Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species.
Simple sequence repeat (SSR) markers are widely used in many plant and animal genomes due to their abundance, hypervariability, and suitability for high-throughput analysis. Development of SSR markers using molecular methods is time consuming, laborious, and expensive. Use of computational approaches to mine ever-increasing sequences such as expressed sequence tags (ESTs) in public databases permits rapid and economical discovery of SSRs. Most of such efforts to date focused on mining SSRs from monocotyledonous ESTs. In this study, we have computationally mined and examined the abundance of SSRs in more than 1.54 million ESTs belonging to 55 dicotyledonous species. The frequency of ESTs containing SSRs among species ranged from 2.65% to 16.82%. Dinucleotide repeats were found to be the most abundant followed by tri- or mono-nucleotide repeats. The motifs A/T, AG/GA/CT/TC, and AAG/AGA/GAA/CTT/TTC/TCT were the predominant mono-, di-, and tri-nucleotide SSRs, respectively. Most of the mononucleotide SSRs contained 15-25 repeats, whereas the majority of the di- and tri-nucleotide SSRs contained 5-10 repeats. The comprehensive SSR survey data presented here demonstrates the potential of in silico mining of ESTs for rapid development of SSR markers for genetic analysis and applications in dicotyledonous crops.
Kumpatla
Siva P
SP
Indiana University School of Informatics, IUPUI, Indianapolis 46202, USA. spkumpatla@dow.com
Mukhopadhyay
Snehasis
S
D019295:Computational Biology / Q000379:methods; D018548:Cotyledon / Q000235:genetics*; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D019684:Magnoliopsida / Q000235:genetics*; D018598:Minisatellite Repeats; D013045:Species Specificity