Dataset Information

Comprehensive analysis of transcriptomics and metabolomics provides insights into the mechanism by plant growth regulators affect the quality of jujube (Ziziphus jujuba Mill.) fruit.

ABSTRACT: A comprehensively analysis of the transcriptomics and metabolomics was conducted to investigate the mechanism of plant growth regulators on the quality of jujube fruit. After the application of plant growth regulators, a total of 3097 differentially expressed genes (DEGs) were identified, which were mainly annotated in 123 pathways such as flavonoid biosynthesis, metabolism of alanine, aspartate, and glutamate. In addition, 1091 differential expressed metabolites (DEMs), including 519 up-regulated and 572 down-regulated metabolites, were significantly altered after application of plant growth regulators. DEGs and DEMs simultaneously annotated 69 metabolic pathways, including biosynthesis of phenylpropane, flavonoid, starch and sucrose. The key genes in flavonoid biosynthesis pathway were revealed, which may play an important role in plant growth regulator regulation quality of jujube fruit. Besides, the application of plant growth regulator during the jujube flowering period increased the contents of gibberellin and indole-3-acetic acid in leaves, and decreased the contents of abscisic acid. The results may help to reveal the metabolic network and molecular mechanism of plant growth regulators in jujube fruit.

SUBMITTER: Liu D

PROVIDER: S-EPMC11343422 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature

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Comprehensive analysis of transcriptomics and metabolomics provides insights into the mechanism by plant growth regulators affect the quality of jujube (Ziziphus jujuba Mill.) fruit.

Liu Defen D Jiang Na N Yuan Yuting Y Liu Hejiang H Ju Yanjun Y Sun Wanjin W Jia Wenzhao W Fang Yi Y Zhao Duoyong D Mao Jiefei J Kang Lu L

PloS one 20240823 8

A comprehensively analysis of the transcriptomics and metabolomics was conducted to investigate the mechanism of plant growth regulators on the quality of jujube fruit. After the application of plant growth regulators, a total of 3097 differentially expressed genes (DEGs) were identified, which were mainly annotated in 123 pathways such as flavonoid biosynthesis, metabolism of alanine, aspartate, and glutamate. In addition, 1091 differential expressed metabolites (DEMs), including 519 up-regulat ...[more]

PMID: 39178226

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Project description:BackgroundJujube is a typical fruit tree species from China. 'Muzao', a cracking-susceptible cultivar, and 'Linhuang No. 1', a cracking-resistant cultivar, were selected in a previous study as contrasting research materials. Whole-genome resequencing and transcriptomic analysis of 'Linhuang No. 1' and 'Muzao' allowed the identification of differentially expressed genes with different gene structures between the two cultivars and could be helpful in explaining the differences and similarities between the two cultivars.ResultsResequencing identified 664,129 polymorphic variable sites between 'Linhuang No. 1' and 'Muzao'. To determine the genetic relationship among 'Linhuang No. 1', 'Muzao' and the jujube genome reference cultivar 'Dongzao', the characteristic polymorphic variable sites were analysed by principal component analysis. The genetic relationship between 'Linhuang No. 1' and 'Muzao' was closer than that of either variety and 'Dongzao'. Nineteen differentially expressed genes were identified by combining transcriptomic analysis with resequencing analysis. LOC107427052 (encoding a nitrite reductase) was identified by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis for further study. The identified insertion was not in the domain region of the LOC107427052 gene coding sequence (CDS) region and was verified by the finding that the insertion did not affect translation of the protein. The LOC107427052 gene expression levels, nitrite reductase activities and nitrite contents of 'Muzao' were significantly higher than the corresponding values of 'Linhuang No. 1' at the young fruit stage. There was no significant difference in the quantity of the product of nitrite reductase, namely, ammonia, between the two cultivars.ConclusionsThe present study was the first to explore the differences between different jujube cultivars ('Linhuang No. 1' and 'Muzao') by combining genome resequencing and transcriptomics. LOC107427052 (encoding a nitrite reductase) was characterized by KEGG enrichment analysis. The insertion in the CDS region of the LOC107427052 gene provides a new direction for the study of nitrogen metabolism in jujube. Our study has laid a foundation for the comparative analysis of nitrite metabolism between the jujube cultivars 'Linhuang No. 1' and 'Muzao'.

Project description:The quality attributes of jujube fruit can be directly and indirectly affected by abiotic stresses associated with climate change. Increased temperature and drought are among the most important factors challenging sustainable jujube production in the temperate semi-arid region in northwest China. The main objective of the present study was to understand the effects of elevated air temperature and drought stress on sugar and acid accumulation and coloration of jujube fruits. The content of soluble sugar, organic acid and pigments of traditional jujube "Linwuchangzao" under different atmospheric temperatures and drought stresses were analyzed during three different fruit ripening stages. The elevated temperature (1.5-2.5° C than normal temperature) significantly increased the fruit sugar content, sugar-acid ratio, anthocyanins, flavonoids and carotenoids content. Under the drought stress where the soil moisture was 30% -50% of the field capacity, sugar content, anthocyanin, flavonoid and carotenoid content of the fruit were significantly reduced at the same temperature, but the chlorophyll and organic acid content increased. No significant interaction of Temperature x Drought was observed for all the analyzed quality parameters. The current results showed that the fruit quality of jujube variety "Lingwuchangzao" could be improved when the atmospheric temperature increases by 2° C in this region. However, drought stress had a negative impact on the fruit's sugar-acid ratio and pigment content. The present results also showed that the synthesis and accumulation of anthocyanins in jujube fruit were positively correlated with sugar content and related enzyme activities, especially Phenylalanine Ammonia-lyase (PAL) activity. This study, therefore, provides novel information for understanding the influence of growth environment on the quality properties of jujube fruits. This knowledge will help develop appropriate crop management practices for jujube production in arid and semi-arid areas in northwest China.

Project description:BackgroundAmong several TF families unique to eukaryotes, the basic leucine zipper (bZIP) family is one of the most important. Chinese jujube (Ziziphus jujuba Mill.) is a popular fruit tree species in Asia, and its fruits are rich in sugar, vitamin C and so on. Analysis of the bZIP gene family of jujube has not yet been reported. In this study, ZjbZIPs were identified firstly, their expression patterns were further studied in different tissues and in response to various abiotic and phytoplasma stresses, and their protein-protein interactions were also analyzed.ResultsAt the whole genome level, 45 ZjbZIPs were identified and classified into 14 classes. The members of each class of bZIP subfamily contain a specific conserved domain in addition to the core bZIP conserved domain, which may be related to its biological function. Relative Synonymous Codon Usage (RSCU) analysis displayed low values of NTA and NCG codons in ZjbZIPs, which would be beneficial to increase the protein production and also indicated that ZjbZIPs were at a relative high methylation level. The paralogous and orthologous events occurred during the evolutionary process of ZjbZIPs. Thirty-four ZjbZIPs were mapped to but not evenly distributed among 10 pseudo- chromosomes. 30 of ZjbZIP genes showed diverse tissue-specific expression in jujube and wild jujube trees, indicating that these genes may have multiple functions. Some ZjbZIP genes were specifically analyzed and found to play important roles in the early stage of fruit development. Moreover, some ZjbZIPs that respond to phytoplasma invasion and abiotic stress environmental conditions, such as salt and low temperature, were found. Based on homology comparisons, prediction analysis and yeast two-hybrid, a protein interaction network including 42 ZjbZIPs was constructed.ConclusionsThe bioinformatics analyses of 45 ZjbZIPs were implemented systematically, and their expression profiles in jujube and wild jujube showed that many genes might play crucial roles during fruit ripening and in the response to phytoplasma and abiotic stresses. The protein interaction networks among ZjbZIPs could provide useful information for further functional studies.

Dataset Information

Comprehensive analysis of transcriptomics and metabolomics provides insights into the mechanism by plant growth regulators affect the quality of jujube (Ziziphus jujuba Mill.) fruit.

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Comprehensive analysis of transcriptomics and metabolomics provides insights into the mechanism by plant growth regulators affect the quality of jujube (Ziziphus jujuba Mill.) fruit.

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