De Novo Assembly, Functional Annotation and Comparative Analysis of Withania somnifera Leaf and Root Transcriptomes to Identify Putative Genes Involved in the Withanolides Biosynthesis

Guleri

Biotechnology and Genetic Engineering Reviews

et al. 2015

Withania somnifera is one of the most valued plants and is extensively used in Indian, Unani, and African systems of traditional medicine. It possess a wide array of therapeutic properties including anti-arthritic, anti-aging, anti-cancer, anti-inflammatory, immunoregulatory, chemoprotective, cardioprotective, and recovery from neurodegenerative disorders. With the growing realization of benefits and associated challenges in the improvement of W. somnifera, studies on exploration of genetic and chemotypic variations, identification and characterization of important genes, and understanding the secondary metabolites production and their modulation has gained significant momentum. In recent years, several in vitro and in vivo preclinical studies have facilitated the validation of therapeutic potential of the phytochemicals derived from W. somnifera and have provided necessary impetus for gaining deeper insight into the mechanistic aspects involved in the mode of action of these important pharmaceutically active constituents. The present review highlights some of the current developments and future prospects of biotechnological intervention in this important medicinal plant.

Section: Transport Of Withanolidesmentioning

confidence: 99%

Section: Ests and Transcriptomics Studiesmentioning

confidence: 99%

Section: Ests and Transcriptomics Studiesmentioning

confidence: 99%

See 1 more Smart Citation

Biotechnological interventions inWithania somnifera(L.) Dunal

Guleri

Biotechnology and Genetic Engineering Reviews

et al. 2015

“…It has now reached a level where large volumes of sequence data can be collected without a major investment in DNA sequencing infrastructure He et al 2012;Yan et al 2013;Dang et al 2013). Digital gene expression (DGE) is a tag-based transcriptome sequencing approach where short raw tags are generated by endonuclease (Mortazavi et al 2008;Gupta et al 2013). The advantage of the DGE approach is that it generates a transcriptional profile which more closely resembles the in vivo situation with low cost (Xu et al 2002;Wei et al 2013;Zhang et al 2013).…”

Section: Introductionmentioning

confidence: 99%

De novo characterization of the Rehmannia glutinosa leaf transcriptome and analysis of gene expression associated with replanting disease

Yang

Chen

et al. 2014

Mol Breeding

The perennial herbaceous plant, Rehmannia glutinosa Libosch, is a traditional Chinese medicine because of the active extracts from its dried tuberous roots. However, R. glutinosa productivity and quality has been seriously affected by replanting (continuous monoculture) disease, which cannot at present be effectively prevented or controlled. Since very little is known about the molecular mechanism of replanting disease, we aimed to investigate transcriptional changes in replanted R. glutinosa leaves and identify genes responding to the disease. Here, we constructed a cDNA library from total RNA isolated from the mixture of leaves of the first year planted (L1) and the second year replanted R. glutinosa (L2) at the tuberous root expansion stage. We generated about 37 million high-quality reads from the cDNA library using deep sequencing and obtained 94,544 distinct sequences by de novo assembly and gap-filling. From this set, a total of 54,490 transcripts containing a complete or partial encoding region was annotated in public protein databases. Based on this resource, we screened differentially expressed genes in the L1 and L2 libraries by the digital gene expression (DGE) technique. Finally, a set of 1,954 genes was found to be differentially expressed in L2. Using bioinformatics and qRT-PCR, the 117 most strongly differentially expressed genes were considered to be prime candidates responsible for replanting disease. Functional analysis of the candidates showed that ethylene signaling was exaggerated and the genes in key metabolism pathways were abnormally expressed in L2. The study provides an important resource for further investigating the cause of replanting disease and developing methods to control or reduce its harmful effects.

“…In addition, transcriptome datasets of the high papaverine mutant (pap1) and normal cultivar (BR086) developed in our laboratory were used for the analysis. These reads were processed and trimmed for weak signals by GS FLX pyrosequencing software to yield high-quality (HQ) (≥99.5 % accuracy of single-base reads) sequences and assembled using Roche GS Assembler (version 2.5.3) with 40 bp overlap and 95 % identity for independent libraries forming contigs and singletons as described in Gupta et al (2013). Contigs and singletons obtained from combined assembly were utilized for the purpose of quantifying differential expression of the members of the different gene families.…”

Section: Transcriptome Datasets Assembly and Annotationmentioning

confidence: 99%

Comparative analysis of transcription factor gene families from Papaver somniferum: identification of regulatory factors involved in benzylisoquinoline alkaloid biosynthesis

et al. 2015

Self Cite

Opium poppy (Papaver somniferum L.), known for biosynthesis of several therapeutically important benzylisoquinoline alkaloids (BIAs), has emerged as the premier organism to study plant alkaloid metabolism. The most prominent molecules produced in opium poppy include narcotic analgesic morphine, the cough suppressant codeine, the muscle relaxant papaverine and the anti-microbial agent sanguinarine and berberine. Despite several health benefits, biosynthesis of some of these molecules is very low due to tight temporal and spatial regulation of the genes committed to their biosynthesis. Transcription factors, one of the prime regulators of secondary plant product biosynthesis, might be involved in controlled biosynthesis of BIAs in P. somniferum. In this study, identification of members of different transcription factor gene families using transcriptome datasets of 10 cultivars of P. somniferum with distinct chemoprofile has been carried out. Analysis suggests that most represented transcription factor gene family in all the poppy cultivars is WRKY. Comparative transcriptome analysis revealed differential expression pattern of the members of a set of transcription factor gene families among 10 cultivars. Through analysis, two members of WRKY and one member of C3H gene family were identified as potential candidates which might regulate thebaine and papaverine biosynthesis, respectively, in poppy.