title: Transcriptome analysis reveals in vitro cultured Withania somnifera leaf and root tissues as a promising source for targeted withanolide biosynthesis.
abstract: BACKGROUND
  The production of metabolites via in vitro culture is promoted by the availability of fully defined metabolic pathways. Withanolides, the major bioactive phytochemicals of Withania somnifera, have been well studied for their pharmacological activities. However, only a few attempts have been made to identify key candidate genes involved in withanolide biosynthesis. Understanding the steps involved in withanolide biosynthesis is essential for metabolic engineering of this plant to increase withanolide production.
  
  
  RESULTS
  Transcriptome sequencing was performed on in vitro adventitious root and leaf tissues using the Illumina platform. We obtained a total of 177,156 assembled transcripts with an average unigene length of 1,033 bp. About 13% of the transcripts were unique to in vitro adventitious roots but no unique transcripts were observed in in vitro-grown leaves. A putative withanolide biosynthetic pathway was deduced by mapping the assembled transcripts to the KEGG database, and the expression of candidate withanolide biosynthesis genes -were validated by qRT PCR. The accumulation pattern of withaferin A and withanolide A varied according to the type of tissue and the culture period. Further, we demonstrated that in vitro leaf extracts exhibit anticancer activity against human gastric adenocarcinoma cell lines at sub G1 phase.
  
  
  CONCLUSIONS
  We report here a validated large-scale transcriptome data set and the potential biological activity of in vitro cultures of W. somnifera. This study provides important information to enhance tissue-specific expression and accumulation of secondary metabolites, paving the way for industrialization of in vitro cultures of W. somnifera.
authors.affiliation: Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India. kalaiselvi_bc@avinuty.ac.in.
authors.forename: Kalaiselvi
authors.initials: K
authors.lastname: Senthil
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. murukarthick@snu.ac.kr.
authors.forename: Murukarthick
authors.initials: M
authors.lastname: Jayakodi
authors.affiliation: Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India. pankajavallimscbt@gmail.com.
authors.forename: Pankajavalli
authors.initials: P
authors.lastname: Thirugnanasambantham
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. sclee0923@snu.ac.kr.
authors.forename: Sang Choon
authors.initials: SC
authors.lastname: Lee
authors.affiliation: Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India. pradeepaduraisamy@gmail.com.
authors.forename: Pradeepa
authors.initials: P
authors.lastname: Duraisamy
authors.affiliation: Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India. preethi.contact@gmail.com.
authors.forename: Preethi M
authors.initials: PM
authors.lastname: Purushotham
authors.affiliation: Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India. kalaibcbt@gmail.com.
authors.forename: Kalaiselvi
authors.initials: K
authors.lastname: Rajasekaran
authors.affiliation: Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India. nancycharles90@gmail.com.
authors.forename: Shobana
authors.initials: S
authors.lastname: Nancy Charles
authors.affiliation: Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India. ira.roy69@gmail.com.
authors.forename: Irene
authors.initials: I
authors.lastname: Mariam Roy
authors.affiliation: Lab of Biochemistry, School of Veterinary Medicine, Gyeongsang National University, Gyeongsangnam-do, Republic of Korea. arulbiotechtnau@gmail.com.
authors.forename: Arul Kumar
authors.initials: AK
authors.lastname: Nagappan
authors.affiliation: Lab of Biochemistry, School of Veterinary Medicine, Gyeongsang National University, Gyeongsangnam-do, Republic of Korea. gonskim@gnu.ac.kr.
authors.forename: Gon Sup
authors.initials: GS
authors.lastname: Kim
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. yame1234@snu.ac.kr.
authors.forename: Yun Sun
authors.initials: YS
authors.lastname: Lee
authors.affiliation: Genomics and Proteomics Laboratory, Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, Tamil Nadu, India. senthil_natesan@yahoo.com.
authors.forename: Senthil
authors.initials: S
authors.lastname: Natesan
authors.affiliation: National Research Foundation, Seoul, Republic of Korea. tsmin@nrf.re.kr.
authors.forename: Tae-Sun
authors.initials: TS
authors.lastname: Min
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. tjyang@snu.ac.kr.
authors.forename: Tae Jin
authors.initials: TJ
authors.lastname: Yang
mesh_terms: D000975:Antioxidants / Q000378:metabolism; D059447:Cell Cycle Checkpoints / Q000187:drug effects; D045744:Cell Line, Tumor; D049109:Cell Proliferation / Q000187:drug effects; D002470:Cell Survival / Q000187:drug effects; D020224:Expressed Sequence Tags; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics; D018515:Plant Leaves / Q000166:cytology / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000166:cytology / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D032341:Withania / Q000235:genetics / Q000378:metabolism*; D054358:Withanolides / Q000302:isolation & purification / Q000378:metabolism* / Q000633:toxicity
chemical_list: D000975:Antioxidants; D054358:Withanolides; C009684:withaferin A