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Systems-based characterization of specialized metabolites biosynthesis in Cornus officinalis

ABSTRACT: Systems-based characterization of specialized metabolites biosynthesis in Cornus officinalis

PROVIDER: PRJNA603009 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10960792_1.fastq.gz	Fastqsanger.gz
	SRR10960792_2.fastq.gz	Fastqsanger.gz
	SRR10960793.fastq.gz	Fastqsanger.gz
	SRR10960793_1.fastq.gz	Fastqsanger.gz
	SRR10960793_2.fastq.gz	Fastqsanger.gz

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Systems-based characterization of specialized metabolites biosynthesis in Cornus officinalis

Project description:In this study, we performed LC-QTOFMS-based metabolomics and RNA-seq based transcriptome analysis using seven tissues of C. officinalis.

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Multiomics-based characterization of specialized metabolites biosynthesis in Cornus Officinalis.

Project description:Cornus officinalis, an important traditional medicinal plant, is used as major constituents of tonics, analgesics, and diuretics. While several studies have focused on its characteristic bioactive compounds, little is known on their biosynthesis. In this study, we performed LC-QTOF-MS-based metabolome and RNA-seq-based transcriptome profiling for seven tissues of C. officinalis. Untargeted metabolome analysis assigned chemical identities to 1,215 metabolites and showed tissue-specific accumulation for specialized metabolites with medicinal properties. De novo transcriptome assembly established for C. officinalis showed 96% of transcriptome completeness. Co-expression analysis identified candidate genes involved in the biosynthesis of iridoids, triterpenoids, and gallotannins, the major group of bioactive metabolites identified in C. officinalis. Integrative omics analysis identified 45 cytochrome P450s genes correlated with iridoids accumulation in C. officinalis. Network-based integration of genes assigned to iridoids biosynthesis pathways with these candidate CYPs further identified seven promising CYPs associated with iridoids' metabolism. This study provides a valuable resource for further investigation of specialized metabolites' biosynthesis in C. officinalis.

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Project description:de novo transcriptome Raw sequence reads of leaf(coYP) and fruit(coGS) of Cornus officinalis

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ArcZ regulation of specialized metabolites

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De novo transcriptome assembly based on RNA-seq and dynamic expression of key enzyme genes in loganin biosynthetic pathway of Cornus officinalis

Project description:Cornus officinalis Sieb. et Zucc., a perennial woody plant which is recognized with high medicinal, economic and ecological values, has been used as traditional Chinese medicine (TCM) for thousands of years in China. Modern pharmacological research has revealed that cornel iridoid glycosides (CIGs, e.g. loganin and morroniside) in dried pericarp of C. officinalis have significant medicinal activities for strengthening immune functions. However, little is known on the molecular processes responsible for the medical properties of this species, owing to the absence of genomic resources such as available sequences of key enzyme genes in biosynthetic pathways. In this study, the RNA sequencing data of C. officinalis were first generated and used for transcriptome analysis. A total of 54,827 unigenes with an average length of 817 bp, an N50 of 1,379 bp, and an average GC content of 44.91% were yielded by de novo assembly, of which 31,780 unigenes were successfully annotated. As potential molecular markers, 121, 118, 96, 89, and 82 transcription factors belonged to bHLH, MYB, PHD, WRKY, and AP2-ERF were further analyzed, respectively. The results of qRT-PCR confirmed that geraniol 10-hydroxylase (G10H) and loganin synthase (SLS) were differentially expressed in fruits and leaves during different growing stages. Furthermore, we found that loganin accumulation was positively related to G10H expression but was negatively correlated with SLS expression. Collectively, the genomic information and gene expression results presented in this study will be helpful for future studies on gene discovery and molecular process of loganin synthesis in C. officinalis.

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De novo transcriptome assembly and characterization of medicinal plant Lithospermum officinale to discover putative genes involved in specialized metabolites biosynthesis

Project description:In this study, we have performed Illumina based RNA sequencing to characterize the transcriptome and expression profiles of genes expressed in 3 tissues of L. officinale. RNA sequencing and de novo transcriptome assembly of L. officinale resulted in a total of 77,047 unigenes with N50 value as 1524 bps. KEGG pathway and GO enrichment analysis using highly expressed unigenes across three tissues showed active secondary metabolic processes specifically enriched to the root of L. officinale. Expression of identified candidate unigenes for specialized metabolites biosynthesis were consistent with previous reports on accumulation of metabolites across different tissues of L. officinale.

2018-07-01 | GSE111375 | GEO

Uncovering production of specialized metabolites by Streptomyces argillaceus by activating cryptic biosynthesis gene clusters

Project description:Activation of cryptic biosynthesis gene clusters for specialized metabolites in Streptomyces argillaceus using nutritional and genetic approaches

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