In silico analysis of polymorphic microsatellites in penaeid shrimp and construction of a free-access database

Abstract

We performed an in silico analysis of all microsatellites so far described for penaeid shrimp and for which the polymorphic behavior has previously been analyzed. The objective of the study was to evaluate the structural characteristics of these microsatellites and identifying patterns which allow the characterization of the nature of these sequences in the penaeid genome. All data were compiled in a free-access database specially constructed for this study. Three hundred non-mononucleotide polymorphic microsatellite loci described for 12 shrimp species belonging to the family Penaeidae were analyzed and simple and compound microsatellites with di-, tri-, tetra-, penta-and hexanucleotide motifs were found. Dinucleotides and trinucleotides were the most frequent motifs among both the simple and the compound microsatellites. Although a certain bias related to different microsatellite isolation methodology could not be discarded, it is possible that part of this microsatellite abundance reflects some degree of conservation of microsatellite motifs among the different species. There was a pronounced motif variability within and between species, indicating high differentiation dynamism of these repetitions in this animal group. This study not only sheds light on the structure of the microsatellites present in the penaeid shrimp genome but also resulted in the free-access Penaeid Shrimp Microsatellite Database (available at http://www.shrimp.ufscar.br) which may be very useful for optimizing the use of these microsatellites.Key words: Crustacea, microsatellite structure, Penaeidae, SSR.Received: September 19, 2006; Accepted: May 7, 2007. Over the last few decades, microsatellite sequences have been widely used in many animal groups, including shrimp, and principally in economically important species (Wolfus et al., 1997;Bierne et al., 2000;Xu et al., 2001). Due to their high level of allelic variation and codominant nature, microsatellite loci have been extremely useful for the determination of genetic diversity, stock discrimination, identification of lineages and individuals, the establishment of pedigrees, the development of breeding programs, linkage map studies and the identification of loci related to commercially important characteristics (Moore et al., 1999;Ozaki et al., 2000).In the past half decade, different research groups have been striving to characterize microsatellite markers in the genome of a number of penaeid shrimp species (Cruz et al., 2002;Meehan et al., 2003;Pérez et al., 2005). However, the validation of these sequences has generally not been easy. The penaeid genome seems to contain very long microsatellite repetitions, hindering the cloning and sequencing of microsatellites containing both flanking regions. A few comparisons demonstrate that the microsatellites found in penaeids (Tassanakajon et al., 1998;Cruz et al., 2002) are approximately twice the size of the sequences found in other animal groups (Estoup et al., 1993;Brooker et al., 1994), being four or five times larger in so...