Ontology highlight
ABSTRACT:
PROVIDER: PRJNA669362 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12908177_1.fastq.gz | Fastqsanger.gz | |||
| SRR12908177_2.fastq.gz | Fastqsanger.gz |
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Project description:Putative terpene synthase ORFs
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Project description:MicroRNAs (miRNAs) are essential small RNA molecules that regulate the expression of target mRNAs in plants and animals. Here, we aimed to identify miRNAs and their putative targets in Hibiscus syriacus, the national flower of South Korea. Therefore, we employed high-throughput sequencing of small RNAs obtained from four different tissues (i.e., leaf, root, flower, and ovary) and identified 33 conserved and 30 novel miRNA families, many of which showed differential tissue-specific expressions. In addition, we computationally predicted novel targets of miRNAs and validated some of them using 5′ rapid amplification of cDNA ends analysis. One of the validated novel targets of miR477 was a terpene synthase, the primary gene involved in the formation of disease-resistant terpene metabolites such as sterols and phytoalexins. In addition, a predicted target of conserved miRNAs, miR396, is SHORT VEGETATIVE PHASE, which is involved in flower initiation and is duplicated in Hibiscus syriacus. Collectively, this study provides the first reliable draft of the Hibiscus syriacus miRNA transcriptome that should constitute a basis for understanding the biological roles of miRNAs in Hibiscus syriacus.
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Project description:Comprehensive identification of terpene synthase genes from a traditional medicinal plant Angelica archangelica
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Project description:we employed integrated transcriptomic and metabolomic analyses to elucidate the molecular basis of cannabinoid biosynthesis during early and late flowering stages in two hemp cultivars, CBG-Ambit and CBG-Limonene. A total of 338 differentially expressed genes (DEGs) were identified at the early stage (ES), while 342 at the late stage (LS) between CBG-Ambit (Amb) and CBG-Limonene (Lim) cultivars. Additionally, 1342 DEGs were identified between the early and late stages of Ambit, whereas 1152 DEGs among early and late stages in Limonene. Key candidate genes including cytochrome P450 78A9 (CYP78A9), 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (HMGCR1), auxin transporter-like protein 2 (LAX2), myrcene synthase (MyrS), terpene synthase 29 (TS-29), geranylpyrophosphate: olivetolate geranyltransferase (GPP), ABSCISIC ACID-INSENSITIVE 5-like protein 7 isoform X1 (ABI5), MYB transcription factor 1, histone-lysine N-methyltransferase (SUVH6), TIFY 10A, tetraketide alpha-pyrone reductase 2 (TPKR2), ethylene-responsive transcription factor (ERF109), berberine bridge enzyme-like 8 (BBE8) and monoterpene synthase (MTS1), were implicated as central regulators of CBD biosynthesis and conformed by RT-qPCR. Functional enrichment (GO and KEGG) analysis demonstrated that these genes are concentrated in secondary metabolic processes, oxidoreductase activity, and transcriptional regulation, highlighting their central roles in cannabinoid and terpenoid biosynthesis. Along with ultra-performance liquid chromatography-mass spectrometry (UPLC-MS), metabolomic profiling further showed increased accumulation of CBDA and CBGA in late stage.
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Project description:Analysis of white adipose tissue of PPARb/d knockout mice. Data may point towards putative target genes of PPARb/d and thus the function of PPARb/d in white adipose tissue. Datasets were used to identify glycogen synthase 2 as novel PPAR target. Keywords: gene expression array-based, count
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Project description:<p><strong>BACKGROUND:</strong> Plants exhibit wide chemical diversity due to the production of specialized metabolites that function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs, as well as sources of insect repellents, health-promoting compounds, and fragrance.</p><p><strong>FINDINGS:</strong> We report the chromosome-scale genome assembly of Callicarpa americana L. (American beautyberry), a species within the early-diverging Callicarpoideae clade of Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long-read sequencing and Hi-C scaffolding, we generated a 506.1-Mb assembly spanning 17 pseudomolecules with N50 contig and N50 scaffold sizes of 7.5 and 29.0 Mb, respectively. In all, 32,164 genes were annotated, including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Our analyses revealed 3 putative whole-genome duplication events, which, together with local tandem duplications, contributed to gene family expansion of terpene synthases. Kolavenyl diphosphate is a gateway to many of the bioactive terpenoids in C. americana; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with Tectona grandis L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 C. americana syntelogs.</p><p><strong>CONCLUSIONS:</strong> Access to the C. americana genome provides a road map for rapid discovery of genes encoding plant-derived agrichemicals and a key resource for understanding the evolution of chemical diversity in Lamiaceae.</p>
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