Berry transcriptome: insights into a novel resource to understand development dependent secondary metabolism in Withania somnifera (Ashwagandha). 
Withania somnifera (Ashwagandha) is considered as Rasayana in Indian systems of medicine.  This study reports a novel transcriptome of W. somnifera berries, with high depth, quality and coverage.  Assembled and annotated transcripts for nearly all genes related with the withanolide biosynthetic pathway were obtained.  Tissue-wide gene expression analysis reflected almost similar definitions for the terpenoid pathway in leaf, root and berry tissues with relatively higher abundance of transcripts linked to steroid, phenylpropanoid metabolism as well as flavonoid metabolism in berries.  The metabolome map generated from the data embodied transcripts from 143 metabolic pathways connected together and mediated collectively by about 1792 unique enzyme functions specific to berry, leaf and root tissues, respectively.  Transcripts specific to cytochrome p450 (CYP450), methyltransferases and glycosyltransferases were distinctively located in a tissue specific manner and exhibited a complex network.  Significant distribution of transcription factor genes such as MYB, early light inducible protein (ELI), minichromosome maintenance1, agamous, deficiens and serum response factor (MADS) and WRKY etc.  was observed, as the major transcriptional regulators of secondary metabolism.  Validation of the assembly was ascertained by cloning WsELI, which has a light dependent regulatory role in development.  Quantitative expression of WsELI was observed to be considerably modulated upon exposure to abiotic stress and elicitors.  Co-relation of over-expression of WsELI, may provide new aspects for the functional role of ELI proteins in plants linked to secondary metabolism.  The study offers the first comprehensive and comparative evaluation of W. somnifera transcriptome data between the three tissues and across other members of Solanaceae (Nicotiana, Solanum and Capsicum) with respect to major pathways and their metabolome regulation.