SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng

Abstract Panax notoginseng is one of the most widely used traditional Chinese herbs with particularly valued roots. Triterpenoid saponins are mainly specialized secondary metabolites, which medically act as bioactive components. Knowledge of the ginsenoside biosynthesis in P. notoginseng, which is of great importance in the industrial biosynthesis and genetic breeding program, remains largely undetermined. Here we combined single molecular real time (SMRT) and Second-Generation Sequencing (SGS) technologies to generate a widespread transcriptome atlas of P. notoginseng. We mapped 2,383 full-length non-chimeric (FLNC) reads to adjacently annotated genes, corrected 1,925 mis-annotated genes and merged into 927 new genes. We identified 8,111 novel transcript isoforms that have improved the annotation of the current genome assembly, of which we found 2,664 novel lncRNAs. We characterized more alternative splicing (AS) events from SMRT reads (20,015 AS in 6,324 genes) than Illumina reads (18,498 AS in 9,550 genes), which contained a number of AS events associated with the ginsenoside biosynthesis. The comprehensive transcriptome landscape reveals that the ginsenoside biosynthesis predominantly occurs in flowers compared to leaves and roots, substantiated by levels of gene expression, which is supported by tissue-specific abundance of isoforms in flowers compared to roots and rhizomes. Comparative metabolic analyses further show that a total of 17 characteristic ginsenosides increasingly accumulated, and roots contained the most ginsenosides with variable contents, which are extraordinarily abundant in roots of the three-year old plants. We observed that roots were rich in protopanaxatriol- and protopanaxadiol-type saponins, whereas protopanaxadiol-type saponins predominated in aerial parts (leaves, stems and flowers). The obtained results will greatly enhance our understanding about the ginsenoside biosynthetic machinery in the genus Panax.

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Five New Oleanane Triterpenoid Saponins from the Aerial Parts ofElsholtzia bodinieri

Helvetica Chimica Acta ◽

10.1002/hlca.00003 ◽

2016 ◽

pp. n/a-n/a

Author(s):

Jin-Dong Zhong ◽

Xue-Wei Zhao ◽

Hong-Mei Li ◽

Ling-Huan Gao ◽

Rong-Tao Li

Keyword(s):

Triterpenoid Saponins ◽

Aerial Parts ◽

Oleanane Triterpenoid

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Transcriptome Analysis of Ginkgo biloba L. Leaves across Late Developmental Stages Based on RNA-Seq and Co-Expression Network

Forests ◽

10.3390/f12030315 ◽

2021 ◽

Vol 12 (3) ◽

pp. 315

Author(s):

Hailin Liu ◽

Xin Han ◽

Jue Ruan ◽

Lian Xu ◽

Bing He

Keyword(s):

Ginkgo Biloba ◽

Leaf Development ◽

Developmental Stages ◽

Leaf Growth ◽

Rna Seq ◽

Final Size ◽

Dioecious Species ◽

Related Factors ◽

New Genes ◽

Gene Modules

The final size of plant leaves is strictly controlled by environmental and genetic factors, which coordinate cell expansion and cell cycle activity in space and time; however, the regulatory mechanisms of leaf growth are still poorly understood. Ginkgo biloba is a dioecious species native to China with medicinally and phylogenetically important characteristics, and its fan-shaped leaves are unique in gymnosperms, while the mechanism of G. biloba leaf development remains unclear. In this study we studied the transcriptome of G. biloba leaves at three developmental stages using high-throughput RNA-seq technology. Approximately 4167 differentially expressed genes (DEGs) were obtained, and a total of 12,137 genes were structure optimized together with 732 new genes identified. More than 50 growth-related factors and gene modules were identified based on DEG and Weighted Gene Co-expression Network Analysis. These results could remarkably expand the existing transcriptome resources of G. biloba, and provide references for subsequent analysis of ginkgo leaf development.

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Analysis of saponins detoxification genes in Ilyonectria mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

Archives of Microbiology ◽

10.1007/s00203-021-02502-4 ◽

2021 ◽

Author(s):

Guohong Zeng ◽

Jin Li ◽

Yuxiu Ma ◽

Qian Pu ◽

Tian Xiao ◽

...

Keyword(s):

Root Rot ◽

Molecular Mechanisms ◽

Management Strategies ◽

Panax Notoginseng ◽

Glycoside Hydrolases ◽

Rna Seq ◽

Host Interaction ◽

Excellent Starting Point ◽

Starting Point ◽

Genes Encoding

AbstractSaponins are kinds of antifungal compounds produced by Panax notoginseng to resist invasion by pathogens. Ilyonectria mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4H (Hours) and 12H (Hours) compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4H and 12H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation–reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen–Host Interaction) genes out of those 93 up-regulated genes. In this report, we analyzed virulence-associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

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Plant buffering against the high-light stress-induced accumulation of CsGA2ox8 transcripts via alternative splicing to finely tune gibberellin levels and maintain hypocotyl elongation

Horticulture Research ◽

10.1038/s41438-020-00430-w ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Bin Liu ◽

Shuo Zhao ◽

Pengli Li ◽

Yilu Yin ◽

Qingliang Niu ◽

...

Keyword(s):

Alternative Splicing ◽

Light Intensity ◽

Intron Retention ◽

Light Stress ◽

Photosynthetic Photon Flux Density ◽

Photon Flux ◽

Photon Flux Density ◽

Rna Seq ◽

Multiple Transcripts ◽

Novel Transcript

AbstractIn plants, alternative splicing (AS) is markedly induced in response to environmental stresses, but it is unclear why plants generate multiple transcripts under stress conditions. In this study, RNA-seq was performed to identify AS events in cucumber seedlings grown under different light intensities. We identified a novel transcript of the gibberellin (GA)-deactivating enzyme Gibberellin 2-beta-dioxygenase 8 (CsGA2ox8). Compared with canonical CsGA2ox8.1, the CsGA2ox8.2 isoform presented intron retention between the second and third exons. Functional analysis proved that the transcript of CsGA2ox8.1 but not CsGA2ox8.2 played a role in the deactivation of bioactive GAs. Moreover, expression analysis demonstrated that both transcripts were upregulated by increased light intensity, but the expression level of CsGA2ox8.1 increased slowly when the light intensity was >400 µmol·m−2·s−1 PPFD (photosynthetic photon flux density), while the CsGA2ox8.2 transcript levels increased rapidly when the light intensity was >200 µmol·m−2·s−1 PPFD. Our findings provide evidence that plants might finely tune their GA levels by buffering against the normal transcripts of CsGA2ox8 through AS.

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Maximizing prediction of orphan genes in assembled genomes

10.1101/2019.12.17.880294 ◽

2019 ◽

Cited By ~ 2

Author(s):

Arun Seetharam ◽

Urminder Singh ◽

Jing Li ◽

Priyanka Bhandary ◽

Zeb Arendsee ◽

...

Keyword(s):

Sequence Homology ◽

Evolutionary History ◽

Direct Evidence ◽

Gene Annotation ◽

Rna Seq ◽

Orphan Genes ◽

Orphan Gene ◽

New Genes ◽

Conserved Genes ◽

Rapid Emergence

ABSTRACTThe evolutionary rapid emergence of new genes gives rise to “orphan genes” that share no sequence homology to genes in closely related genomes. These genes provide organisms with a reservoir of genetic elements to quickly respond to changing selection pressures. Gene annotation pipelines that combine ab initio machine-learning with sequence homology-based searches are efficient in identifying basal genes with a long evolutionary history. However, their ability to identify orphan genes and other young genes has not been systematically evaluated. Here, we classify the phylostrata of curated Arabidopsis thaliana genes and use these to assess the ability of two of the most prevalent annotation pipelines, MAKER and BRAKER, to predict orphans and other young genes. MAKER predictions are highly dependent on the RNA-Seq evidence, predicting between 11% and 60% of the orphan-genes and 95% to 98% of basal-genes in the annotated genome of Arabidopsis. In contrast, BRAKER consistently predicts 33% of orphan-genes and 98% of basal-genes. A less used method to identify genes is by directly aligning RNA-Seq data to the genome sequence. We present a Findable, Accessible, Interoperable and Reusable (FAIR) approach, called BIND, that mitigates the under-prediction of orphan genes. BIND combines BRAKER predictions with direct evidence-based inference of transcripts based on RNA-Seq alignments to the genome. BIND increases the number and accuracy of orphan gene predictions, identifying 68% of Araport11-annotated orphan genes and 99% of the conserved genes.

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Antifungal activity and cytotoxicity of extracts and triterpenoid saponins obtained from the aerial parts of Anagallis arvensis L.

Journal of Ethnopharmacology ◽

10.1016/j.jep.2017.03.056 ◽

2017 ◽

Vol 203 ◽

pp. 233-240 ◽

Cited By ~ 12

Author(s):

José R. Soberón ◽

Melina A. Sgariglia ◽

Ana C. Pastoriza ◽

Estela M. Soruco ◽

Sebastián N. Jäger ◽

...

Keyword(s):

Antifungal Activity ◽

Triterpenoid Saponins ◽

Aerial Parts

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The Chromosome-Level Reference Genome Assembly for Panax notoginseng and Insights into Ginsenoside Biosynthesis

Plant Communications ◽

10.1016/j.xplc.2020.100113 ◽

2020 ◽

pp. 100113 ◽

Cited By ~ 1

Author(s):

Zhouqian Jiang ◽

Lichan Tu ◽

Weifei Yang ◽

Yifeng Zhang ◽

Tianyuan Hu ◽

...

Keyword(s):

Genome Assembly ◽

Reference Genome ◽

Panax Notoginseng ◽

Ginsenoside Biosynthesis ◽

Reference Genome Assembly ◽

Chromosome Level

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The transcriptome variations of Panaxnotoginseng roots treated with different forms of nitrogen fertilizers

BMC Genomics ◽

10.1186/s12864-019-6340-7 ◽

2019 ◽

Vol 20 (S9) ◽

Cited By ~ 4

Author(s):

Xiaohong Ou ◽

Shipeng Li ◽

Peiran Liao ◽

Xiuming Cui ◽

Binglian Zheng ◽

...

Keyword(s):

Crop Production ◽

Tca Cycle ◽

Panax Notoginseng ◽

Ammonium Nitrogen ◽

Nitrogen Fertilizers ◽

Rna Seq ◽

Root Yield ◽

Qrt Pcr ◽

The Tca Cycle ◽

Nitrate Fertilizer

Abstract Background The sensitivity of plants to ammonia is a worldwide problem that limits crop production. Excessive use of ammonium as the sole nitrogen source results in morphological and physiological disorders, and retarded plant growth. Results In this study we found that the root growth of Panax notoginseng was inhibited when only adding ammonium nitrogen fertilizer, but the supplement of nitrate fertilizer recovered the integrity, activity and growth of root. Twelve RNA-seq profiles in four sample groups were produced and analyzed to identify deregulated genes in samples with different treatments. In comparisons to NH${~}_{4}^{+}$ 4 + treated samples, ACLA-3 gene is up-regulated in samples treated with NO${~}_{3}^{-}$ 3 − and with both NH$_{4}^{+}$ 4 + and NO${~}_{3}^{-}$ 3 − , which is further validated by qRT-PCR in another set of samples. Subsequently, we show that the some key metabolites in the TCA cycle are also significantly enhanced when introducing NO${~}_{3}^{-}$ 3 − . These potentially enhance the integrity and recover the growth of Panax notoginseng roots. Conclusion These results suggest that the activated TCA cycle, as demonstrated by up-regulation of ACLA-3 and several key metabolites in this cycle, contributes to the increased Panax notoginseng root yield when applying both ammonium and nitrate fertilizer.

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Dammarane triterpenoid saponins from Bacopa monnieri

Canadian Journal of Chemistry ◽

10.1139/v09-111 ◽

2009 ◽

Vol 87 (9) ◽

pp. 1230-1234 ◽

Cited By ~ 10

Author(s):

Pamita Bhandari ◽

Neeraj Kumar ◽

Bikram Singh ◽

Inderjeet Kaur

Keyword(s):

Medicinal Plant ◽

2D Nmr ◽

Bacopa Monnieri ◽

Spectroscopic Methods ◽

Triterpenoid Saponins ◽

Enhancing Effect ◽

Indian Medicinal Plant ◽

Aerial Parts ◽

Memory Enhancer ◽

Memory Enhancing

Bacopa monnieri is a well-known Ayurvedic Indian medicinal plant traditionally used as a memory enhancer. Its memory-enhancing effect is mainly attributed to dammarane triterpenoid saponins. In the present study, two new dammarane-type triterpenoid saponins, bacopaside-XI (1) and bacopaside-XII (2), together with known compounds, bacopaside IV, bacopaside V, and apigenin, were isolated from the aerial parts of the B. monnieri . The structures of the new saponins were elucidated as 3-O-[α-L-arabinofuranosyl(1→3)]-6-O-sulfonyl-β-D-glucopyranosyl pseudojujubogenin (1) and 3-O-{β-D-glucopyranosyl(1→3)[α-L-arabinofuranosyl(1→2)]-β-D-glucopyranosyl}-20-O-α-L-arabinopyranosyl pseudojujubogenin (2) on the basis of extensive investigations of 1D and 2D NMR (HMQC and HMBC), ESI-QTOF-MS/MS spectroscopic methods, and chemical evidences.

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