukaryotic organisms, are named for the conserved MYB DNA-binding domains in their N-terminus (Lipsick, 1996; Chen et al, 2009; Dubos et al, 2010), which typically consist of 1–4 imperfect repeat (R) motifs (Du et al, 2009; Feller et al, 2011). Dendrobium catenatum MYBs Analysis tryptophan residues with an interval of 18–19 amino acids, forming a helix-turn-helix (HTH) structure (Stracke et al, 2001). The HTH structure interacts with the major groove of DNA at the recognition site C/TAACG/TG and stabilizes the DNA-binding domain (Ogata et al, 1995). The C-terminus of MYB proteins are regulatory domains and highly divergent, which is consistent with the extensive range of regulatory roles for the MYB gene family (Jin and Martin, 1999)
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