Genome Wide Identification and Characterization of Apple WD40 Proteins and Expression Analysis in Response to ABA, Drought, and Low Temperature

Genome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsii

WD40 transcription factors (TFs) constitute a large gene family in eukaryotes, playing diverse roles in cellular processes. However, their functions in the major ornamental plant, Rhododendron simsii, remain poorly understood. In this study, we identified 258 WD40 proteins in the R. simsii genome, which exhibited an uneven distribution across chromosomes. Based on domain compositions and phylogenetic analysis, we classified these 258 RsWD40 proteins into 42 subfamilies and 47 clusters. Comparative genomic analysis suggested that the expansion of the WD40 gene family predates the divergence of green algae and higher plants, indicating an ancient origin. Furthermore, by analyzing the duplication patterns of RsWD40 genes, we found that transposed duplication played a major role in their expansion. Notably, the majority of RsWD40 gene duplication pairs underwent purifying selection during evolution. Synteny analysis identified significant orthologous gene pairs between R. simsii and Arabidopsis thaliana, Oryza sativa, Vitis vinifera, and Malus domestica. We also investigated potential candidate genes involved in anthocyanin biosynthesis during different flower development stages in R. simsii using RNA-seq data. Specifically, we identified 10 candidate genes during the bud stage and 7 candidate genes during the full bloom stage. GO enrichment analysis of these candidate genes revealed the potential involvement of the ubiquitination process in anthocyanin biosynthesis. Overall, our findings provide a valuable foundation for further investigation and functional analysis of WD40 genes, as well as research on the molecular mechanisms underlying anthocyanin biosynthesis in Rhododendron species.

Genome-wide identification of WD40 superfamily in Cerasus humilis and functional characteristics of ChTTG1

The WD40 superfamily plays an important role in a wide range of developmental and physiological processes. It is a large gene family in eukaryotes. Unfortunately, the research on the WD40 superfamily genes in Cerasus humilis has not been reported. 198 ChWD40s were identified and analyzed in the present study, along with evolutionary relationships, gene structure, chromosome distribution, and collinearity. Then, 5 pairs of tandem duplication and 17 pairs of segmental duplication were found. Based on RNA-Seq data analysis, we screened 31 candidate genes whose expression was up-regulated during the four developmental stages of fruit peel. In addition, we also demonstrated that ChWD40-140, namely ChTTG1, located in the nucleus, cytoplasm, and cytomembrane, has transcriptional activation activity and can form homodimers. ChTTG1 is involved in anthocyanin biosynthesis through heterologous overexpression in Arabidopsis. These research results provide a reference for a comprehensive analysis of the functions of WD40 in the future.

MdMYB110a, directly and indirectly, activates the structural genes for the ALA-induced accumulation of anthocyanin in apple

5-Aminolevulinic acid (ALA), an essential biosynthetic precursor of tetrapyrrole compounds, promotes the anthocyanin accumulation in many plant species. However, the underlying mechanism of ALA-induced accumulation is not yet fully understood. In this study, we identified an important regulator of the anthocyanin accumulation, MdMYB110a, which plays an important role in the ALA-induced anthocyanin accumulation. MdMYB110a activated the expression of MdGSTF12 by binding to its promoter. Additionally, two interacting MdMYB110a proteins, MdWD40-280 and MdHsfB3a, were isolated and confirmed as positive regulators of the ALA-induced anthocyanin accumulation. Both MdWD40-280 and MdHsfB3a enhanced the ability of MdMYB110a to transcribe MdGSTF12. A yeast one-hybrid assay revealed that MdWD40-280 did not bind to most structural genes in the anthocyanin biosynthetic and transport pathways, thus promoting anthocyanin accumulation by MdWD40-280 to depend on MdMYB110a. However, MdHsfB3a could bind to both the MdDFR and MdANS promoters, thereby directly regulating anthocyanin biosynthesis. Collectively, these results provide new insight into the mechanism of ALA-induced anthocyanin accumulation.

Plasma Membrane-Localized Transporter MdSWEET12 Is Involved in Sucrose Unloading in Apple Fruit

Sugar content is an important factor determining the flavor in apple fruit. Sugar unloading is a prerequisite step for sugar accumulation. However, little is known about sugar unloading mechanisms in apple. Transcriptomic sequencing of two apple varieties, "Envy" and "Pacific Rose," with significantly different sugar content was performed. MdSWEET12a from the SWEET transporter family was differentially expressed. Further study of the MdSWEET12a showed that this plasma membrane-localized transporter protein-encoding gene was mainly expressed in sieve element-companion cells (SE-CC) in the fruit, which was positively correlated with the sucrose accumulation during the development of "Envy" apple. Consistently manipulating the gene expression through either transient overexpression or silencing significantly increased or decreased the sugar content in apple fruit, respectively. Complementary growth experiments in mutant yeast cells indicated that MdSWEET12a transported sucrose. Heterologous expression of MdSWEET12a in tomato increased the expression of genes related to sugar metabolism and transport, leading to increased sugar content. These findings underpin the involvement of MdSWEET12a in sugar unloading in apple fruit.