In silico analysis of carotenoid biosynthesis pathway in cassava (Manihot esculenta C.)

Abstract

The project entitled “In silico analysis of carotenoid biosynthesis pathway in cassava (Manihot esculenta C.)” was conducted at ICAR-CTCRI, Sreekariyam, Thiruvananthapuram during 2016-2017. The main objective of the study was to identify the genes involved in the carotenoid biosynthesis pathways in cassava, construction of the carotenoid biosynthesis pathway in cassava, regulatory sequence analysis of carotenoid genes in cassava and visualization of the constructed carotenoid pathway. The preliminary template data set of carotenoid genes were obtained from NCBI and Phytozome database. 39 carotenoid genes were identified from cassava through comparative genomic analysis and BLAST-p search Functional annotation of carotenoid genes was done using E2P2 tool and NCBI conserved domain analysis tool. This ensures the function of the carotenoid genes in cassava. The identified genes were used for the regulatory sequence analysis. TF prediction analysis shows that about 18 TF associated with identified carotenoid genes in cassava, CpG island analysis facilitated to understand the carotenoid gene expression pattern in cassava and miRNA analysis showed six significant miRNAs targeting carotenoid genes in cassava. Phylogenetic analysis and chromosomal location analysis revealed the gene duplication events and conserved genes between cassava and the template plants such as Arabidopsis thaliana, Solanum lycopersicum, Solanum tuberosum, Ipomea batatas and Populus trichocarpa. Carotenoid biosynthesis pathway in cassava constructed by integrating the identified genes and regulatory elements using cell illustrator software. MEP pathway, core carotenoid pathway and apocarotenoid pathway was interconnected into a single pathway and subcellular localization analysis data was united with this novel pathway.Study of the carotenoid biosynthetic genes and pathways in cassava will provide insight into carotenoid metabolic mechanisms and enrichment of carotenoids in cassava.