Evaluation of Perfect Microsatellites in Nile Tilapia (Oreochromis niloticus) Genome

Abstract

Microsatellites or simple sequence repeats (SSRs) consist of a sizable part of genomes and 
play a crucial role in the function of genes and the organization of the genome. The complete 
availability of a genome sequence for Nile tilapia (Oreochromis niloticus) provides the possibility of 
accomplishing a genome-wide analysis of SSRs in this species. I analyzed the abundance and density 
of perfect SSRs in the Nile tilapia genome and observed a sum of 252,047 microsatellites with 1–6 bp 
nucleotide motifs. This indicates that about 2.7 % of the Nile tilapia whole genome sequence 
(927.77Mb) is made up of perfect SSRs, with an average length of 135.68bp/Mb. The average density 
and frequency of perfect SSRs were 271.69 loci/Mb and 5834.46 bp/Mb, respectively. The six classes 
of perfect SSRs proportional distribution within the Nile tilapia genome were not even. Dinucleotide 
repeats (40.13 %) with a total count of 101145 of an average length of 26.11 bp happen to be the most 
abundant class of SSRs, while the percentages of mononucleotide, trinucleotide, tetranucleotide, 
pentanucleotide, and hexanucleotide repeats was 31.88 %, 11.98 %, 11.52 %, 4.22 %, and 0.26 %, 
accordingly. The various classes of SSRs repeat differ in their number of repeats with the highest 
being 95. My results indicate that 21 motifs contain the prevalent categories with a frequency above 1 
locus/Mb: A, AAC, AAG, AATAG, AATTC, AC, AG, AGAT, AT, ATCT, ATG, ATGG, ATT, 
ATTT, C, CCT, CTG, CTTT, GT,  GTTT.