Bioinformatics Analysis of Perfect Microsatellite in the Whole Genomes of Channel Catfish,Ictalurus punctatus

The perfect microsatellite sequences were searched in channel catfish（Ictalurus punctatus） genome, and their number, frequency, density and distribution were analyzed by bioinformatics methods in this study. The results showed that there were 678 681 perfect microsatellites with a length of 15.8 Mb, accounting for 2.25% of the genome sequence. The relative abundance was 963 loci/Mb. Among the 6 types of microsatellites, dinucleotide repeats had the largest quantity, reaching a total of 341 143, which accounted for 50.26% of the total microsatellites. Mononucleotide repeats（22.50%）, tetranucleotide repeats（14.00%）, trinucleotide repeats（11.93%）, pentanucleotide repeats（1.14%）, and hexanucleotide repeats（0.17%） were followed. The top 10 microsatellite classes in channel catfish genome were: GT/AC,A/T,AG/CT,AT,ATT/AAT,ATTT/AAAT,C/G,GTTT/AAAC,AGAT/ATCT and ACT/AGT. Among the 29 chromosomes, chromosome 13 contained the largest number of microsatellites（39 089）, and the chromosome 16 had the least（10 692）. A highly positive correlation was observed between microsatellite numbers and chromosome lengths of DNA sequences. In addition, chromosome 16 had the highest frequency of microsatellite occurrence（1 478 loci/Mb） and chromosome 3 had the lowest（713 loci/Mb）. The result showed that the frequency of microsatellite was also positively related to chromosome length. The present study provides a basis for the further research on microsatellite marker screening, genetic analysis and molecular breeding of channel catfish.