Biodiversity Mining Through Transcriptome Analysis

Secondary metabolites or chemical constituents of plants are functional products synthesized through more complex multienzymatic secondary metabolite pathways. The release of few secondary metabolites is related to the exertion of morphological differentiation and maturation during plant development. Secondary metabolite compounds designate huge chemical diversity, i.e., each plant possesses its own complex diverse set of metabolites. This diversity imparts analytical challenges, characterization of a number of metabolites in parallel, and quantification of particular compound of interest. These compounds itself are related to significant plant traits (color and fragrance of flowers, taste and color of food, and resistance toward pests and pathogens) and also for the synthesis of fine chemicals such as medicines (anticancer, anti-inflammatory, antioxidants, etc.), flavors, fragrances, dyes, insecticides, pheromones, and antimicrobial agents. The emergence of cost-effective high throughput sequencing or next-generation sequencing (NGS) technology quickly expanded transcriptome information of several plant species, which could be analyzed for quick identification of previously unknown genes and enzymes and elucidation of biosynthetic pathways. The present chapter details diverse secondary metabolites, gene expression patterns, molecular basis of chemical diversity of the compounds, and application of NGS based transcriptome profiling for biosynthetic pathway elucidation.

Citation: Sabu, K. K. and F. Nadiya. 2017. Biodiversity Mining Through Transcriptome Analysis. In: Bioresources and Bioprocess in Biotechnology, Volume 1: Status and Strategies for Exploration, Part II. Eds. Sabu A, N.S. Pradeep, S. Shiburaj. pp 207-246. doi: 10.1007/978-981-10-3573-9_10. Springer, Singapore.

Development and validation of EST-SSR and identification of EST-SNP markers for snake gourd (Trichosanthes cucumerina var. cucumerina L.)

Snake gourd is a natural antibiotic and the plant is commonly used in folk medicines throughout India. The present study was carried out using transcriptomic sequence of Trichosanthes kirilowii Maxim. for the development and validation of EST-SSR markers and EST sequences of T. dioica Roxb. for identification of EST-SNPs in T. cucumerina var. cucumerina L. A total of 382 primers were developed and out of which 58 were found to be suitable for genetic analysis. For experimental validation, 20 primers were randomly selected and amplified in T. cucumerina var. cucumerina and two related genera, viz. Coccinia grandis and Momordica charantia. It was found that 90% of the primers generated PCR products in T. cucumerina var. cucumerina and considerable cross generic amplification in M. charantia and C. grandis. Further, identification of EST-SNPs in T. cucumerina var. cucumerina was also carried out. The SNPs detected were converted to CAPS markers using the tool SNP2CAPS. The newly developed SSR and SNP markers offer novel additions to the genomic resources of this important medicinal herb for population studies, phylogenetics analyses and estimation of genetic diversity.

Citation: Silpa S, Shinsy M Y, Sabu K K. 2016. Development and validation of EST-SSR and identification of EST-SNP markers for snake gourd (Trichosanthes cucumerina var. cucumerina L.). Abrahamia 2: 51-56