Integrated Transcriptome and Metabolome Analyses Provide Insights into the Coloring Mechanism of Dark-red and Yellow Fruits in Chinese Cherry [Cerasus pseudocerasus (Lindl.) G. Don]

Molecular evolution of Phytocyanin gene and analysis of expression at different coloring periods in apple (Malus domestica)

BACKGROUND

PC (phytocyanin) is a class of copper-containing electron transfer proteins closely related to plant photosynthesis, abiotic stress responses growth and development in plants, and regulation of the expression of some flavonoids and phenylpropanoids, etc., however, compared with other plants, the PC gene family has not been systematically characterized in apple.

RESULTS

A total of 59 MdPC gene members unevenly distributed across 12 chromosomes were identified at the genome-wide level. The proteins of the MdPC family were classified into four subfamilies based on differences in copper binding sites and glycosylation sites: Apple Early nodulin-like proteins (MdENODLs), Apple Uclacyanin-like proteins (MdUCLs), Apple Stellacyanin-like proteins (MdSCLs), and Apple Plantacyanin-like proteins (MdPLCLs). Some MdPC members with similar gene structures and conserved motifs belong to the same group or subfamily. The internal collinearity analysis revealed 14 collinearity gene pairs among members of the apple MdPC gene. Interspecific collinearity analysis showed that apple had 31 and 35 homologous gene pairs with strawberry and grape, respectively. Selection pressure analysis indicated that the MdPC gene was under purifying selection. Prediction of protein interactions showed that MdPC family members interacted strongly with the Nad3 protein. GO annotation results indicated that the MdPC gene also regulated the biosynthesis of phenylpropanoids. Chip data analysis showed that (MdSCL3, MdSCL7 and MdENODL27) were highly expressed in mature fruits and peels. Many cis-regulatory elements related to light response, phytohormones, abiotic stresses and flavonoid biosynthetic genes regulation were identified 2000 bp upstream of the promoter of the MdPC gene, and qRT-PCR results showed that gene members in Group IV (MdSCL1/3, MdENODL27) were up-regulated at all five stages of apple coloring, but the highest expression was observed at the DAF13 (day after fruit bag removal) stage. The gene members in Group II (MdUCL9, MdPLCL3) showed down-regulated or lower expression in the first four stages of apple coloring but up-regulated and highest expression in the DAF 21 stage.

CONCLUSION

Herein, one objective of these findings is to provide valuable information for understanding the structure, molecular evolution, and expression pattern of the MdPC gene, another major objective in this study was designed to lay the groundwork for further research on the molecular mechanism of PC gene regulation of apple fruit coloration.

Comparative metabolomics profiling highlights unique color variation and bitter taste formation of Chinese cherry fruits

Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don], native to China, is an economically important fruit crop with attractive colors and delicious flavors. However, the specific metabolites present in cherry fruits have remained unknown. Here, we firstly characterized 1439 metabolite components of Chinese cherry fruits, predominantly including amino acids, flavonoids, and phenolic acids. Moreover, we screened ten biomarkers of Chinese cherry accessions by ROC curve analysis. Among 250 flavonoids, 26 structurally unique anthocyanins collectively determined fruit color, with cyanidins playing a dominant role. Differences in accumulated metabolites between anthocyanin and proanthocyanidin pathways were likely responsible for the variation in fruit color, ranging from yellow to black purple. Meanwhile, we found limocitrin-7-O-glucoside, along with eight other compounds, as underlying contributors to bitter off-taste experienced in fruits. This study provides insights into the regulatory network of metabolites involved in color variation and bitterness formation and genetic improvement of Chinese cherry fruits.

Metabolome integrated with transcriptome reveals the mechanism of three different color formations in Taxus mairei arils

Maire yew (Taxus mairei), an evergreen conifer, has high ornamental and medicinal value. The arils of this species has three different colors. However, the variation mechanisms of arils color formation remains unclear. Here, the gene expression and metabolite concentration were profiled for red (RTM), yellow (YTM), and purple (PTM) arils in different developmental stages. A total of 266 flavonoids and 35 carotenoids were identified. The predominant pigments identified in YTM were epiafzelechin, lutein, and β-Cryptoxanthin, while malvidin-3,5-di-O-glucoside and apigenin played crucial roles in PTM. And significant differential expression was observed among the HCT, DFR, LAR, ANS, crtB, NCED, and CCoAOMT genes across different color arils. During the maturation of yellow arils, the upregulation of HCT was strongly correlated with the accumulation of epiafzelechin. The diminished expression of DFR, LAR, and ANS seemed to inhibit the production of delphinidin-3-O-rutinoside. The decrease in crtB expression and concurrent increase in NCED expression potentially regulate the heightened accumulation of lutein. Meanwhile, the accumulation of β-cryptoxanthin appeared seemed to be positively influenced by NCED. As aril turning purple, the decreased expression of CCoAOMT seemed to facilitate the synthesis of apigenin. The substantial upregulation of DFR promoted the production of malvidin-3,5-di-O-glucoside. Additionally, the overexpression of MYBs may plays the important role in regulating the formation of different colored arils. In total, 14 genes were selected for qRT-PCR validation, the results indicated the reliability of the transcriptome sequences data. Our findings could provide valuable insight into the molecular breeding, development, and application of Maire yew resources.

Metabolomics and transcriptomics analyses for characterizing the alkaloid metabolism of Chinese jujube and sour jujube fruits

Introduction

Jujube is an important economic forest tree whose fruit is rich in alkaloids. Chinese jujube (Ziziphus jujuba Mill.) and sour jujube (Ziziphus spinosa Hu.) are the two most important species of the jujube genus. However, the mechanisms underlying the synthesis and metabolism of alkaloids in jujube fruits remain poorly understood.

Methods

In this study, the fruits of Ziziphus jujuba 'Hupingzao' and Ziziphus spinosa 'Taigusuanzao' in different harvest stages were used as test materials, we first integrated widely targeted metabolomics and transcriptomics analyses to elucidate the metabolism of alkaloids of jujube fruits.

Results

In the metabolomics analysis, 44 alkaloid metabolites were identified in 4 samples, 3 of which were unique to sour jujube fruit. The differential alkaloid metabolites (DAMs) were more accumulated in sour jujube than in Chinese jujube; further, they were more accumulated in the white ripening stage than in the red stage. DAMs were annotated to 12 metabolic pathways. Additionally, transcriptomics data revealed 259 differentially expressed genes (DEGs) involved in alkaloid synthesis and metabolism. By mapping the regulatory networks of DAMs and DEGs, we screened out important metabolites and 11 candidate genes.

Discussion

This study preliminarily elucidated the molecular mechanism of jujube alkaloid synthesis. The candidate genes regulated the synthesis of key alkaloid metabolites, but the specific regulation mechanism is unclear. Taken together, our results provide insights into the metabolic networks of alkaloid synthesis in Chinese jujube and sour jujube fruits at different harvest stages, thereby providing a theoretical reference for further research on the regulatory mechanism of jujube alkaloids and their development and utilization.

Comparative physiological and transcriptomic analyses provide insights into fruit softening in Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don]

Fruit softening is a complex, genetically programmed and environmentally regulated process, which undergoes biochemical and physiological changes during fruit development. The molecular mechanisms that determine these changes in Chinese cherry [Cerasus peseudocerasus (Lindl.) G.Don] fruits are still unknown. In the present study, fruits of hard-fleshed 'Hongfei' and soft-fleshed 'Pengzhoubai' varieties of Chinese cherry were selected to illustrate the fruit softening at different developmental stages. We analyzed physiological characteristics and transcriptome profiles to identify key cell wall components and candidate genes related to fruit softening and construct the co-expression networks. The dynamic changes of cell wall components (cellulose, hemicellulose, pectin, and lignin), the degrading enzyme activities, and the microstructure were closely related to the fruit firmness during fruit softening. A total of 6,757 and 3,998 differentially expressed genes (DEGs) were screened between stages and varieties, respectively. Comprehensive functional enrichment analysis supported that cell wall metabolism and plant hormone signal transduction pathways were involved in fruit softening. The majority of structural genes were significantly increased with fruit ripening in both varieties, but mainly down-regulated in Hongfei fruits compared with Pengzhoubai, especially DEGs related to cellulose and hemicellulose metabolism. The expression levels of genes involving lignin biosynthesis were decreased with fruit ripening, while mainly up-regulated in Hongfei fruits at red stage. These obvious differences might delay the cell all degrading and loosening, and enhance the cell wall stiffing in Hongfei fruits, which maintained a higher level of fruit firmness than Pengzhoubai. Co-expressed network analysis showed that the key structural genes were correlated with plant hormone signal genes (such as abscisic acid, auxin, and jasmonic acid) and transcription factors (MADS, bHLH, MYB, ERF, NAC, and WRKY). The RNA-seq results were supported using RT-qPCR by 25 selected DEGs that involved in cell wall metabolism, hormone signal pathways and TF genes. These results provide important basis for the molecular mechanism of fruit softening in Chinese cherry.