scholarly journals De novo transcriptome and tissue specific expression analysis of genes associated with biosynthesis of secondary metabolites in Operculina turpethum (L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bhagyashree Biswal ◽  
Biswajit Jena ◽  
Alok Kumar Giri ◽  
Laxmikanta Acharya
Keyword(s):  
Secondary Metabolite ◽  
De Novo ◽  
Differentially Expressed Gene ◽  
Homology Search ◽  
Biosynthesis Pathway ◽  
Terpenoid Biosynthesis ◽  
De Novo Transcriptome ◽  
Illumina Hiseq ◽  
Secondary Metabolite Biosynthesis ◽  
Root Tissues

AbstractThis study reported the first-ever de novo transcriptome analysis of Operculina turpethum, a high valued endangered medicinal plant, using the Illumina HiSeq 2500 platform. The de novo assembly generated a total of 64,259 unigenes and 20,870 CDS (coding sequence) with a mean length of 449 bp and 571 bp respectively. Further, 20,218 and 16,458 unigenes showed significant similarity with identified proteins of NR (non-redundant) and UniProt database respectively. The homology search carried out against publicly available database found the best match with Ipomoea nil sequences (82.6%). The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis identified 6538 unigenes functionally assigned to 378 modules with phenylpropanoid biosynthesis pathway as the most enriched among the secondary metabolite biosynthesis pathway followed by terpenoid biosynthesis. A total of 17,444 DEGs were identified among which majority of the DEGs (Differentially Expressed Gene) involved in secondary metabolite biosynthesis were found to be significantly upregulated in stem as compared to root tissues. The qRT-PCR validation of 9 unigenes involved in phenylpropanoid and terpenoid biosynthesis also showed a similar expression pattern. This finding suggests that stem tissues, rather than root tissues, could be used to prevent uprooting of O. turpethum in the wild, paving the way for the plant's effective conservation. Moreover, the study formed a valuable repository of genetic information which will provide a baseline for further molecular research.

scholarly journals De novo Transcriptome and tissue specific expression analysis of gene associated with biosynthesis of medicinally active metabolites in a high valued medicinal plant Operculina turpethum (L.)

2021 ◽  
Author(s):  
Bhagyashree Biswal ◽  
Biswajit Jena ◽  
Alok Kumar Giri ◽  
Laxmikanta Acharya
Keyword(s):  
Medicinal Plant ◽  
De Novo ◽  
Homology Search ◽  
Root Bark ◽  
Biosynthesis Pathway ◽  
De Novo Transcriptome ◽  
Active Metabolites ◽  
Illumina Hiseq ◽  
Specific Expression ◽  
Triterpenoid Saponins

Abstract Operculina turpethum (L.) Silva Manso (Nisoth), an important medicinal plant whose root and stem tissues are found to be key ingredient in more than 135 herbal formulation in both Unani and Ayurvedic medicine system and is used for the treatment of various health disorders. It has a very high demand in the Indian Pharmaceutical industry with an annual average consumption of about 660 metric tonne (dry weight). The plant because of its wide usability is also exported to countries like Sri Lanka, Singapore, Netherlands, Japan, United States, etc. leading to a total export value of approximately 2.4 million USD. Terpenoids, steroid glycosides, resin glycosides, dammarane type triterpenoid saponins, flavonoids, coumarins are the major bioactive principles present in O. turpethum. However, overexploitation of root/root bark over the other part of the plant has caused depletion of its germplasm resources from the wild while bringing it to Near Threatened category which subsequently lead to unavailability of the requisite plant material followed by adulteration. Additionally, the limited genomics and transcriptomic resource is a major hindrance in the genetic and molecular research including elucidation of biosynthetic pathway, identification of enhanced traits and proper authentication and genetic diversity study of the plant. Hence, de novo transcriptome sequencing of root and stem tissues of O. turpethum was performed using Illumina HiSeq platform which generated a total of 64259 unigenes and 20870 CDS (coding sequence) with a mean length of 449bp and 571bp respectively. Further, 20218 and 16458 unigenes showed significant similarity with the identified proteins of NR(non-redundant) and Uniprot database respectively. The homology search carried out against publicly available database found the best match with Ipomoea nil sequences (82.6%). The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis identified 6538 unigenes functionally assigned to 378 modules with phenylpropanoid biosynthesis pathway as the most enriched among the secondary metabolite biosynthesis pathway followed by terpenoid biosynthesis. Moreover, transcription factors, SSRs (Simple sequence repeats) and SNPs (single nucleotide polymorphism) were also identified in this study. Apparently, the present investigation reported the first ever transcriptome analysis of the root and stem tissues of the non-model plant O. turpethum of family Convolvulaceae, which will provide a baseline for further molecular research.

scholarly journals De novo transcriptome analysis of the critically endangered alpine Himalayan herb Nardostachys jatamansi reveals the biosynthesis pathway genes of tissue-specific secondary metabolites

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Nisha Dhiman ◽  
Anil Kumar ◽  
Dinesh Kumar ◽  
Amita Bhattacharya
Keyword(s):  
Secondary Metabolites ◽  
Transcriptome Analysis ◽  
Vegetative Growth ◽  
De Novo ◽  
Biosynthesis Pathway ◽  
De Novo Transcriptome ◽  
Tissue Specific ◽  
Nardostachys Jatamansi ◽  
Secondary Metabolite Biosynthesis

Abstract The study is the first report on de novo transcriptome analysis of Nardostachys jatamansi, a critically endangered medicinal plant of alpine Himalayas. Illumina GAIIx sequencing of plants collected during end of vegetative growth (August) yielded 48,411 unigenes. 74.45% of these were annotated using UNIPROT. GO enrichment analysis, KEGG pathways and PPI network indicated simultaneous utilization of leaf photosynthates for flowering, rhizome fortification, stress response and tissue-specific secondary metabolites biosynthesis. Among the secondary metabolite biosynthesis genes, terpenoids were predominant. UPLC-PDA analysis of in vitro plants revealed temperature-dependent, tissue-specific differential distribution of various phenolics. Thus, as compared to 25 °C, the phenolic contents of both leaves (gallic acid and rutin) and roots (p-coumaric acid and cinnamic acid) were higher at 15 °C. These phenolics accounted for the therapeutic properties reported in the plant. In qRT-PCR of in vitro plants, secondary metabolite biosynthesis pathway genes showed higher expression at 15 °C and 14 h/10 h photoperiod (conditions representing end of vegetative growth period). This provided cues for in vitro modulation of identified secondary metabolites. Such modulation of secondary metabolites in in vitro systems can eliminate the need for uprooting N. jatamansi from wild. Hence, the study is a step towards effective conservation of the plant.

De novo assembly of Eugenia uniflora L. transcriptome and identification of genes from the terpenoid biosynthesis pathway

Plant Science ◽  
2014 ◽  
Vol 229 ◽  
pp. 238-246 ◽  
Author(s):  
Frank Guzman ◽  
Franceli Rodrigues Kulcheski ◽  
Andreia Carina Turchetto-Zolet ◽  
Rogerio Margis
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Biosynthesis Pathway ◽  
Terpenoid Biosynthesis ◽  
Eugenia Uniflora

scholarly journals Transcriptomic analyses reveal molecular mechanisms underlying regulation of floral attributes in Lonicera japonica Thunb.

2021 ◽  
Author(s):  
Lei Shi ◽  
Yuan Shen ◽  
Yuhao Chi
Keyword(s):  
Flower Development ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Floral Scent ◽  
Expression Profiles ◽  
Lonicera Japonica ◽  
Biosynthesis Pathway ◽  
Terpenoid Biosynthesis ◽  
Genes Encoding

Abstract Background Lonicera Japonica Thunb. is a perennial, semi-evergreen and twining vine in the family of Caprifoliaceae, which is widely cultivated in Asia. Thus far, L. japonica is often used to treat some human diseases including COVID-19, H1N1 influenza and hand-foot-and-mouth diseases, however, the regulatory mechanism of intrinsic physiological processes during different floral developmental stages of L. japonica remain largely unknown. Results The complete transcriptome of L. japonica was de novo-assembled and annotated, generating a total of 195850 unigenes, of which 84657 could be functionally annotated. 70 candidate genes involved in flowering transition were identified and the flowering regulatory network of five pathways was constructed in L. japonica. The mRNA transcripts of AGL24 and SOC1 exhibited a downward trend during flowering transition and followed by a gradual increase during the flower development. The transcripts of AP1 was only detected during the floral development, whereas the transcript level of FLC was high during the vegetative stages. The expression profiles of AGL24, SOC1, AP1 and FLC genes indicate that these key integrators might play the essential and evolutionarily conserved roles in control of flowering switch across the plant kingdom. We also identified 54 L. japonica genes encoding enzymes involved in terpenoid biosynthesis pathway. Most highly expressed genes centered on the MEP pathway, suggesting that this plastid pathway might represent the major pathway for terpenoid biosynthesis in L. japonica. In addition, 33 and 31 key genes encoding enzymes involved in the carotenogenesis and anthocyanin biosynthesis pathway were identified, respectively. PSY transcripts gradually increased during the flower development, supporting its role as the first rate-limiting enzyme in carotenoid skeleton production. The expression level of most anthocyanin biosynthetic genes was dramatically decreased during the flower developmental stages, consistent with the decline in the contents of anthocyanin. Conclusion These results identified a large number of potential key regulators controlling flowering time, flower color and floral scent formation in L. japonica, which improves our understanding of the molecular mechanisms underlying the flower traits and flower metabolism, as well as sets the groundwork for quality improvement and molecular breeding of L. japonica.

scholarly journals De novo Transcriptome Assembly of Senna occidentalis Sheds Light on the Anthraquinone Biosynthesis Pathway

2022 ◽  
Vol 12 ◽  
Author(s):  
Sang-Ho Kang ◽  
Woo-Haeng Lee ◽  
Joon-Soo Sim ◽  
Niha Thaku ◽  
Saemin Chang ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Differential Expression Analysis ◽  
Biosynthesis Pathway ◽  
Rna Seq ◽  
Pharmacological Activities ◽  
Secondary Metabolite Biosynthesis ◽  
Long Read ◽  
Gene Expression Levels

Senna occidentalis is an annual leguminous herb that is rich in anthraquinones, which have various pharmacological activities. However, little is known about the genetics of S. occidentalis, particularly its anthraquinone biosynthesis pathway. To broaden our understanding of the key genes and regulatory mechanisms involved in the anthraquinone biosynthesis pathway, we used short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) to perform a spatial and temporal transcriptomic analysis of S. occidentalis. This generated 121,592 RNA-Seq unigenes and 38,440 Iso-Seq unigenes. Comprehensive functional annotation and classification of these datasets using public databases identified unigene sequences related to major secondary metabolite biosynthesis pathways and critical transcription factor families (bHLH, WRKY, MYB, and bZIP). A tissue-specific differential expression analysis of S. occidentalis and measurement of the amount of anthraquinones revealed that anthraquinone accumulation was related to the gene expression levels in the different tissues. In addition, the amounts and types of anthraquinones produced differ between S. occidentalis and S. tora. In conclusion, these results provide a broader understanding of the anthraquinone metabolic pathway in S. occidentalis.

scholarly journals De novo transcriptome analysis of Lantana camara L. revealed candidate genes involved in phenylpropanoid biosynthesis pathway

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Muzammil Shah ◽  
Hesham F. Alharby ◽  
Khalid Rehman Hakeem ◽  
Niaz Ali ◽  
Inayat Ur Rahman ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Lantana Camara ◽  
Biosynthesis Pathway ◽  
De Novo Transcriptome ◽  
Phenylpropanoid Biosynthesis

scholarly journals Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing

2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Gang Nie ◽  
Linkai Huang ◽  
Xiao Ma ◽  
Zhongjie Ji ◽  
Yajie Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Regulatory Networks ◽  
De Novo ◽  
Profile Analysis ◽  
Abiotic Stress Tolerance ◽  
Differentially Expressed Gene ◽  
Miscanthus Sinensis ◽  
Illumina Hiseq ◽  
Genomic Databases ◽  
Transcriptional Profile Analysis

Miscanthus × giganteus is wildly cultivated as a potential biofuel feedstock around the world; however, the narrow genetic basis and sterile characteristics have become a limitation for its utilization. As a progenitor of M. × giganteus, M. sinensis is widely distributed around East Asia providing well abiotic stress tolerance. To enrich the M. sinensis genomic databases and resources, we sequenced and annotated the transcriptome of M. sinensis by using an Illumina HiSeq 2000 platform. Approximately 316 million high-quality trimmed reads were generated from 349 million raw reads, and a total of 114,747 unigenes were obtained after de novo assembly. Furthermore, 95,897 (83.57%) unigenes were annotated to at least one database including NR, Swiss-Prot, KEGG, COG, GO, and NT, supporting that the sequences obtained were annotated properly. Differentially expressed gene analysis indicates that drought stress 15 days could be a critical period for M. sinensis response to drought stress. The high-throughput transcriptome sequencing of M. sinensis under drought stress has greatly enriched the current genomic available resources. The comparison of DEGs under different periods of drought stress identified a wealth of candidate genes involved in drought tolerance regulatory networks, which will facilitate further genetic improvement and molecular studies of the M. sinensis.

scholarly journals De novo transcriptome sequence of Senna tora provides insights into anthraquinone biosynthesis

2019 ◽  
Author(s):  
Sang-Ho Kang ◽  
Woo-Haeng Lee ◽  
Chang-Muk Lee ◽  
Joon-Soo Sim ◽  
So Youn Won ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Regulatory Mechanism ◽  
De Novo ◽  
Differential Expression Analysis ◽  
Rna Seq ◽  
De Novo Transcriptome ◽  
Secondary Metabolite Biosynthesis ◽  
Long Read ◽  
Annual Herb ◽  
Key Genes

AbstractSenna tora is an annual herb with rich source of anthraquinones that have tremendous pharmacological properties. However, there is little mention of genetic information for this species, especially regarding the biosynthetic pathways of anthraquinones. To understand the key genes and regulatory mechanism of anthraquinone biosynthesis pathways, we performed spatial and temporal transcriptome sequencing of S. tora using short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) technologies, and generated two unigene sets composed of 118,635 and 39,364, respectively. A comprehensive functional annotation and classification with multiple public databases identified array of genes involved in major secondary metabolite biosynthesis pathways and important transcription factor (TF) families (MYB, MYB-related, AP2/ERF, C2C2-YABBY, and bHLH). Differential expression analysis indicated that the expression level of genes involved in anthraquinone biosynthetic pathway regulates differently depending on the degree of tissues and seeds development. Furthermore, we identified that the amount of anthraquinone compounds were greater in late seeds than early ones. In conclusion, these results provide a rich resource for understanding the anthraquinone metabolism in S. tora.

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