Dataset Information

De novo assembly and analysis of Artemisia argyi transcriptome and identification of genes involved in terpenoid biosynthesis

ABSTRACT: Artemisia argyi Lev. et Vant., a common ancient compositae species, is widely utilized in traditional Chinese medicine. The underlying mechanism of terpenoid biosynthesis in leaf has been suggested to play an important role in this medicine. However, the transcriptome of A. argyi has not been established. Here, we performed RNA sequencing in leaf, root and stem tissues to identify all possibly transcribed genes. We assembled a total of 99,807 unigenes by analyzing the expression profiling that were generated from the three tissues. Of them, 67,446 unigenes (67.58%) were annotated from public databases including GO, KEGG, COG. We further performed differential gene expression analysis between leaf with stem and root tissue. Our findings revealed that a total of 7,725 unigenes were specified transcribed in leaf. In particular, we determined multiple genes, which encode significant enzymes including HMGR, MVD, DXS, DXR, HDS and HDR, and transcription factors related to terpenoid synthesis. This study established a valuable resource of transcriptome and identified many transcribed genes related to terpenoid biosynthesis, providing the genomic basis for further studies on the molecular mechanism of the medicine for this species.

ORGANISM(S): Artemisia argyi

PROVIDER: GSE102404 | GEO | 2017/12/21

SECONDARY ACCESSION(S): PRJNA397671

REPOSITORIES: GEO

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Project description:Zanthoxylum armatum (Z. armatum) is one of the most economical trees with the unique numbing taste. However, the underlying regulation mechanism involved in the numbing-taste remains scarce. Thus, uncovering the vital genes associated with numbing-taste biosythesis pathways is critical for revealing the genetic information and breeding the high-quality Z. armatum germplasms. Here, a de novo transcriptome assembly of the five major organs was performed in Z. armatum, including roots, stems, leaf buds, mature leaves and fruits. A total of 111 318 unigenes were generated with an average of 1 014 bp. Meanwhile, a large number of SSR and SNP/Indel loci were obtained to improve our understanding about the phylogenetic and genetic information in Z. armatum. The organ specific unigenes of five major samples were screened and annotated with GO and KEGG enrichment analysis, respectively. Additionally, 53 and 34 unigenes were exclusively up-regulated in fruit samples, and identified as candidate unigenes for terpenoid biosynthesis process and fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, he forty days after fertilization (Fr4 stage) could be a important period to accumulate the terpenoid compounds in the fruit development and maturation process of Z. armatum. The Fr4 stage could be a vital point to promote the first few steps of fatty acid biosynthesis process, and the subsequent reactions could be significantly catalyzed at sixty two days after fertilization (Fr6 stage). The present study conducted the de novo transcriptome assembly of the five major organs in Z. armatum. To the best of our knowledge, this study is the first comprehensive analysis to reveal the underlying genes related to the unique numbing taste in Z. armatum. The assembled transcriptome profiles will expand the genetic information and improve our understanding for gene functional studies, which helps in engineering high-quality cultivars of Z. armatum.

Project description:Cryptomeria fortunei (Chinese cedar) has outstanding medicinal value due to its abundant flavonoid and terpenoid contents. The metabolite contents of C. fortunei needles differ across different seasons. However, the biosynthetic mechanism of these differentially synthesized metabolites (DSMs) is poorly understood. To improve our understanding of this process, we performed integrated non-targeted metabolomic liquid chromatography and gas chromatography mass spectrometry (LC-MS and GC-MS), and transcriptomic analyses of summer and winter needles. In winter, the C. fortunei needle ultrastructure was damaged, and the chlorophyll content and Fv/Fm were significantly (p < 0.05) reduced. Based on GC-MS and LC-MS, we obtained 106 and 413 DSMs, respectively; based on transcriptome analysis, we obtained a total of 41.17 Gb of clean data and assembled 33,063 unigenes, including 14,057 differentially expressed unigenes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DSMs/DEGs were significantly (p < 0.05) enriched in many biosynthesis pathways, such as terpenoids, photosynthates, and flavonoids. Integrated transcriptomic and metabonomic analyses showed that seasonal changes have the greatest impact on photosynthesis pathways, followed by terpenoid and flavonoid biosynthesis pathways. In summer Chinese cedar (SCC) needles, DXS, DXR, and ispH in the 2-methyl-pentaerythritol 4-phosphate (MEP) pathway and GGPS were highly expressed and promoted the accumulation of terpenoids, especially diterpenoids. In winter Chinese cedar (WCC) needles, 9 genes (HCT, CHS, CHI, F3H, F3'H, F3'5'H, FLS, DFR, and LAR) involved in flavonoid biosynthesis were highly expressed and promoted flavonoid accumulation. This study broadens our understanding of the metabolic and transcriptomic changes in C. fortunei needles caused by seasonal changes and provides a reference regarding the adaptive mechanisms of C. fortunei and the extraction of its metabolites.

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De novo assembly and analysis of Artemisia argyi transcriptome and identification of genes involved in terpenoid biosynthesis

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