Statistical Analysis of Simple Sequence Repeats in Genome Sequence: A Case of Acheta Domesticus (Orthoptera: Gryllidae)

Abstract

Herein, we have described genome wide screening of microsatellites (Simple Sequence Repeats: SSRs) and their distribution in the Acheta domesticus genome using a custom python script. A total of 232,179 microsatellites were identified, in which trinucleotide repeats were found to be the most abundant repeats in the genome, representing 60 % of the total microsatellite, followed by dinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides. Among trinucleotides, dinucleotides, and tetranucleotides, the most prevalent microsatellite motifs were AAT/ATT, TG/CA, and AAAT/ATTT, respectively. Notably, statistical analysis of the SSR repetition frequency distribution showed that SSR motifs that were repeated four times were the most recurrent. Additionally, the SSR length distribution showed that SSRs with a12 bp size were the most common. As a result, the statistical analysis of the SSR dataset in A. domesticus will be a useful resource for a better understanding of microsatellite distribution in crickets for evolutionary genetics.

Microsatellite-Marker-Based Evaluation of Stock Enhancement for Kuruma Prawn Penaeus japonicus in Beibu Gulf, South China Sea

“…Microsatellites (microsatellite DNA), also known as simple sequence repeats (SSRs), simple tandem repeats (STRs), or simple sequences, are composed of repeated DNA motifs (usually 1-6 base pairs) [13,14]. They have many advantages as molecular markers: high polymorphism, genetic codominance, easy detection, and low requirements for template DNA compared with that for other genetic markers [15].…”