Characteristic Analysis of Microsatellite DNA in the Genome of Gobiidae

Abstract:

The family Gobiidae is one of the largest fish families consisting of more than 200 genera and 2000 species. This family was found in near shore seawater, brackish water, and freshwater in the temperate and tropical areas all over the world. In this study we applied microsatellite DNA (short sequence repeat, SSR) to characterize the genetic structure of Gobiidae. We analyzed 153 SSR sequences amplified in our laboratory and 535 SSR sequences downloaded and screened from GenBank. The 686 sequences originated from 19 different species of Gobiidae. The total length of these sequences was about 295062 bp, in which 473 microsatellite repeat loci were found by using the bio-software Tandem Repeats Finder. The length of the repeat sequences was 33370 bp. We found that 361 dinucleotide repeat sequences accounted for the majority (76.32%) of the 473 repeat loci. Moreover, the AC repeat sequences were the most common (94.18) in the dinucleotide repeat sequences, whereas AT and GC repeat sequences were not observed. The number of the trinucleotide repeat sequences was 35 (7.4%), including 12 ACT repeat sequences that were the majority (34.29%). There were 68 tetranuleotide repeat sequences including 31 CTAT that was the dominant (14.38%). The numbers of both petranucleotide and hexanucleotide repeat sequences were 2 (0.42%) and 7 (1.48%) respectively. Intriguingly repeats of single nucleotide sequences were absent. Our results about the distribution of microsatellite contributed to a better understanding of the genomic structure of goby fish, and might provide important information for the development and application of goby fish microsatellite markers.