title: De novo leaf and root transcriptome analysis identified novel genes involved in steroidal sapogenin biosynthesis in Asparagus racemosus.
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.
authors.forename: Swati
authors.initials: S
authors.lastname: Upadhyay
authors.forename: Ujjal J
authors.initials: UJ
authors.lastname: Phukan
authors.forename: Sonal
authors.initials: S
authors.lastname: Mishra
authors.affiliation: Biotechnology Division, Central Institute of Medicinal and Aromatic Plants, P,O, CIMAP, Near Kukrail Picnic Spot, Lucknow, U,P, India. rk.shukla@cimap.res.in.
authors.forename: Rakesh Kumar
authors.initials: RK
authors.lastname: Shukla
mesh_terms: D000085:Acetates / Q000494:pharmacology; D019295:Computational Biology; D003517:Cyclopentanes / Q000494:pharmacology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing; D019684:Magnoliopsida / Q000235:genetics* / Q000378:metabolism*; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D054883:Oxylipins / Q000494:pharmacology; D018515:Plant Leaves / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics* / Q000378:metabolism; D015203:Reproducibility of Results; D012502:Sapogenins / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D000085:Acetates; D003517:Cyclopentanes; D054883:Oxylipins; D012502:Sapogenins; C072239:methyl jasmonate