Purple cowpea accumulates abundant anthocyanins in its epidermis, with R2R3-MYB transcription factors serving as potential regulators of anthocyanin accumulation. This study systematically deciphered the genome-wide characteristics of cowpea R2R3-MYB transcription factors, elucidating their critical roles in plant anthocyanin accumulation. Employing a combined strategy of HMMER Hidden Markov Model searches and BLASTP homology alignment, we successfully identified 127 non-redundant VuR2R3-MYB transcription factors. The encoded proteins exhibited remarkable physicochemical diversity: the average length reached 338.8 amino acid residues, with theoretical isoelectric points distributed between 4.79 and 10.91 residues. When performing a phylogenetic analysis with Arabidopsis homologs, 27 distinct subgroups were identified. Among them, the S4–S7 clades showed conserved protein architectures, which might play a role in regulating the phenylpropanoid pathway. An analysis of the gene architecture revealed patterns of intron/exon organization. Specifically, 85 out of 127 loci (66.9%) presented the typical two-intron configuration, whereas 18 genes had no introns. An investigation of the promoters found that, on average, each gene had 52 cis-regulatory elements. These elements were mainly light-responsive motifs and phytohormone-related elements. Chromosomal mapping indicated an uneven distribution of these genes across 11 chromosomes. Duplication analysis further showed 13 tandem repeats and 54 segmentally duplicated pairs. An analysis of evolutionary constraints demonstrated that purifying selection was predominant (Ka/Ks < 0.5) among paralogous pairs. Through comparative transcriptomics of pod color variants, 19 differentially expressed MYB regulators were identified. These included VuR2R3-MYB23 (MYB3 homolog), VuR2R3-MYB95 (MYB4 homolog), VuR2R3-MYB53 (MYB114 homolog), and VuR2R3-MYB92 (MYB5 homolog), which showed a strong correlation with the patterns of anthocyanin accumulation. Our findings are expected to contribute to elucidating the potential regulatory mechanisms through which R2R3-MYB transcription factors mediate anthocyanin biosynthesis and accumulation.

De-etiolation consists of a series of developmental and physiological changes that a plant undergoes in response to light. During this process light, an important environmental signal, triggers the inhibition of mesocotyl elongation and the production of photosynthetically active chloroplasts, and etiolated leaves transition from the “sink” stage to the “source” stage. De-etiolation has been extensively studied in maize ( Zea mays L ). However, little is known about how this transition is regulated. In this study, we describe a quantitative proteomic and phosphoproteomic atlas of the de-etiolation process in maize. We identified 16,420 proteins and quantified 14,168. In addition, 8,746 phosphorylation sites within 3,110 proteins were identified. From the proteomic and phosphoproteomic data combined, we identified a total of 17,436 proteins, 27.6% of which are annotated protein coding genes in the Zea_mays AGPv3.28 database. Only 6% of proteins significantly changed in abundance during de-etiolation. In contrast, the phosphorylation levels of more than 25% of phosphoproteins significantly changed; these included proteins involved in gene expression and homeostatic pathways and rate-limiting enzymes involved in photosynthesis light and carbon reactions. Based on phosphoproteomic analysis, 34% (1,057) of all phosphoproteins identified in this study contained more than three phosphorylation sites, and 37 proteins contained more than 16 phosphorylation sites, which shows that multi-phosphorylation is ubiquitous during the de-etiolation process. Our results suggest that plants might preferentially regulate the level of PTMs rather than protein abundance for adapting to changing environments. The study of PTMs could thus better reveal the regulation of de-etiolation.