Characterization of microsatellite DNAs in Takifugu rubripes genome and their utilization in the genetic diversity analysis of T. rubripes and T. pseudommus

Abstract

By screening the whole genome sequence of Takifugu rubripes available in DDBJ, a total of 49 647 simple sequence repeats (SSRs) were identified. One SSR was found every 7351 bp and the total length of all SSRs accounts for 0.77% of the whole genome, about 365 Mb in length. The most frequent six SSR types are di-, tetra-, tri-, penta-, hexa- and mononucleotide types, accounting for 71.30%, 13.77%, 7.14%, 3.73%, 3.23% and 0.80% of the total respectively. In decreasing order, The 20 most frequently occurring microsatellites were AC, AG, AGAT, ACAG, AT, AAT, AGGT, AGAGG, ACCT, AGG, ATC, ACT, ACAT, AACT, ACGC, AATC, A, TCCA, ACT and AATCCC, representing 90.81% of the total. The polymorphism of these SSRs will certainly facilitate the genetic diversity analysis of puffer fish and the comparative studies of diverse genomes. Nine microsatellites were used to study (1) the genetic diversity of wild T. rubripes (WR) and cultured stock (CR); and (2) the phylogenetic relationships of wild T. rubripes and Takifugu pseudommus (WP). All nine microsatellite DNA loci were polymorphic. A total of 106 alleles are found at all loci. The total number of alleles per locus ranges from 5 to 25. The genetic diversity index values of three populations were 0.8661 (WR), 0.8272 (WP) and 0.7832 (CR). The values of genetic distance and G ST (genetic differentiation) showed genetic differentiation among the three populations. All the data showed that H 0 values of cultured stock were less than those of wild T. rubripes, suggesting a significant decrease in genetic diversity. Genetic distance and G ST between WR and WP was smaller than those between WR and CR, suggesting that T. rubripes and T. pseudommus may be the same species.