Mining and Survey of Simple Sequence Repeats in Expressed Sequence Tags of Tomato Species

Abstract

Expressed Sequence Tags (ESTs) of three tomato species were computationally mined for simple sequence repeats (SSRs). A total of 4,490, 291 and 1,270 simple sequence repeats identified in analyzed non-redundant ESTs of Solanum lycoperisicum, Solanum pennellii and Solanum habrochaites, respectively. In S. lycopersucum, 416 sequences contained more than one SSR and 264 motifs were present in compound formation. 24 and 137 EST sequences contained more than one SSR, and 16 and 93 motifs were found in compound formation in S. pennellii and S. habrochaites, respectively. The frequency of repeats within all retrieved S. lycopersicum EST sequences were 7.6%, whereas this number was corresponded to 6.5% in S. pennellii and 9% in S. habrochaites. An average density was one SSR per 9 kb in S. lycopersicum, per 7.9 kb in S. pennellii and per 9.4 kb in S. habrochaites. AT/AT, AG/CT and AAG/CTT motifs, considering sequence complementary, detected more frequently among all types of identified repeats.