Article

cid: a rapid and efficient bioinformatic tool for the detection of SSRs from genomic libraries.

Departamento de Genética e Evolução, Universidade Federal de São Carlos, Via Washington Luiz km 235, Caixa Postal 676, CEP 13565-905, São Carlos, SP, Brazil.
Molecular Ecology Resources (Impact Factor: 7.43). 01/2008; 8(1):107-8. DOI: 10.1111/j.1471-8286.2007.01950.x
Source: PubMed

ABSTRACT cid is a computational tool developed in the Web environment to process cloned DNA fragments with the objective of masking the vector and adaptor regions, detecting the presence of microsatellites and designing the most appropriate primer pairs for the amplification of the identified repetitive sequences. This entire process is executed by the user in a simple and automated manner with the data input as a Zip file of chromatograms or a multiFASTA file. Thus, it is possible to analyse dozens of sequences at the same time, optimizing data processing and the search for the information of interest. cid is freely available on http://www.shrimp.ufscar.br/cid/index.php.

0 Bookmarks
 · 
50 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: We characterize thirteen polymorphic microsatellite loci isolated from Naja atra genomic libraries, which were enriched for AC-motif microsatellites. The thirteen loci were screened on a group of 48 individuals from two populations, one in Yong'an and the other in Ganzhou. These markers revealed a relatively high degree of genetic diversity (4-12 alleles per locus) and heterozygosity (Ho ranged from 0.213-0.854 and He ranged from 0.301-0.838). Tests for departure from Hardy-Weinberg equilibrium and for linkage disequilibrium were conducted for each of the two populations separately. After sequential Bonferroni correction, none of the 13 loci showed significant departures from Hardy-Weinberg equilibrium. Hierarchical analysis of molecular variance indicated that a small but significant (P < 0.001) proportion (16.0%) of the total variation in the microsatellite DNA data were attributable to differences among populations, indicating geographical structuring and restricted gene flow. It could be attributable to the Wuyi mountains in the area having a sufficiently isolating effect to significantly reduce gene flow. Our microsatellite data also showed a low N(m) (1.31) value in the two populations from mainland China. Thus, the Yong'an and Ganzhou populations could be treated as distinct evolutionarily significant units (ESUs). The high level of polymorphism revealed by these microsatellite markers will be useful for the study of gene flow, population structure and evolutionary history of N. atra.
    International Journal of Molecular Sciences 01/2011; 12(7):4435-40. · 2.46 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The leaf-cutter ant Atta laevigata (Formicidae: Attini) is an agricultural pest largely distributed in the Neotropics and a model organism for studies of evolution, speciation and population genetics. Microsatellites are a very powerful tool for these kind of studies, but such markers are not available for studies on A. laevigata. In the present report, we describe the isolation and characterization of nine microsatellite loci in A. laevigata and the testing of these markers across other species of leaf-cutter ants. Nine microsatellite loci, consisting of six dinucloeotide, one trinucleotide, one tetranucleotide, and one di/trinucleotide repeat motifs, were isolated and characterized. Primers and protocols were successfully designed to selectively amplify these markers. To test effectiveness of these markers for detailed population genetic studies, we genotyped female workers collected from 36 monogynic nests of A. laevigata and found that eight loci were within Hardy-Weinberg expectations, while the remaining locus had a deficiency of heterozygotes. Micro-Checker analysis of individuals from 55 monogynic nests indicated that loci Alae11, Alae24, Alae18 showed signs of null alleles. For the remaining six loci, the number of alleles per locus ranged between 2 and 11, with expected heterozygosity ranging between 0.07 and 0.88. All of these loci cross-amplified in other species of Atta. These six polymorphic microsatellite loci should prove useful for future genetic investigations of the pest species Atta laevigata, as well as studies of other species of leaf-cutter ants in the genus Atta.
    BMC Research Notes 01/2013; 6(1):328.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Ten microsatellite loci were isolated and characterized from the spiny-rat (Clyomy bishopi), a mediumsize Neotropical rodent that inhabits some of the last remaining savannas from Sa˜o Paulo state, Brazil. Between 5 and 17 alleles were detected per locus, with expected heterozygosity ranging from 0.605 to 0.921. All but one locus were found to be in Hardy–Weinberg equilibrium, and no linkage disequilibrium was detected among pairs of loci. These microsatellites should provide useful markers in genetic studies including parentage analyses and determining genetic and social structure of populations.
    Conservation Genetics Resources 10/2012; 4(4):335-337. · 1.14 Impact Factor