Starch is the major source of storage carbohydrate, which is important product for plant and animal as well as for industrial use. Starch synthase (SS) enzyme encoded by several genes is the key factors in starch biosynthetic pathway. Genome wide exploration and characterization of these starch synthase (SS) genes are still limited in the literature. Therefore, intensive bioinformatic tools were approached to identify and in silico characterize the SS genes in potato genome. We identified several orthologues of SS in Arabidopsis by using the term starch synthase in Arabidopsis genome database (TAIR) and National Centre for Biotechnology Information (NCBI). These orthologues were blast in Sol Genomics network and ten SS genes were confirmed as member of the family following Hidden Markov Model (HMM). The genes were characterized in silico for chromosomal locations, phylogeny, exon-intron, domains and motif content, molecular weight and nature of proteins and predicted the functions using different online bioinformatic tools. Chromosomal map and phylogenetic tree were constructed for analyzing evolutionary pattern and relationship with the SS genes of other crop species. The SS genes are distributed on 4 chromosomes (chromosome number 2, 3, 7 and 8) out of 12 potato basic chromosomes and originated from Arabidopsis. The results of this study will be provided basic information in planning future research regarding the regulatory mechanism of search synthesis both under normal and stress condition.
Key words: In silico, Starch synthase, Potato, Phylogeny, Motif
|
