In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

Author(s)

Tambarussi, Evandro Vagner ^[1] ; Melotto-Passarin, Danila Montewka ^[1] ; Gonzalez, Simone Guidetti ^[1] ; Brigati, Joice Bissoloti ^[1] ; de Jesus, Frederico Almeida ^[1] ; Barbosa, Andre Luis ^[1] ; Dressano, Keim ^[1] ; Carrer, Helaine ^[1]

Affiliation

^[1] Univ Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Ciencias Biol, BR-13418900 Piracicaba, SP - Brazil

• Document type: Journal article
• Source: Crop Breeding and Applied Biotechnology; v. 9, n. 4, p. 344-352, DEC 2009.
• Web of Science Citations: 8

Abstract

The availaibilty 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 sequence 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 analyses and biotechnological approaches (AU)

• FAPESP's process: 07/05797-3 - Study of SnRK gen family related to sucorse acumulation in sugarcane
• Grantee: Frederico Almeida de Jesus
• Support Opportunities: Scholarships in Brazil - Master
• FAPESP's process: 07/05795-0 - Development of biotechnological methods for micropropagation, regeneration and genetic transformation of teak (Tectona grandis L. f.) to resistance for Hyblaea puera
• Grantee: Evandro Vagner Tambarussi
• Support Opportunities: Scholarships in Brazil - Master