title: Characterization of chloroplast DNA microsatellites from Saccharum spp and related species.
abstract: Microsatellites,  or simple sequence repeats (SSRs), and their flanking regions in chloroplast  genomes (plastomes) of some species of the family Poaceae were analyzed in  silico to look for DNA sequence variations. Comparison of the complete  chloroplast DNA sequences (cpDNAs) of sugarcane (Saccharum hybrid cv.  SP-80-3280 and S. officinarum cv. NCo310) and related species, Agrostis  stolonifera, Brachypodium distachyon, Hordeum vulgare subsp vulgare, Lolium perenne, Oryza nivara, O. sativa subsp indica, O. sativa subsp japonica, Sorghum bicolor, Triticum  aestivum, Zea mays, and Z. mays cv. B73, allowed us to  examine the organization of chloroplast SSRs (cpSSRs) in genic and intergenic  regions. We identified 204 cpSSRs in the sugarcane cpDNA; 22.5% were in genic  regions. The ndh, rps, trn, and rpl gene clusters  of the chloroplasts had the most repeats. Mononucleotide repeats were the most  abundant cpSSRs in these species; however, di-, tri-, tetra-, penta-, and  hexanucleotide repeats were also identified. Many base substitutions and  deletions/insertions were identified in the cpSSR loci and their flanking  regions. Multiple alignments of all cpSSR sequences of Poaceae species made  identification of nucleotide variability possible; repeat motifs are not  uniformly distributed across the Poaceae plastomes, but are mostly confined to  intergenic regions. Phylogeny was determined by maximum parsimony and  neighbor-joining inference methods. The cpSSRs of these species were found to  be polymorphic. It appears that individual cpSSRs in the Poaceae are stable, at  least over short periods of evolutionary time. We conclude that the plastome  database can be exploited for phylogenetic analysis and biotechnological  development.
authors.affiliation: Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brasil.
authors.forename: D M
authors.initials: DM
authors.lastname: Melotto-Passarin
authors.forename: E V
authors.initials: EV
authors.lastname: Tambarussi
authors.forename: K
authors.initials: K
authors.lastname: Dressano
authors.forename: V F
authors.initials: VF
authors.lastname: De Martin
authors.forename: H
authors.initials: H
authors.lastname: Carrer
mesh_terms: D001483:Base Sequence; D002736:Chloroplasts / Q000235:genetics; D018742:DNA, Chloroplast / Q000235:genetics*; D005819:Genetic Markers; D014644:Genetic Variation; D054628:Genome, Chloroplast; D018745:Genome, Plant; D018895:Microsatellite Repeats / Q000235:genetics*; D010802:Phylogeny; D011110:Polymorphism, Genetic; D031786:Saccharum / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D018742:DNA, Chloroplast; D005819:Genetic Markers