title: Transcriptome sequencing of rhizome tissue of Sinopodophyllum hexandrum at two temperatures.
abstract: BACKGROUND
  Sinopodophyllum hexandrum is an endangered medicinal herb, which is commonly present in elevations ranging between 2,400-4,500 m and is sensitive to temperature. Medicinal property of the species is attributed to the presence of podophyllotoxin in the rhizome tissue. The present work analyzed transcriptome of rhizome tissue of S. hexandrum exposed to 15°C and 25°C to understand the temperature mediated molecular responses including those associated with podophyllotoxin biosynthesis.
  
  
  RESULTS
  Deep sequencing of transcriptome with an average coverage of 88.34X yielded 60,089 assembled transcript sequences representing 20,387 unique genes having homology to known genes. Fragments per kilobase of exon per million fragments mapped (FPKM) based expression analysis revealed genes related to growth and development were over-expressed at 15°C, whereas genes involved in stress response were over-expressed at 25°C. There was a decreasing trend of podophyllotoxin accumulation at 25°C; data was well supported by the expression of corresponding genes of the pathway. FPKM data was validated by quantitative real-time polymerase chain reaction data using a total of thirty four genes and a positive correlation between the two platforms of gene expression was obtained. Also, detailed analyses yielded cytochrome P450s, methyltransferases and glycosyltransferases which could be the potential candidate hitherto unidentified genes of podophyllotoxin biosynthesis pathway.
  
  
  CONCLUSIONS
  The present work revealed temperature responsive transcriptome of S. hexandrum on Illumina platform. Data suggested expression of genes for growth and development and podophyllotoxin biosynthesis at 15°C, and prevalence of those associated with stress response at 25°C.
authors.forename: Anita
authors.initials: A
authors.lastname: Kumari
authors.forename: Heikham Russiachand
authors.initials: HR
authors.lastname: Singh
authors.forename: Ashwani
authors.initials: A
authors.lastname: Jha
authors.forename: Mohit Kumar
authors.initials: MK
authors.lastname: Swarnkar
authors.affiliation: Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, PO Box No, 6, Palampur 176 061, Himachal Pradesh, India. ravish@ihbt.res.in.
authors.forename: Ravi
authors.initials: R
authors.lastname: Shankar
authors.forename: Sanjay
authors.initials: S
authors.lastname: Kumar
mesh_terms: D028141:Berberidaceae / Q000166:cytology / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D005875:Gibberellins / Q000378:metabolism; D007210:Indoleacetic Acids / Q000378:metabolism; D058977:Molecular Sequence Annotation; D011034:Podophyllotoxin / Q000096:biosynthesis; D027343:Rhizome / Q000166:cytology / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D017421:Sequence Analysis; D015398:Signal Transduction / Q000235:genetics; D013213:Starch / Q000378:metabolism; D013696:Temperature; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D005875:Gibberellins; D007210:Indoleacetic Acids; D014157:Transcription Factors; D013213:Starch; D011034:Podophyllotoxin