Analysis of Simple Sequence Repeats (SSRs) Dynamics in Reticulitermes chinensis

Abstract

: An abundance of potential inherent variation in SSR or microsatellite repeats has resulted in a valuable genetic marker in eukaryotes. We describe how SSRs in Reticulitermes chinensis castes are organized and abundant. Collectively we sequence 184,436 unigenes through the Trinity system, ranging from 201-43, 214 bp length from transcriptome data. Using MISA to find out SSRs in uni-genes and a total of 10740 SSRs loci were identified as di-, tri-, tetra-, penta-, and hexanucleotide. Among them, trinucleotide SSRs were the most abundant in R. chinensis genome 2702, followed by chromosome six (tri-) 1110. Pentanucleotide repeats were found at frequency 1 from each chromosome 8, 9 and 13, respectively. The frequency of AC/GT motif was (21.91%) reported, followed by others motif (16.6%), AAG/CTT (8.49%) and AGC/CTG (8.2%). The minimum motif types were AATG/ATTC (1.27%), followed by ACG/CGT (1.32%) and AAT/ATT (1.77%). Thes abundance and inherent variations in SSRs provide valuable information for taxonomics, phylogenetic, genome mapping, and population genetic research studies. SSR-based markers have high degrees of allelic variability and codominant legacy ( inheritance), and analytical ease.