MYB transcription factor family in sweet cherry (Prunus avium L.): genome-wide investigation, evolution, structure, characterization and expression patterns

Back ground MYB Transcription factors (TFs) are most imperative and largest gene family in plants, which participate in development, metabolism, defense, differentiation and stress response. The MYB TFs has been studied in various plant species. However, comprehensive studies of MYB gene family in the sweet cherry (Prunus avium L.) are still unknown. Results In the current study, a total of 69 MYB genes were investigated from sweet cherry genome and classified into 28 subfamilies (C1-C28 based on phylogenetic and structural analysis). Microcollinearity analysis revealed that dispersed duplication (DSD) events might play an important role in the MYB genes family expansion. Chromosomal localization, the synonymous (Ks) and nonsynonymous (Ka) analysis, molecular characteristics (pI, weight and length of amino acids) and subcellular localization were accomplished using several bioinformatics tools. Furthermore, the members of distinct subfamilies have diverse cis-acting regions, conserved motifs, and intron-exon architectures, indicating functional heterogeneity in the MYB family. Moreover, the transcriptomic data exposed that MYB genes might play vital role in bud dormancy. The quantitative real-time qRT-PCR was carried out and the expression pattern indicated that MYB genes significantly expressed in floral bud as compared to flower and fruit. Conclusion Our comprehensive findings provide supportive insights into the evolutions, expansion complexity and functionality of PavMYB genes. These PavMYB genes should be further investigated as they seem to be brilliant candidates for dormancy manipulation in sweet cherry.

Characterization of the MYB Genes Reveals Insights Into Their Evolutionary Conservation, Structural Diversity, and Functional Roles in Magnaporthe oryzae

The myeloblastosis (MYB) transcription factor family is evolutionarily conserved among plants, animals, and fungi, and contributes to their growth and development. We identified and analyzed 10 putative MYB genes in Magnaporthe oryzae (MoMYB) and determined their phylogenetic relationships, revealing high divergence and variability. Although MYB domains are generally defined by three tandem repeats, MoMYBs contain one or two weakly conserved repeats embedded in extensive disordered regions. We characterized the secondary domain organization, disordered segments, and functional contributions of each MoMYB. During infection, MoMYBs are distinctively expressed and can be subdivided into two clades of being either up- or down-regulated. Among these, MoMYB1 and MoMYB8 are up-regulated during infection and vegetative growth, respectively. We found MoMYB1 localized predominantly to the cytosol during the formation of infection structures. ΔMomyb1 exhibited reduced virulence on intact rice leaves corresponding to the diminished ability to form hypha-driven appressorium (HDA). We discovered that MoMYB1 regulates HDA formation on hard, hydrophobic surfaces, whereas host surfaces partially restored HDA formation in ΔMomyb1. Lipid droplet accumulation in hyphal tips and expression of HDA-associated genes were strongly perturbed in ΔMomyb1 indicating genetic interaction of MoMYB1 with downstream components critical to HDA formation. We also found that MoMYB8 is necessary for fungal growth, dark-induced melanization of hyphae, and involved in higher abiotic stress tolerance. Taken together, we revealed a multifaceted picture of the MoMYB family, wherein a low degree of conservation has led to the development of distinct structures and functions, ranging from fungal growth to virulence.

Genome-Wide Identification and Expression Analysis of R2R3-MYB Family Genes Associated with Petal Pigment Synthesis in Liriodendron

The MYB transcription factor family is one of the largest families in plants, and its members have various biological functions. R2R3-MYB genes are involved in the synthesis of pigments that yield petal colors. Liriodendron plants are widely cultivated as ornamental trees owing to their peculiar leaves, tulip-like flowers, and colorful petals. However, the mechanism underlying petal coloring in this species is unknown, and minimal information about MYB genes in Liriodendron is available. Herein, this study aimed to discern gene(s) involved in petal coloration in Liriodendron via genome-wide identification, HPLC, and RT-qPCR assays. In total, 204 LcMYB superfamily genes were identified in the Liriodendron chinense genome, and 85 R2R3-MYB genes were mapped onto 19 chromosomes. Chromosome 4 contained the most (10) R2R3-MYB genes, and chromosomes 14 and 16 contained the fewest (only one). MEME analysis showed that R2R3-MYB proteins in L. chinense were highly conserved and that their exon-intron structures varied. The HPLC results showed that three major carotenoids were uniformly distributed in the petals of L. chinense, while lycopene and β-carotene were concentrated in the orange band region in the petals of Liriodendron tulipifera. Furthermore, the expression profiles via RT-qPCR assays revealed that four R2R3-MYB genes were expressed at the highest levels at the S3P/S4P stage in L. tulipifera. This result combined with the HPLC results showed that these four R2R3-MYB genes might participate in carotenoid synthesis in the petals of L. tulipifera. This work laid a cornerstone for further functional characterization of R2R3-MYB genes in Liriodendron plants.

Evolution of flower color genes in petunias and their wild relatives

Evolutionary transitions in flower color often trace back to changes in the flavonoid biosynthetic pathway and its regulators. In angiosperms, this pathway produces a range of red, purple, and blue anthocyanin pigments. Transcription factor (TF) complexes involving members of the MYB, bHLH, and WD40 protein families control the expression of pathway enzymes. Here, we investigate flavonoid pathway evolution in the Petunieae clade of the tomato family (Solanaceae). Using transcriptomic data from 69 species of Petunieae, we estimated a new phylogeny for the clade. For the 65 species with floral transcriptomes, we retrieved transcripts encoding homologs of 18 enzymes and transcription factors to investigate patterns of evolution across genes and lineages. We found that TFs exhibit faster rates of molecular evolution than their targets, with the highly specialized MYB genes evolving fastest. Using the largest comparative dataset to date, we recovered little support for the hypothesis that upstream enzymes evolve slower than those occupying more downstream positions. However, expression levels inversely correlated with molecular evolutionary rates, while shifts in floral pigmentation were weakly related to changes affecting coding regions. Nevertheless, shifts in floral pigmentation and presence/absence patterns of MYB transcripts are strongly correlated. Intensely pigmented and patterned species express homologs of all three main MYB anthocyanin activators in petals, while pale or white species express few or none. Our findings reinforce the notion that regulators of the flavonoid pathway have a dynamic history, involving higher rates of molecular evolution than structural components, along with frequent changes in expression during color transitions.

Serial Transcriptome Analysis Reveals Genes Associated with Late Blight Resistance in Potato Cultivar Qingshu 9

The late blight caused by Phytophthora infestans (P. infestans) has been a major constraint for worldwide sustainable potato production. Chinese potato cultivar Qingshu 9 has shown excellent field performance against late blight. To understand the mechanism underlying its resistance, the transcriptomic dynamics of Qingshu 9 infected with P. infestans was systematically investigated to identify the resistance-related genes. In total, 2027 shared differentially expressed genes (DEGs) were identified when infected with P. infestans at 24, 48 and 72 h post-inoculation. Based on k-mean cluster analysis, the DEGs showed four types of expression patterns, suggesting their divergent functions in response to P. infestans infection. KEGG enrichment analysis showed that the significantly enriched DEGs were involved in the biosynthesis of secondary metabolites, plant–pathogen interaction, and photosynthesis. Furthermore, 980 transcription factor genes belonging to 68 families were found in the DEGs, of which AP2-EREBP and MYB genes were the most abundant. Moreover, many genes related to disease resistance showed differential expression during infection. Finally, the expression of nine DEGs was validated by quantitative real-time PCR. These results provide valuable information for understanding late resistance in potato cultivar Qingshu 9.

R2R3-MYB Transcription Factor Family in Boehmeria nivea (L.) Gaudich: Potential Associations between Cd2+ Stress and Flavonoid Metabolism

Background: The characterization of gene families especially MYB being the largest transcription factor (TFs) families in plants is a crucial step for functional studies. The completion of ramie genome sequencing provides a great opportunity to investigate the organization and evolutionary traits of ramie MYB genes at the genome-wide level. Results: A total of 105 BnGR2R3-MYB genes were identified in ramie and divided into 35 distinct subfamilies according to phylogeny divergence and sequences similarity. These genes were unevenly distributed among 14 chromosomes. Collinearity analysis showed that the segmental and tandem duplication events is the dominant form of the gene family expansion, and duplications prominent in distal telomeric regions. 88 BnGR2R3-MYB genes showed syntenic relationship with those in Apocynum venetum, followed by Cannabis sativa (58), Arabidopsis (53), maize (8) and rice (4). 103 of the 105 BnGMYB proteins were predicted nuclear subcellular, the remaining two were in either chloroplast or cytoplasm. The combination of transcriptome data and phylogenetic tree allows us to propose some powerful MYB candidates that might be involved in the regulation of secondary wall-associated cellulose synthases (BnGMYB14) secondary cell wall thickening (BnGMYB66/67) and flavonoids synthesis (BnGMYB60). The MYBs subgroups involve in regulating anthocyanin were different from arabidopsis and tomato pointing that BnGMYB in other groups play a role in regulating anthocyanin synthesis. qPCR results revealed 8 MYB TFs candidate genes for cadmium stress in ramie. There was an increased in synthesis of procyanidins under the cadmium stress, which suggest a new regulatory pathway in response to the stress. The predicted network identifies the interface between flavonoid metabolic pathways and adversity stress, and found evidence for the involvement of flavonoid synthetic pathways in the stress regulation.Conclusions: This work provides a basic understanding of BnGR2R3-MYB gene family characteristics and provides valuable information that may contribute in improving the tolerance of ramie to cadmium stress and fiber quality.

Genome-Wide Comparative Analysis of R2R3 MYB Gene Family in Populus and Salix and Identification of Male Flower Bud Development-Related Genes

The MYB transcription factor (TF) family is one of the largest plant transcription factor gene family playing vital roles in plant growth and development, including defense, cell differentiation, secondary metabolism, and responses to biotic and abiotic stresses. As a model tree species of woody plants, in recent years, the identification and functional prediction of certain MYB family members in the poplar genome have been reported. However, to date, the characterization of the gene family in the genome of the poplar’s sister species willow has not been done, nor are the differences and similarities between the poplar and willow genomes understood. In this study, we conducted the first genome-wide investigation of the R2R3 MYB subfamily in the willow, identifying 216 R2R3 MYB gene members, and combined with the poplar R2R3 MYB genes, performed the first comparative analysis of R2R3 MYB genes between the poplar and willow. We identified 81 and 86 pairs of R2R3 MYB paralogs in the poplar and willow, respectively. There were 17 pairs of tandem repeat genes in the willow, indicating active duplication of willow R2R3 MYB genes. A further 166 pairs of poplar and willow orthologs were identified by collinear and synonymous analysis. The findings support the duplication of R2R3 MYB genes in the ancestral species, with most of the R2R3 MYB genes being retained during the evolutionary process. The phylogenetic trees of the R2R3 MYB genes of 10 different species were drawn. The functions of the poplar and willow R2R3 MYB genes were predicted using reported functional groupings and clustering by OrthoFinder. Identified 5 subgroups in general expanded in woody species, three subgroups were predicted to be related to lignin synthesis, and we further speculate that the other two subgroups also play a role in wood formation. We analyzed the expression patterns of the GAMYB gene of subgroup 18 (S18) related to pollen development in the male flower buds of poplar and willow at different developmental stages by qRT-PCR. The results showed that the GAMYB gene was specifically expressed in the male flower bud from pollen formation to maturity, and that the expression first increased and then decreased. Both the specificity of tissue expression specificity and conservation indicated that GAMYB played an important role in pollen development in both poplar and willow and was an ideal candidate gene for the analysis of male flower development-related functions of the two species.

Newly developed MAGIC population allows identification of strong associations and candidate genes for anthocyanin pigmentation in eggplant

SummaryMAGIC populations facilitate the genetic dissection of complex quantitative traits in plants and are valuable breeding materials. We report the development of the first eggplant MAGIC population (S3MEGGIC; 8-way), constituted by 420 S3 individuals developed from the intercrossing of seven cultivated eggplant (Solanum melongena) and one wild relative (S. incanum) parents. The S3MEGGIC recombinant population was genotyped with the eggplant 5k probes SPET platform and phenotyped for anthocyanins presence in vegetative plant tissues (PA) and fruit epidermis (FA), and for the light-sensitive anthocyanic pigmentation under the calyx (PUC). The 7,724 filtered high-confidence SNPs confirmed a low residual heterozygosity (6.87%) and a lack of genetic structure in the S3MEGGIC population, including no differentiation among subpopulations carrying cultivated or wild cytoplasm. Inference of haplotype blocks of the nuclear genome revealed an unbalanced representation of founder genomes, suggesting cryptic selection in favour or against specific parental genomes. GWAS analysis for PA, FA and PUC detected strong associations with two MYB genes similar to MYB113 involved in the anthocyanin biosynthesis pathway and with a COP1 gene, which encodes for a photo-regulatory protein and may be responsible for the PUC phenotype. Evidence was found of a duplication of an ancestral MYB113 gene with a translocation from chromosome 10 to chromosome 1. Parental genotypes for the three genes were in agreement with the candidate genes identification performed in the S3MEGGIC population. Our new eggplant MAGIC population is the largest recombinant population in eggplant and is a powerful tool for eggplant genetics and breeding studies.