Phylogenic analysis based on intergenic spacer of rpl32-ccsA segment in chloroplasts genome of cacao (Theobroma cacao L.).

Complete chloroplast genome of cacao (Theobroma cacao L.) provides information not only about the size of genome, and the number of genes (81 genes) on it, but also indicates a lot of untranslated regions which vary in between sub species. The genome size is about 160 kbp (kilo base pairs), and having highly conserved regions among chloroplast genome in other plants. Recently, studies on chloroplast genome, indicate there are universal primers in certain locus, which compatible in amplification of DNA fragment for various plants. Therefore, that regions were suitable for genetic marker in developing DNA fingerprinting, including in sub species level. Here in this study, we used the universal primer for analyzing intergenic spacer of rpl32-ccsA on chloroplast genome of Sulawesi cacao, and utilize available sequences homologue in database, in constructing phylogenetic analysis. The outcome, indicating that the variation on nucleotide sequences of this region can be potentially used in identification on sub species level. [ABSTRACT FROM AUTHOR]