title: Comparative whole-transcriptome analysis in Podophyllum species identifies key transcription factors contributing to biosynthesis of podophyllotoxin in P. hexandrum.
abstract: Podophyllum species (Podophyllum hexandrum Royle and Podophyllum peltatum) are a major source of deriving anticancer drugs from their major chemical constituent, podophyllotoxin. However, information lacks on regulatory components of podophyllotoxin biosynthesis; therefore, different classes of transcription factors were identified through mining transcriptomes of Podophyllum species and validated through qRT-PCR analysis vis-à-vis podophyllotoxin contents in different tissues/organs of Podophyllum hexandrum. A total of 82, 278, 70, and 90 transcripts were identified in shoots and 89, 273, 72, and 91 transcripts in rhizomes of P. hexandrum transcriptome; 70, 268, 48, and 92 transcripts were in shoots and 58, 245, 41, and 85 transcripts in rhizomes of P. peltatum transcriptome corresponding to bZIP, MYB, WRKY, and bHLH families of transcription factors, which have been shown in regulating biosynthesis of secondary metabolites. Two unique transcripts encoding bHLH and MYB/SANT TFs in shoots of P. peltatum (medp_podpe_41091 and medp_podpe_2547) and bZIP and MYB TFs in rhizomes of P. hexandrum (medp_podhe_163581 and medp_podhe_147614) correlated with podophyllotoxin content. Quantification of podophyllotoxin and comparative expression analysis between high (2.51 %) versus low (0.59) podophyllotoxin content accessions revealed 0.04 to ~16-folds increase in transcripts of transcription factors, thereby further supporting the association of identified transcription factors with podophyllotoxin content. bZIP TF showed the highest transcript abundance (19.60-folds) in P. hexandrum rhizomes (2.51 % podophyllotoxin) compared to shoots (0.01 %). In silico analysis of putative promoter regions of pathway genes in other plant species revealed the presence of sequence elements for MYB and WRKY transcription factors, thereby suggesting their role in controlling the production of podophyllotoxin. A repertoire of additional transcription factors has been provided, which can be functionally validated and used in designing a suitable genetic intervention strategy towards enhanced production of podophyllotoxin.
authors.affiliation: Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234, Solan, Himachal Pradesh, India.
authors.forename: Pawan
authors.initials: P
authors.lastname: Kumar
authors.affiliation: Department of Computer Science and Bioinformatics, Shoolini University, Solan, 173212, Himachal Pradesh, India.
authors.forename: Varun
authors.initials: V
authors.lastname: Jaiswal
authors.affiliation: Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234, Solan, Himachal Pradesh, India.
authors.forename: Tarun
authors.initials: T
authors.lastname: Pal
authors.affiliation: Agroforestry and Extension Division, Himalayan Forest Research Institute, Panthaghati, 171009, Shimla, Himachal Pradesh, India.
authors.forename: Jagdish
authors.initials: J
authors.lastname: Singh
authors.affiliation: Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234, Solan, Himachal Pradesh, India. rajinder.chauhan@juit.ac.in.
authors.forename: Rajinder S
authors.initials: RS
authors.lastname: Chauhan
mesh_terms: D003198:Computer Simulation; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018520:Plant Shoots / Q000235:genetics; D011034:Podophyllotoxin / Q000096:biosynthesis*; D011035:Podophyllum / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D027343:Rhizome / Q000235:genetics; D064210:Secondary Metabolism / Q000235:genetics; D013045:Species Specificity; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics
chemical_list: D012333:RNA, Messenger; D014157:Transcription Factors; D011034:Podophyllotoxin
keywords: Podophyllotoxin; Podophyllum; Regulation; Transcription factors; Transcriptome