Comparative transcriptome analysis reveals sesquiterpenoid biosynthesis among 1-, 2- and 3-year old Atractylodes chinensis

Zhao, Jianhua; Sun, Chengzhen; Shi, Fu-Ming; Ma, Shanshan; Zheng, Jinshuang; Du, Xin; Zhang, Liping

doi:10.1186/s12870-021-03131-1

Cited by 19 publications

(7 citation statements)

References 39 publications

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“…This phenomenon also occurred in Atractylodes atractylodes . By comparing A. atractylodes with different growth years, suggesting that the productivity of secondary metabolism of A. atractylodes increased with cultivation years, possibly because it was used to resist the pressure in old plants [ 26 ].…”

Section: Discussionmentioning

confidence: 99%

Effects of growth years on ginsenoside biosynthesis of wild ginseng and cultivated ginseng

et al. 2022

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Background Ginsenoside, as the main active substance in ginseng, has the function of treating various diseases. However, the ginsenosides content of cultivated ginseng is obviously affected by the growth years, but the molecular mechanism is not clear. In addition, there are significant differences in morphology and physiology between wild ginseng and cultivated ginseng, and the effect of growth years on ginsenoside synthesis not yet understood in wild ginseng. Results Transcriptome sequencing on the roots, stems and leaves of cultivated ginseng and wild ginseng with different growth years was performed in this study, exploring the effect of growth years on gene expression in ginseng. The number of differentially expressed genes (DEGs) from comparison groups in cultivated ginseng was higher than that in wild ginseng. The result of weighted gene co-expression network analysis (WGCNA) showed that growth years significantly affected the gene expression of Mitogen-activated protein kinases (MAPK) signaling pathway and terpenoid backbone biosynthesis pathway in cultivated ginseng, but had no effects in wild ginseng. Furthermore, the growth years had significant effects on the genes related to ginsenoside synthesis in cultivated ginseng, and the effects were different in the roots, stems and leaves. However, it had little influence on the expression of genes related to ginsenoside synthesis in wild ginseng. Growth years might affect the expression of genes for ginsenoside synthesis by influencing the expression of these transcription factors (TFs), like my elob lastosis (MYB), NAM, ATAF1 and 2, and CUC2 (NAC), APETALA2/ethylene-responsive factor (AP2/ERF), basic helix-loop-helix (bHLH) and WRKY, etc., thereby affecting the content of ginsenosides. Conclusions This study complemented the gaps in the genetic information of wild ginseng in different growth periods and helped to clarify the potential mechanisms of the effect of growth years on the physiological state in wild ginseng and cultivated ginseng, which also provided a new insight into the mechanism of ginsenoside regulation.

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Section: Discussionmentioning

confidence: 99%

Effects of growth years on ginsenoside biosynthesis of wild ginseng and cultivated ginseng

et al. 2022

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“…The significance of the MCL survival differences between two patient groups dichotomized based on the expression of transcripts or immunocyte ratios was evaluated by calculating p values based on the log-rank test [ 48 ]. To evaluate the consistency between expression values obtained with whole transcriptome sequencing and qRT-PCR for selected transcripts, the p values were calculated via Pearson correlation testing for paired expressions [ 49 ].…”

Section: Methodsmentioning

confidence: 99%

Whole Transcriptome Sequencing Reveals Cancer-Related, Prognostically Significant Transcripts and Tumor-Infiltrating Immunocytes in Mantle Cell Lymphoma

Sönmez

Hatipoğlu

Kurşun

et al. 2022

Cells

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Mantle cell lymphoma (MCL) is an aggressive B-cell non-Hodgkin lymphoma (NHL) subtype characterized by overexpression of CCND1 and SOX11 genes. It is generally associated with clinically poor outcomes despite recent improvements in therapeutic approaches. The genes associated with the development and prognosis of MCL are still largely unknown. Through whole transcriptome sequencing, we identified mRNAs, lncRNAs, and alternative transcripts differentially expressed in MCL cases compared with reactive tonsil B-cell subsets. CCND1, VCAM1, and VWF mRNAs, as well as MIR100HG and ROR1-AS1 lncRNAs, were among the top 10 most significantly overexpressed, oncogenesis-related transcripts. Survival analyses with each of the top upregulated transcripts showed that MCL cases with high expression of VWF mRNA and low expression of FTX lncRNA were associated with poor overall survival. Similarly, high expression of MSTRG.153013.3, an overexpressed alternative transcript, was associated with shortened MCL survival. Known tumor suppressor candidates (e.g., PI3KIP1, UBXN) were significantly downregulated in MCL cases. Top differentially expressed protein-coding genes were enriched in signaling pathways related to invasion and metastasis. Survival analyses based on the abundance of tumor-infiltrating immunocytes estimated with CIBERSORTx showed that high ratios of CD8+ T-cells or resting NK cells and low ratios of eosinophils are associated with poor overall survival in diagnostic MCL cases. Integrative analysis of tumor-infiltrating CD8+ T-cell abundance and overexpressed oncogene candidates showed that MCL cases with high ratio CD8+ T-cells and low expression of FTX or PCA3 can potentially predict high-risk MCL patients. WTS results were cross-validated with qRT-PCR of selected transcripts as well as linear correlation analyses. In conclusion, expression levels of oncogenesis-associated transcripts and/or the ratios of microenvironmental immunocytes in MCL tumors may be used to improve prognostication, thereby leading to better patient management and outcomes.

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“…RNA extraction and sequencing were performed as described by Zhao et al (2021) [36]. RNA of A. chinensis was extracted using TRIzol Reagent (Invitrogen).…”

Section: Rna Sequencing and Core Ssr Marker Screeningmentioning

confidence: 99%

“…Transcriptome data of A. chinensis were acquired based on the Illumina Hiseq Xten PE150 platform, by Novogene Co. (Beijing, China). All SSR primers used in this study were designed from the transcriptomic database as reported by Zhao et al 2021 [36], and they are available in the SRA (BioProject ID PRJNA698794, https:// www. ncbi.…”

Section: Rna Sequencing and Core Ssr Marker Screeningmentioning

confidence: 99%

Transcriptome-derived SSR markers for DNA fingerprinting and inter-populations genetic diversity assessment of Atractylodes chinensis

Zhao²,

Su³

et al. 2022

Nucleus

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Atractylodes chinensis (fam. Asteraceae) is an important medicinal plant due to its unique pharmacological activity. The species is widely distributed in most areas of northern China. It is difficult to identify different populations of A. chinensis due to their similarity in characteristics. This study was the first investigation to date that assessed the genetic diversity of A. chinensis from different geographical counties of northern China using simple sequence repeat (SSR) markers. Of the 106 SSR primers in the clusters classified in the sesquiterpenoid biosynthesis pathway in the transcriptomic database of A. chinensis, ten with high polymorphism were used to analyze the inter-populations genetic diversity and construct DNA fingerprinting of 19 A. chinensis populations. A total of 78 alleles were detected, with an average number of 6.5 alleles per primer. The PIC value ranged from 0.4748 to 0.8918 with a mean of 0.6265. The neighbor-joining tree was used to classify 19 populations of A. chinensis into three clusters. DNA fingerprinting was performed according to these ten SSR markers. The results revealed that geographic origin is not exactly related to genetic diversity, as populations belonging to different provinces are grouped in the same cluster. The results of this study confirm that SSR markers are effective for genetic diversity analysis. The inter-populations genetic diversity and fingerprinting of A. chinensis in this study could provide a scientific basis for species identification and selective breeding.

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Comparative transcriptome analysis reveals sesquiterpenoid biosynthesis among 1-, 2- and 3-year old Atractylodes chinensis

Cited by 19 publications

References 39 publications

Effects of growth years on ginsenoside biosynthesis of wild ginseng and cultivated ginseng

Effects of growth years on ginsenoside biosynthesis of wild ginseng and cultivated ginseng

Whole Transcriptome Sequencing Reveals Cancer-Related, Prognostically Significant Transcripts and Tumor-Infiltrating Immunocytes in Mantle Cell Lymphoma

Transcriptome-derived SSR markers for DNA fingerprinting and inter-populations genetic diversity assessment of Atractylodes chinensis

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