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.

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.

De novo transcriptome analysis reveals tissue-specific differences in gene expression in Salix arbutifolia

Trees ◽  
2016 ◽  
Vol 30 (5) ◽  
pp. 1647-1655 ◽  
Author(s):  
Guodong Rao ◽  
Yanfei Zeng ◽  
Jinkai Sui ◽  
Jianguo Zhang
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
De Novo ◽  
De Novo Transcriptome ◽  
Tissue Specific

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 Tissue-specific de novo transcriptome analysis in kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson]

2019 ◽  
Author(s):  
JUAN SALAZAR ◽  
Cristian Vergara ◽  
Claudia Jorquera ◽  
Patricio Zapata ◽  
Pedro Martínez Gómez ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Actinidia Deliciosa ◽  
De Novo Transcriptome ◽  
Tissue Specific

Abstract The authors have withdrawn this preprint from Research Square

De novo transcriptome analysis of bamboo in vitro shoots for identification of genes differentiating juvenile and aged plants

2022 ◽  
Vol 176 ◽  
pp. 114353
Author(s):  
Pooja Thapa ◽  
Bhuvnesh Sareen ◽  
Mohit Kumar Swarnkar ◽  
Anil Sood ◽  
Amita Bhattacharya
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
De Novo Transcriptome ◽  
In Vitro Shoots

scholarly journals De novo transcriptome analysis of Perna viridis highlights tissue-specific patterns for environmental studies

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 804 ◽  
Author(s):  
Priscilla TY Leung ◽  
Jack CH Ip ◽  
Sarah ST Mak ◽  
Jian Qiu ◽  
Paul KS Lam ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Environmental Studies ◽  
Perna Viridis ◽  
De Novo Transcriptome ◽  
Tissue Specific

scholarly journals Elucidation of the core betalain biosynthesis pathway in Amaranthus tricolor

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yu-Cheng Chang ◽  
Yi-Ching Chiu ◽  
Nai-Wen Tsao ◽  
Yuan-Lin Chou ◽  
Choon-Meng Tan ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Natural Antioxidants ◽  
Biosynthesis Pathway ◽  
Comparative Transcriptome ◽  
Amaranthus Tricolor ◽  
Enzymatic Assays ◽  
Comparative Transcriptome Analysis ◽  
Elevated Expression ◽  
Green Coloration

AbstractAmaranthus tricolor L., a vegetable Amaranthus species, is an economically important crop containing large amounts of betalains. Betalains are natural antioxidants and can be classified into betacyanins and betaxanthins, with red and yellow colors, respectively. A. tricolor cultivars with varying betalain contents, leading to striking red to green coloration, have been commercially produced. However, the molecular differences underlying betalain biosynthesis in various cultivars of A. tricolor remain largely unknown. In this study, A. tricolor cultivars with different colors were chosen for comparative transcriptome analysis. The elevated expression of AmCYP76AD1 in a red-leaf cultivar of A. tricolor was proposed to play a key role in producing red betalain pigments. The functions of AmCYP76AD1, AmDODAα1, AmDODAα2, and AmcDOPA5GT were also characterized through the heterologous engineering of betalain pigments in Nicotiana benthamiana. Moreover, high and low L-DOPA 4,5-dioxygenase activities of AmDODAα1 and AmDODAα2, respectively, were confirmed through in vitro enzymatic assays. Thus, comparative transcriptome analysis combined with functional and enzymatic studies allowed the construction of a core betalain biosynthesis pathway of A. tricolor. These results not only provide novel insights into betalain biosynthesis and evolution in A. tricolor but also provide a basal framework for examining genes related to betalain biosynthesis among different species of Amaranthaceae.

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