MYB Genes Research Articles

Terpenoid biosynthesis in Dendrobium officinale: Identification of (E)-β-caryophyllene synthase and the regulatory MYB genes

Dendrobium officinale Kimura et Migo is a well-known medicinal plant producing terpenoid alkaloids as the main medicinal constituents. D. officinale also produces many volatile terpenoids, including monoterpenes and sesquiterpenes. However, little is known about the biosynthetic and regulatory mechanisms underlying terpenoid biosynthesis in this plant. This study first analyzed the terpenoid profiles of D. officinale PLBs treated with lovastatin (LOV) and fosmidomycin (FOS), two chemical inhibitors of terpenoid pathways, and produced corresponding transcriptomes. The volatile products of PLBs were mainly sesquiterpenes, and the contents of (E)-β-caryophyllene and α-humulene were decreased by 42.05% and 27.27%, respectively, after LOV treatment. A candidate sesquiterpene synthase gene identified from the transcriptome and terpene metabolic profiling as (E)-β-caryophyllene synthase (DoECS), localized in the cytoplasm. The emission of (E)-β-caryophyllene decreased by 26.70% in DoECS RNA interference PLBs compared with the control group. Based on co-expression analysis, four MYB genes (DoMYB26, DoMYB29, DoMYB31 and DoMYB32) were involved in the transcriptional regulation of DoECS. Yeast one-hybrid assays and fluorometric GUS assay provided evidence that DoMYB26 and DoMYB31 positively regulated the expression of DoECS, while DoMYB29 negatively regulated the expression of DoECS. In summary, this study produced novel knowledge about the catalytic and regulatory mechanisms responsible for the biosynthesis of volatile terpenoids in D. officinale.

Transposon insertions regulate genome‐wide allele‐specific expression and underpin flower colour variations in apple (Malus spp.)

SummaryAllele‐specific expression (ASE) can lead to phenotypic diversity and evolution. However, the mechanisms regulating ASE are not well understood, particularly in woody perennial plants. In this study, we investigated ASE genes in the apple cultivar ‘Royal Gala’ (RG). A high quality chromosome‐level genome was assembled using a homozygous tetra‐haploid RG plant, derived from anther cultures. Using RNA‐sequencing (RNA‐seq) data from RG flower and fruit tissues, we identified 2091 ASE genes. Compared with the haploid genome of ‘Golden Delicious’ (GD), a parent of RG, we distinguished the genomic sequences between the two alleles of 817 ASE genes, and further identified allele‐specific presence of a transposable element (TE) in the upstream region of 354 ASE genes. These included MYB110a that encodes a transcription factor regulating anthocyanin biosynthesis. Interestingly, another ASE gene, MYB10 also showed an allele‐specific TE insertion and was identified using genome data of other apple cultivars. The presence of the TE insertion in both MYB genes was positively associated with ASE and anthocyanin accumulation in apple petals through analysis of 231 apple accessions, and thus underpins apple flower colour evolution. Our study demonstrated the importance of TEs in regulating ASE on a genome‐wide scale and presents a novel method for rapid identification of ASE genes and their regulatory elements in plants.

Transcriptome profiling provides preliminary molecular insights into adventitious bud formation in herbaceous peony (Paeonia × ‘Coral Charm’)

ABSTRACT Herbaceous peony is a kind of perennial herbaceous flowering plant and most varieties are highly dependent on ramet propagation. Some varieties, such as Paeonia × ‘Coral Charm’, have characteristics of relatively easy root cutting propagation. However, underlying adventitious buds of root cutting, the molecular mechanisms are still not completely understood. Here, we collected four key stages of adventitious bud formation of P. × ‘Coral Charm’ for transcriptome sequencing, and assembled and annotated 326,139 transcripts. By carrying out weighted gene co-expression network analysis, three functional modules and several biological and metabolic pathways related to the adventitious bud formation were identified. Finally, we determined six transcription factors in the MYB, HD-ZIP, C2H2 and bZIP gene family that may play a key role in the adventitious bud formation. These results provided insights into the adventitious bud formation of herbaceous peony, and laid a theoretical foundation for the rapid propagation of Paeonia.

Genome-wide Identification and Expression Analysis of RcMYB Genes in Rhodiola crenulata.

Modern research has proved that the main medicinal component of Rhodiola crenulata, which has a wide range of medicinal value, is its secondary metabolite salidroside. The MYB transcription factor family is widely involved in biosynthesis of second metabolism and other roles in the stress response in plants, so a genome-wide identification and analysis for this family in R. crenulata is worth conducting. In this research, genome-wide analysis identified 139 MYB genes based on conserved domains in the R. crenulata genome, and 137 genes were used to construct a phylogenetic tree and modified with expression files to reveal evolutionary characteristics. Physical and chemical characteristics, gene structure, and conserved motif analysis were also used to further analyze RcMYBs. Additionally, cis-acting elements related to transcription, hormone, and MYB binding were found in the promoter region of the selected RcMYBs. Four RcMYBs were cloned, sequenced, and their gene expression pattern was analyzed for further analysis of their functions. The research results lay the foundation for further research on the function of RcMYB and R. crenulata.

Differential environmental and genomic architectures shape the natural diversity for trichome patterning and morphology in different Arabidopsis organs.

Despite the adaptive and taxonomic relevance of the natural diversity for trichome patterning and morphology, the molecular and evolutionary mechanisms underlying these traits remain mostly unknown, particularly in organs other than leaves. In this study, we address the ecological, genetic and molecular bases of the natural variation for trichome patterning and branching in multiple organs of Arabidopsis (Arabidopsis thaliana). To this end, we characterized a collection of 191 accessions and carried out environmental and genome‐wide association (GWA) analyses. Trichome amount in different organs correlated negatively with precipitation in distinct seasons, thus suggesting a precise fit between trichome patterning and climate throughout the Arabidopsis life cycle. In addition, GWA analyses showed small overlapping between the genes associated with different organs, indicating partly independent genetic bases for vegetative and reproductive phases. These analyses identified a complex locus on chromosome 2, where two adjacent MYB genes (ETC2 and TCL1) displayed differential effects on trichome patterning in several organs. Furthermore, analyses of transgenic lines carrying different natural alleles demonstrated that TCL1 accounts for the variation for trichome patterning in all organs, and for stem trichome branching. By contrast, two other MYB genes (TRY and GL1), mainly showed effects on trichome patterning or branching, respectively.

Genome-Wide Identification and Expression Analysis of the R2R3-MYB Transcription Factor Family Revealed Their Potential Roles in the Flowering Process in Longan (Dimocarpus longan).

Longan (Dimocarpus longan Lour.) is a productive fruit crop with high nutritional and medical value in tropical and subtropical regions. The MYB gene family is one of the most widespread plant transcription factor (TF) families participating in the flowering regulation. However, little is known about the MYB TFs involved in the flowering process in longan and its regulatory network. In this study, a total of 119 DlR2R3-MYB genes were identified in the longan genome and were phylogenetically grouped into 28 subgroups. The groupings were supported by highly conserved gene structures and motif composition of DlR2R3-MYB genes in each subgroup. Collinearity analysis demonstrated that segmental replications played a more crucial role in the expansion of the DlR2R3-MYB gene family compared to tandem duplications, and all tandem/segmental duplication gene pairs have evolved under purifying selection. Interspecies synteny analysis among longan and five representative species implied the occurrence of gene duplication events was one of the reasons contributing to functional differentiation among species. RNA-seq data from various tissues showed DlR2R3-MYB genes displayed tissue-preferential expression patterns. The pathway of flower development was enriched with six DlR2R3-MYB genes. Cis-acting element prediction revealed the putative functions of DlR2R3-MYB genes were related to the plant development, phytohormones, and environmental stresses. Notably, the orthologous counterparts between Arabidopsis and longan R2R3-MYB members tended to play conserved roles in the flowering regulation and stress responses. Transcriptome profiling on off-season flower induction (FI) by KClO3 indicated two up-regulated and four down-regulated DlR2R3-MYB genes involved in the response to KClO3 treatment compared with control groups. Additionally, qRT-PCR confirmed certain genes exhibited high expression in flowers/flower buds. Subcellular localization experiments revealed that three predicted flowering-associated MYB proteins were localized in the nucleus. Future functional studies on these potential candidate genes involved in the flowering development could further the understanding of the flowering regulation mechanism.

Automatic identification and annotation of MYB gene family members in plants

BackgroundMYBs are among the largest transcription factor families in plants. Consequently, members of this family are involved in a plethora of processes including development and specialized metabolism. The MYB families of many plant species were investigated in the last two decades since the first investigation looked at Arabidopsis thaliana. This body of knowledge and characterized sequences provide the basis for the identification, classification, and functional annotation of candidate sequences in new genome and transcriptome assemblies.ResultsA pipeline for the automatic identification and functional annotation of MYBs in a given sequence data set was implemented in Python. MYB candidates are identified, screened for the presence of a MYB domain and other motifs, and finally placed in a phylogenetic context with well characterized sequences. In addition to technical benchmarking based on existing annotation, the transcriptome assembly of Croton tiglium and the annotated genome sequence of Castanea crenata were screened for MYBs. Results of both analyses are presented in this study to illustrate the potential of this application. The analysis of one species takes only a few minutes depending on the number of predicted sequences and the size of the MYB gene family. This pipeline, the required bait sequences, and reference sequences for a classification are freely available on github: https://github.com/bpucker/MYB_annotator.ConclusionsThis automatic annotation of the MYB gene family in novel assemblies makes genome-wide investigations consistent and paves the way for comparative studies in the future. Candidate genes for in-depth analyses are presented based on their orthology to previously characterized sequences which allows the functional annotation of the newly identified MYBs with high confidence. The identification of orthologs can also be harnessed to detect duplication and deletion events.

Silicon Nanoparticles Enhance Ginger Rhizomes Tolerance to Postharvest Deterioration and Resistance to Fusarium solani.

Postharvest deterioration of ginger rhizome caused by microorganisms or wound infections causes significant economic losses. Fusarium solani is one of the important causal agents of prevalent ginger disease soft rot across the world. The massive and continuous use of chemical fungicides in postharvest preservation pose risks to human health and produce environmental contamination. Hence, new alternative tools are required to reduce postharvest deterioration and extend the postharvest life of ginger. In this study, the use of silicon nanoparticles (SiNPs) on the storability of ginger rhizomes during postharvest storage and their resistance to Fusarium solani was investigated. The results showed that 50, 100, and 150 mg L−1 of SiNPs increased the firmness of the ginger rhizome during storage but decreased the decay severity, water loss, total color difference, and the reactive oxygen species (ROS; H2O2 and superoxide anion) accumulation. Specifically, 100 mg L−1 (SiNP100) demonstrated the best effect in the extension of postharvest life and improved the quality of the ginger rhizomes. SiNP100 application increased the activities of antioxidant enzymes (SOD and CAT) and the total phenolics and flavonoid contents, thereby reducing the ROS accumulation and malondialdehyde (MDA) content. Meanwhile, SiNP100 treatment negatively impacts the peroxidase (POD) and polyphenol oxidase (PPO) activities, which may have contributed to the lower level of lignin and decreased total color difference. SiNP100 likely decreased water loss and the transfer of water by altering the expression of aquaporin genes. Moreover, SiNP100 modulated the expression of lignin synthesis and phytopathogenic responses genes including MYB and LysM genes. Furthermore, SiNP100 inhibited Fusarium solani by preventing the penetration of hyphae into cells, thus decreasing the severity of postharvest pathogenic decay. In summary, this study revealed the physiology and molecular mechanisms of SiNPs-induced tolerance to postharvest deterioration and resistance to disease, which provides a foundation for using SiNPs resources as a promising alternative tool to maintain ginger quality and control postharvest diseases.

Identification of MYB genes reveals their potential functions in cadmium stress response and the regulation of cannabinoid biosynthesis in hemp

Cadmium (Cd) is an inorganic heavy mutant pollutant in China. Industrial hemp (Cannabis sativa L.) is an important fiber crop used to remediate soils contaminated with heavy metals. Studies have shown that exogenous Cd stress can affect the production of secondary metabolites in industrial hemp plants. In the industrial hemp genome, we identified a total of 113 MYB genes, which are members of one of the largest and most important gene families that influences plant growth and secondary metabolite production. This study characterized 17 genes within the 1R-MYB subfamily, 88 genes in the 2R-MYB subfamily, and eight genes in the 3R-MYB subfamily. Synteny analysis indicated that there were three pairs of tandemly repeated CsMYBs, 21 pairs of segmental duplication, six CsMYBs were present before species differentiation, and 60 may be cannabis-specific CsMYBs. These results suggested that segmental duplication was the main factor during the evolutionary process that resulted in the expansion of the MYB family in hemp. Importantly, seven of these are key genes in response to Cd stress. Based on changes in gene expression and cannabinoid content under Cd stress, it was shown that CsMYB024 was affected by Cd stress and induced the cannabidiol biosynthesis pathway. Taken together, this study provides a comprehensive analysis of the cannabis MYB family and lays the foundation for the further study of biological functions of CsMYBs.

Clear Cell Neoplasms of Salivary Glands: A Diagnostic Challenge.

This review focuses on the heterogenous group of clear cell neoplasms of salivary glands and attempts to identify major differential diagnostic features. Within the head and neck region, clear cells are found most commonly in salivary gland tumors, but may also be seen in tumors of squamous or odontogenic epithelial origin, primary or metastatic carcinomas, benign or malignant melanocytic lesions, or benign or malignant mesenchymal tumors. Clear cells occur fairly commonly among a wide variety of salivary gland neoplasms, but mostly they constitute only a minor component of the tumor cell population. Clear cells represent a major diagnostic feature in two salivary gland neoplasms, epithelial-myoepithelial carcinoma and hyalinizing clear cell carcinoma. In addition, salivary gland neoplasms composed predominantly of clear cells could also include clear cell variants of other salivary neoplasms, such as mucoepidermoid carcinoma and myoepithelial carcinoma, but their tumor type-specific histologic features may only be available in limited nonclear cell areas of the tumor. Diagnosing predominantly clear cell salivary gland tumors is difficult because the immunoprofiles and morphologic features may overlap and the same tumor entity may also have a wide range of other histologic presentations. Many salivary gland tumors are characterized by tumor type-specific genomic alterations, particularly gene fusions of the ETV6 gene in secretory carcinoma, the MYB and MYBL1 genes in adenoid cystic carcinoma, the MAML2 gene in mucoepidermoid carcinoma, the EWSR1 gene in hyalinizing clear cell carcinoma, and others. Thus, along with conventional histopathologic examination and immunoprofiling, molecular and genetic tests may be important in the diagnosis of salivary gland clear cell tumors by demonstrating genetic alterations specific to them.

Integrated Metabolome and Transcriptome Analyses Reveal Dissimilarities in the Anthocyanin Synthesis Pathway Between Different Developmental Leaf Color Transitions in Hopea hainanensis (Dipterocarpaceae).

Changes in plant leaf color during development are directly related to the accumulation or degradation of certain phytochemicals such as anthocyanins. Since some anthocyanins can be beneficial to human health and provide insights into the biology of leaves, the underlying processes and timing by which plants produce these molecules has been the focus of numerous studies. The tree species Hopea hainanensis generally produces green leaves at all growth stages; however, a few explored individuals have been identified possessing red leaves on the top of the seedlings at a young stage. While the phenomenon of leaf color varying with age has been studied in several species, the underlying mechanisms are largely unknown in H. hainanensis. Using a metabolomics approach, the young red leaves in H. hainanensis were found to contain higher levels of anthocyanins and flavonoids than the young green-leaved individuals. Among anthocyanins, pelargonidin and cyanidin were the most likely candidates contributing to the red color of the young leaves. Transcriptome results indicated the genes related to the production of these anthocyanins were significantly upregulated, leading to greater accumulation of red pigments. Specifically, the expression of several MYB and bHLH genes in young red leaf lines was significantly higher than that in the young green leaf lines, especially HhMYB66, HhMYB91, HhMYB6, and HhbHLH70. As such these four transcription factors are probably the main regulatory genes resulting in young red leaves in H. hainanensis. From these results, comparative analyses with other species can be made to better understand the evolution of pigment biosynthesis and how anthocyanins function in plant metabolism and evolution/adaptation.

Genome wide characterization of R2R3 MYB transcription factor from Apocynum venetum revealed potential stress tolerance and flavonoid biosynthesis genes.

MYB transcription factors are crucial in regulating stress tolerance and expression of major genes involved in flavonoid biosynthesis. The functions of MYBs is well explored in a number of plants, yet no study is reported in Apocynum venetum. We identified a total of 163 MYB candidates, that comprised of 101 (61.96%) R2R3, 6 3R, 1 4R and 55 1R. Syntenic analysis of A. venetum R2R3 (AvMYBs) showed highest orthologous pairs with Vitis vinifera MYBs followed by Arabidopsis thaliana among the four species evaluated. Thirty segmental duplications and 6 tandem duplications were obtained among AvMYB gene pairs signifying their role in the MYB gene family expansion. Nucleotide substitution analysis (Ka/Ks) showed the AvMYBs to be under the influence of strong purifying selection. Expression analysis of selected AvMYBs under low temperature and cadmium stresses resulted in the identification of AvMYB48, AvMYB97, AvMYB8, AvMYB4 as potential stress responsive genes and AvMYB10 and AvMYB11 in addition, proanthocyanidin biosynthesis regulatory genes which is consistent with their annotated homologues in Arabidopsis. Tissue specific expression profile analysis of the AvMYBs further supported the qPCR analysis result. MYBs with higher transcript levels in root, stem and leaf like AvMYB4 for example, was downregulated under the stresses and such with low transcript level such as AvMYB48 which had low transcript in the leaf was upregulated under both stresses. Transcriptome and phylogenetic analyses suggested AvMYB42 as a potential regulator of anthocyanin biosynthesis. Thus, this study provided valuable information on AvR2R3-MYB gene family with respect to stress tolerance and flavonoid biosynthesis.

A new network containing MYB109-ZmCesA5 is involved in kernel development

MYB genes regulate several different aspects of metabolism and development. However, few studies have reported the involvement of MYBs-CesAs network in the regulation of maize kernel development. In this study, yeast one-hybrid (Y1H) assays and dual-luciferase reporter assays showed that ZmMYB109 activated the expression of ZmCesA5 by directly binding to its promoter. Real-time quantitative PCR (RT-qPCR) and transcriptome analyses showed that ZmMYB109 expression increased in ZmCesA5-OE kernels and decreased in ZmCesA5-KO kernels. Overexpression of ZmCesA5 produced heavier kernels, whereas loss of function of ZmCesA5 affected starch and sucrose metabolism, resulting in weight reduction of the maize kernels. Collectively, these findings suggest that a new network containing MYB109-ZmCesA5 is involved in kernel development.

MicroRNA828 negatively regulates lignin biosynthesis in stem of Populus tomentosa through MYB targets.

Lignin biosynthesis in the sclerenchyma cells is strictly controlled by a complex network of genetic and environmental signals. In the last decades, the transcriptional regulation of lignin synthesis in woody species has been established. However, the role of microRNA-mediated post-transcriptional modulation in secondary cell wall biosynthesis remains poorly understood. Here, we identified a microRNA, miR828, involved in the regulation specific to lignin biosynthesis during stem development in Populus tomentosa Carr. miR828 is preferentially expressed in the secondary vascular tissues during stem development. Two MYB genes (MYB171 and MYB011) were validated as direct targets of miR828 by degradome analysis and green fluorescent protein signal detection. Overexpression of miR828 in poplar downregulated genes for lignin biosynthesis, resulting in reduced lignin content in cell walls. Conversely, suppression of miR828 in plants by the short tandem target mimics elevated the expression of lignin biosynthetic genes and increased lignin deposition. We further revealed that poplar MYB171, as the most abundant miR828 target in the stem, is a positive regulator for lignin biosynthesis. Transient expression assays showed that both MYB171 and MYB011 activated PAL1 and CCR2 transcription, whereas the introduction of miR828 significantly suppressed their expression that was induced by MYB171 or MYB011. Collectively, our results demonstrate that the miR828-MYBs module precisely regulates lignin biosynthesis during the stem development in P. tomentosa through transcriptional and post-transcriptional manners.

Transcription Factors Evolve Faster Than Their Structural Gene Targets in the Flavonoid Pigment Pathway.

Dissecting the relationship between gene function and substitution rates is key to understanding genome-wide patterns of molecular evolution. Biochemical pathways provide powerful systems for investigating this relationship because the functional role of each gene is often well characterized. Here, we investigate the evolution of the flavonoid pigment pathway in the colorful Petunieae clade of the tomato family (Solanaceae). This pathway is broadly conserved in plants, both in terms of its structural elements and its MYB, basic helix–loop–helix, and WD40 transcriptional regulators, and its function has been extensively studied, particularly in model species of petunia. We built a phylotranscriptomic data set for 69 species of Petunieae to infer patterns of molecular evolution across pathway genes and across lineages. We found that transcription factors exhibit faster rates of molecular evolution (dN/dS) than their targets, with the highly specialized MYB genes evolving fastest. Using the largest comparative data set to date, we recovered little support for the hypothesis that upstream enzymes evolve slower than those occupying more downstream positions, although expression levels do predict molecular evolutionary rates. Although shifts in floral pigmentation were only weakly related to changes affecting coding regions, we found a strong relationship with the presence/absence patterns of MYB transcripts. Intensely pigmented species express all three main MYB anthocyanin activators in petals, whereas pale or white species express few or none. Our findings reinforce the notion that pathway regulators have a dynamic history, involving higher rates of molecular evolution than structural components, along with frequent changes in expression during color transitions.

Comparative Transcriptome Analysis Reveals Sex-Biased Expression of Hormone-Related Genes at an Early Stage of Sex Differentiation in Red Bayberry (Morella rubra)

The molecular mechanism of sex development and differentiation in the economically important dioecious fruit tree, red bayberry (Morella rubra), was revealed using next-generation transcriptome sequencing (NGS), and comparative analyses were used to identify differentially expressed genes (DEGs) in female and male flower buds. A total of 7029 of these DEGs were identified at two early development stages. KEGG pathway enrichment analysis revealed that plant hormone signal transduction was significantly overrepresented, and 91 genes related to hormones were identified. An analysis of 7029 DEGs revealed 161 hormone-related genes, with the 42 related to auxin and 26 related to ethylene being the most highly represented. A total of 62 genes were significantly up-regulated in females and 29 were in males, with 18 of them specifically expressed in females and 10 in males. A total of 415 transcription factors were identified, with 129 genes up-regulated in females and 53 in males. Moreover, 38 had female-specific expression and 18 had male-specific expression. Using weighted gene co-expression network analysis (WGCNA), two modules were found to be associated with sexual type. In the module coded light-green, there were five genes related to hormones, one to flower development and ten transcription factors with four genes specifically expressed in the males and four in females. The hub gene in the light-green module is MR0TCONS_00017483.1 (ACO), which is involved in ethylene biosynthesis and had male-specific expression. Among the transcription factors, three of the four male-specific expressed genes involved in flavonoid biosynthesis, including the MYB gene MR1TCONS_00020658.1 and two BHLH genes, MR6G001563.1 and MR8G020751.1, played important roles in male floral differentiation. In the dark-cyan module, six hormone-related genes, five transcription factors and three flower development genes were identified with the hub gene MR1G019545.1 (ETR1), which participates in the ethylene signaling pathway, and MR4G023618.1, which encodes the C3H zinc finger transcription factor. These results indicate that ethylene is the key hormone that interacts with other hormones and transcription factors to regulate sex differentiation in the red bayberry, which also provides new insights into the mechanism of sex determination and differentiation in the red bayberry.

Transcriptome and Metabolite Conjoint Analysis Reveals the Seed Dormancy Release Process in Callery Pear.

Seed dormancy transition is a vital developmental process for seedling propagation and agricultural production. The process is precisely regulated by diverse endogenous genetic factors and environmental cues. Callery pear (Pyrus calleryana Decne) is an important rootstock species that requires cold stratification to break seed dormancy, but the mechanisms underlying pear seed dormancy release are not yet fully understood. Here, we analyzed the transcriptome profiles at three different stages of cold stratification in callery pear seeds using RNA sequencing combined with phytohormone and sugar content measurements. Significant alterations in hormone contents and carbohydrate metabolism were observed and reflected the dormancy status of the seeds. The expressions of genes related to plant hormone metabolism and signaling transduction, including indole-3-acetic acid (IAA) biosynthesis (ASAs, TSA, NITs, YUC, and AAO) genes as well as several abscisic acid (ABA) and gibberellic acid (GA) catabolism and signaling transduction genes (CYP707As, GA2ox, and DELLAs), were consistent with endogenous hormone changes. We further found that several genes involved in cytokinin (CTK), ethylene (ETH), brassionolide (BR), and jasmonic acid (JA) metabolism and signaling transduction were differentially expressed and integrated in pear seed dormancy release. In accordance with changes in starch and soluble sugar contents, the genes associated with starch and sucrose metabolism were significantly up-regulated during seed dormancy release progression. Furthermore, the expression levels of genes involved in lipid metabolism pathways were also up-regulated. Finally, 447 transcription factor (TF) genes (including ERF, bHLH, bZIP, NAC, WRKY, and MYB genes) were observed to be differentially expressed during seed cold stratification and might relate to pear seed dormancy release. Our results suggest that the mechanism underlying pear seed dormancy release is a complex, transcriptionally regulated process involving hormones, sugars, lipids, and TFs.

Integrative Analysis of Metabolome and Transcriptome Reveals the Mechanism of Color Formation in Liriope spicata Fruit.

Liriope spicata is an important ornamental ground cover plant, with a fruit color that turns from green to black during the development and ripening stages. However, the material basis and regulatory mechanism of the color variation remains unclear. In this study, a total of 31 anthocyanins and 2 flavonols were identified from the skin of L. spicata fruit via integrative analysis on the metabolome and transcriptome of three developmental stages. The pigments of black/mature fruits are composed of five common anthocyanin compounds, of which Peonidin 3–O–rutinoside and Delphinidin 3–O–glucoside are the most differential metabolites for color conversion. Using dual-omics joint analysis, the mechanism of color formation was obtained as follows. The expression of structural genes including 4CL, F3H, F3′H, F3′5′H and UFGT were activated due to the upregulation of transcription factor genes MYB and bHLH. As a result, a large amount of precursor substances for the synthesis of flavonoids accumulated. After glycosylation, stable pigments were generated which promoted the accumulation of anthocyanins and the formation of black skin.

TERT promoter mutation in a paediatric Spitzoid melanoma – A case report

Optimal classification of skin tumours with Spitz morphology assists patient prognosis and therapy. Deciding between atypical Spitz tumour and Spitzoid melanoma often requires molecular testing. We report a Spitzoid lesion arising on a 12-year-old female’s knee. Microscopic features of marked cytologic atypia, lack of maturation, deep mitotic figures, and loss of p16 expression led to a provisional diagnosis of atypical Spitz tumour and prompted further molecular workup. Alongside copy number abnormalities of the CCND1, MYB and RREB1 genes, the homozygous deletion of CDKN2A and a TERT promoter (TERT-p) hotspot variant were identified.

Assessment of the R2R3 MYB gene expression profile during tomato fruit development using in silico analysis, quantitative and semi-quantitative RT-PCR

Assessment of gene expression is an essential and sensitive indicator of the biological activity and function of a certain gene. The expression profile of R2R3 MYB gene (Solyc02g067760) was investigated at ten development stages of tomato fruits (Lycopersicon esculentum) of Micro-Tom cultivar using three different approaches; quantitative RT-PCR, semi-quantitative RT-PCR and the promising Tomato Expression Atlas (TEA) bioinformatics tool. RNA was extracted from fruit tissues and used for synthesizing cDNA. Quantitative and semi-quantitative expression analyses of R2R3 MYB gene using specific primers consistently showed different expression patterns at the different development stages of tomato fruit. R2R3 MYB exhibited maximum expression at the anthesis stage, suggesting its potential involvement in the pollination and fruit set process. The gene expression was drastically reduced in all other studied stages after anthesis. In the same context, spatiotemporal expression of R2R3 MYB during the ten development stages of tomato fruit using TEA bioinformatics tool revealed a similar expression profile to that obtained by qRT-PCR and semi-qRT-PCR. Comparable results of the three approaches provide new insights into the assessment of tomato gene expression profiling in the presence of Actin gene (Solyc04g011500) as a normalizing expression reference. The obtained results confirm the potentially essential role of the R2R3 MYB in fruit set leading the future research into exploring techniques and stratify of overexpressing this gene in the relevant economic crops.