alexa De novo leaf and root transcriptome analysis identified novel genes involved in steroidal sapogenin biosynthesis in Asparagus racemosus.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Transcriptomics: Open Access

Author(s): Upadhyay S, Phukan UJ, Mishra S, Shukla RK, Upadhyay S, Phukan UJ, Mishra S, Shukla RK

Abstract Share this page

Abstract BACKGROUND: Saponins are mainly amphipathic glycosides that posses many biological activities and confer potential health benefits to humans. Inspite of its medicinal attributes most of the triterpenes and enzymes involved in the saponin biosynthesis remains uncharacterized at the molecular level. Since the major steroidal components are present in the roots of A. racemosus our study is focussed on the comparative denovo transcriptome analysis of root versus leaf tissue and identifying some root specific transcripts involved in saponin biosynthesis using high-throughput next generation transcriptome sequencing. RESULTS: After sequencing, de novo assembly and quantitative assessment, 126861 unigenes were finally generated with an average length of 1200 bp. Then functional annotation and GO enrichment analysis was performed by aligning all-unigenes with public protein databases including NR, SwissProt, and KEGG. Differentially expressed genes in root were initially identified using the RPKM method using digital subtraction between root and leaf. Twenty seven putative secondary metabolite related transcripts were experimentally validated for their expression in root or leaf tissue using q-RT PCR analysis. Most of the above selected transcripts showed preferential expression in root as compared to leaf supporting the digitally subtracted result obtained. The methyl jasmonate application induces the secondary metabolite related gene transcripts leading to their increased accumulation in plants. Therefore, the identified transcripts related to saponin biosynthesis were further analyzed for their induced expression after 3, 5 and 12 hours of exogenous application of Methyl Jasmonate in tissue specific manner. CONCLUSIONS: In this study, we have identified a large set of cDNA unigenes from A. racemosus leaf and root tissue. This is the first transcriptome sequencing of this non-model species using Illumina, a next generation sequencing technology. The present study has also identified number of root specific transcripts showing homology with saponin biosynthetic pathway. An integrated pathway of identified saponin biosynthesis transcripts their tissue specific expression and induced accumulation after methyl jasmonate treatment was discussed.
This article was published in BMC Genomics and referenced in Transcriptomics: Open Access

Relevant Expert PPTs

Relevant Speaker PPTs

  • Bozena Futoma-Koloch
    C3 component deposition on Salmonella O48 cells characterized by sialylated lipopolysaccharide and different pattern of outer membrane proteins
    PPT Version | PDF Version
  • Sumru Savas
    No relationship between lipoprotein-associated phospholipase A2, proinflammatory cytokines, and neopterin   in Alzheimer's disease
    PPT Version | PDF Version
  • Mapitsi S Thantsha
    In vitro antagonistic effects of Listeria adhesion protein (LAP)-expressing Lactobacillus casei against Listeria monocytogenes and Salmonella Typhimurium Copenhagen
    PPT Version | PDF Version
  • Tibor Tot
    Multiparameter characterization of breast carcinoma: subgross, microscopy, proteins, and genes
    PPT Version | PDF Version
  • Monray Edward Williams
    Molecular validation of putative antimicrobial peptides for improved Human Immunodeficiency Virus diagnostics via HIV protein p24
    PPT Version | PDF Version
  • Kuna Yellamma
    Kuna-Yellamma-Sri-Venkateswara-University-India-Evaluation-of-neuroprotective-effect-of-silk-protein
    PPT Version | PDF Version
  • Yosef Yarden
    Classically, the 3’untranslated region (3’UTR) is that region in eukaryotic protein-coding genes from the translation termination codon to the polyA signal. It is transcribed as an integral part of the mRNA encoded by the gene. However, there exists another kind of RNA, which consists of the 3’UTR alone, without all other elements in mRNA such as 5’UTR and coding region. The importance of independent 3’UTR RNA (referred as I3’UTR) was prompted by results of artificially introducing such RNA species into malignant mammalian cells. Since 1991, we found that the middle part of the 3’UTR of the human nuclear factor for interleukin-6 (NF-IL6) or C/EBP gene exerted tumor suppression effect in vivo. Our subsequent studies showed that transfection of C/EBP 3’UTR led to down-regulation of several genes favorable for malignancy and to up-regulation of some genes favorable for phenotypic reversion. Also, it was shown that the sequences near the termini of the C/EBP 3’UTR were important for its tumor suppression activity. Then, the C/EBP 3’UTR was found to directly inhibit the phosphorylation activity of protein kinase CPKC in SMMC-7721, a hepatocarcinoma cell line. Recently, an AU-rich region in the C/EBP 3’UTR was found also to be responsible for its tumor suppression. Recently we have also found evidence that the independent C/EBP 3’UTR RNA is actually exists in human tissues, such as fetal liver and heart, pregnant uterus, senescent fibroblasts etc. Through 1990’s to 2000’s, world scientists found several 3’UTR RNAs that functioned as artificial independent RNAs in cancer cells and resulted in tumor suppression. Interestingly, majority of genes for these RNAs have promoter-like structures in their 3’UTR regions, although the existence of their transcribed products as independent 3’UTR RNAs is still to be confirmed. Our studies indicate that the independent 3’UTR RNA is a novel non-coding RNA species whose function should be the regulation not of the expression of their original mRNA, but of some essential life activities of the cell as a whole.
    PPT Version | PDF Version
  • Shigeomi Horito
    Reconstruction of a transmembrane protein tetraspanin (CD9) into lipid bilayer by interaction of ganglioside GM3 and tetraspanin
    PPT Version | PDF Version
  • Maria A. Miteva
    In silico screening to discover inhibitors of protein-protein interactions targeting angiogenesis
    PPT Version | PDF Version
  • Konrad Sandhoff
    Lysosomal & extracellular degradation of GlcCer: Protein & lipid modifiers
    PPT Version | PDF Version
  • David Ben-Menahem
    O-glycosylation and protein evolution: the case of the LHb to CGb development
    PPT Version | PDF Version
  • Vladimir Sulimov
    “Vladimir Sulimov-Dimonta-Ltd-and-Lomonosov-Moscow-State-University-Russia-Protein-ligand-low-energy-minima-pose-analysis-Docking-target-functions-evaluation-with-the-FLM-program”
    PPT Version | PDF Version
  • Xingmin Sun
    A chimeric protein (mTcd138) comprising the glucosyltransferase and domains of toxin B and the receptor binding domain of toxin A provides full protection against Clostridium difficile infection in mice
    PPT Version | PDF Version
  • Simon J Clark
    The role of complement factor H-like and factor H-related proteins in age-related macular degeneration
    PPT Version | PDF Version
  • Rivan Sidaly
    Hypoxia increases the expression of enamel proteins and cytokines in an ameloblast-derived cell line
    PPT Version | PDF Version

Recommended Conferences

  • 2nd International Conference on Nucleic Acids , Molecular Biology & Biologics
    August 31-September 01, 2017 Philadelphia, Pennsylvania, USA
  • 2nd World Congress on Human Genetics & Genetic Disorders
    November 02-03, 2017 Toronto, Canada
  • 3rd International Conference on Genetic and Protein Engineering
    Nov 08-Nov 09, 2017 Las Vegas, USA

Relevant Topics

Peer Reviewed Journals
 
Make the best use of Scientific Research and information from our 700 + peer reviewed, Open Access Journals
International Conferences 2017-18
 
Meet Inspiring Speakers and Experts at our 3000+ Global Annual Meetings

Contact Us

 
© 2008-2017 OMICS International - Open Access Publisher. Best viewed in Mozilla Firefox | Google Chrome | Above IE 7.0 version
adwords