title: De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments.
abstract: BACKGROUND
  Picrorhiza 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.
  
  
  RESULTS
  Using 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.
  
  
  CONCLUSIONS
  Study 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.
authors.affiliation: Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, PO Box No 6, Palampur 176 061, Himachal Pradesh, India.
authors.forename: Parul
authors.initials: P
authors.lastname: Gahlan
authors.forename: Heikham Russiachand
authors.initials: HR
authors.lastname: Singh
authors.forename: Ravi
authors.initials: R
authors.lastname: Shankar
authors.forename: Niharika
authors.initials: N
authors.lastname: Sharma
authors.forename: Anita
authors.initials: A
authors.lastname: Kumari
authors.forename: Vandna
authors.initials: V
authors.lastname: Chawla
authors.forename: Paramvir Singh
authors.initials: PS
authors.lastname: Ahuja
authors.forename: Sanjay
authors.initials: S
authors.lastname: Kumar
mesh_terms: D001482:Base Composition; D002934:Cinnamates / Q000378:metabolism; D016000:Cluster Analysis; D019295:Computational Biology; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics; D005091:Exons / Q000235:genetics; D020224:Expressed Sequence Tags / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D016695:Glycosyltransferases / Q000235:genetics; D057888:Iridoid Glucosides / Q000378:metabolism; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D032261:Picrorhiza / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D013696:Temperature
chemical_list: D002934:Cinnamates; D057888:Iridoid Glucosides; D012333:RNA, Messenger; D018749:RNA, Plant; C109270:picroside I; C416837:picroside II; D003577:Cytochrome P-450 Enzyme System; D016695:Glycosyltransferases