ArticleBMC genomics2012
De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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63 citing papers in PubMed.
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- Application of metabolomics in quality control of traditional Chinese medicines: a review.Frontiers in plant science · 2024Review
- Transcriptomic and metabolomic profiling reveals the drought tolerance mechanism ofFrontiers in plant science · 2023Article
- Transcriptome and metabolome profiling of the medicinal plantFrontiers in genetics · 2023Article
- Transcriptome and Metabolome Analysis of the Synthesis Pathways of Allelochemicals inACS omega · 2022Article
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- Transcriptome repository of North-Western Himalayan endangered medicinal herbs: a paramount approach illuminating molecular perspective of phytoactive molecules and secondary metabolism.Molecular genetics and genomics : MGG · 2021Review
- The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas.Scientific reports · 2021Article
- miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles.PloS one · 2021Article
- Comparative transcriptome analysis of root, stem, and leaf tissues of Entada phaseoloides reveals potential genes involved in triterpenoid saponin biosynthesis.BMC genomics · 2020Article
- Two light responsive3 Biotech · 2020Article
- De novo transcriptome provides insights into the growth behaviour and resveratrol and trans-stilbenes biosynthesis in Dactylorhiza hatagirea - An endangered alpine terrestrial orchid of western Himalaya.Scientific reports · 2019Article
- Ocimum metabolomics in response to abiotic stresses: Cold, flood, drought and salinity.PloS one · 2019Article
- De novo transcriptome sequencing and metabolite profiling analyses reveal the complex metabolic genes involved in the terpenoid biosynthesis in Blue Anise Sage (Salvia guaranitica L.).DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- De Novo Transcriptome Assembly and Population Genetic Analyses for an Endangered Chinese EndemicGenes · 2018Article
- Comparative transcriptomics uncovers differences in photoautotrophic versus photoheterotrophic modes of nutrition in relation to secondary metabolites biosynthesis in Swertia chirayita.Molecular biology reports · 2018Article
- Transcript profiling and gene expression analysis under drought stress in Ziziphus nummularia (Burm.f.) Wright & Arn.Molecular biology reports · 2018Article
- Transcriptome changes induced by abiotic stresses in Artemisia annua.Scientific reports · 2018Article
- Transcriptome sequence analysis and mining of SSRs in Jhar Ber (Ziziphus nummularia (Burm.f.) Wight & Arn) under drought stress.Scientific reports · 2018Article
3 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
backgroundPicrorhiza kurrooa Royle ex Benth. is an endangered plant species of medicinal importance. The medicinal property is attributed to monoterpenoids picroside I and II, which are modulated by temperature. The transcriptome information of this species is limited with the availability of few hundreds of expressed sequence tags (ESTs) in the public databases. In order to gain insight into temperature mediated molecular changes, high throughput de novo transcriptome sequencing and analyses were carried out at 15 °C and 25 °C, the temperatures known to modulate picrosides content.
resultsUsing paired-end (PE) Illumina sequencing technology, a total of 20,593,412 and 44,229,272 PE reads were obtained after quality filtering for 15 °C and 25 °C, respectively. Available (e.g., De-Bruijn/Eulerian graph) and in-house developed bioinformatics tools were used for assembly and annotation of transcriptome. A total of 74,336 assembled transcript sequences were obtained, with an average coverage of 76.6 and average length of 439.5. Guanine-cytosine (GC) content was observed to be 44.6%, while the transcriptome exhibited abundance of trinucleotide simple sequence repeat (SSR; 45.63%) markers.Large scale expression profiling through "read per exon kilobase per million (RPKM)", showed changes in several biological processes and metabolic pathways including cytochrome P450s (CYPs), UDP-glycosyltransferases (UGTs) and those associated with picrosides biosynthesis. RPKM data were validated by reverse transcriptase-polymerase chain reaction using a set of 19 genes, wherein 11 genes behaved in accordance with the two expression methods.
conclusionsStudy generated transcriptome of P. kurrooa at two different temperatures. Large scale expression profiling through RPKM showed major transcriptome changes in response to temperature reflecting alterations in major biological processes and metabolic pathways, and provided insight of GC content and SSR markers. Analysis also identified putative CYPs and UGTs that could help in discovering the hitherto unknown genes associated with picrosides biosynthesis.
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