In silico analysis on frequency and types of simple sequence repeats in expressed sequence tags (ESTs) of different tomato species

Abstract

The present study focuses on computational mining and survey of the frequency and types of simplesequence repeats in Expressed Sequence Tags (ESTs) of three different tomato species. A thousand ESTs sequences from each of S.lycopersicum L., S.pennellii Corell. and S.habrochaites S.Knapp & D.M.Spooner were retrieved from the National Center for Biotechnology Information (NCBI) databaseand searched for the presence of simple sequence repeat (SSRs) motifs. A total of 35 EST-derived SSRs within 32 unigens of S.lycopersicum, 51 SSRs within 46 unigens of S.pennellii and 64 SSRs in 55unigens of S.habrochaites were identified. Trinucleotide repeats were the most abundant class of microsatellites in all the examined species (54%, 39% and 45% respectively). The hexanucleotide repeats were the second most frequent EST-SSRs in cultivated tomato (26%) and s. pennellii (27%), whereas trinucleotide motifs were followed by pentanucleotides in S. habrochaites (28%). The AGC/CTG motif was the most frequent among all types of repeats identified in S. lycopersicum ESTs, whereas the AAT/ATT and AT/AT were the most abundant in S. pennellii and AAATT/AATTT, ACC/GGT, AAT/ATT, ATC/ATG and AT/AT in S. habrochaites respectively.