In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species
Helaine Carrer; Evandro Vagner Tambarussi; Danila Montewka Melotto-Passarin; Simone Guidetti Gonzalez; Joice Bissoloti Brigati; Frederico Almeida de Jesus; André Luiz Barbosa and Keini Dressano
Abstract: The availability of chloroplast genome (cpDNA) sequences of Atropa belladonna, Nicotiana sylvestris, N. tabacum, N. tomentosiformis, Solanum bulbocastanum, S. lycopersicum and S. tuberosum, which are Solanaceae species, allowed us to analyze the organization of cpSSRs in their genic and intergenic regions. In general, the number of cpSSRs in CpDNA ranged from 161 in S. tuberosum to 226 in N. tabacum, and the number of intergenic cpSSRs was higher than genic CpSSRs. The mononucleotide repeats were the most frequent in studied species, but we also identified di-, tri-, tetra-, penta- and hexanucleotide repeats. Multiple alignments of all cpSSRs sequences from Solanaceae species made the identification of nucleotide variability possible and the phylogeny was estimated by maximum parsimony. Our study showed that the plastome database can be exploited for phylogenetic analysis and biotechnological approaches.