Data mining for simple sequence repeats in expressed sequence tags from Saruma henryi / 中草药

ABSTRACT

Objective To analyze the simple sequence repeat(SSR)information in expressed sequence tag(EST)resource of Saruma henryi and lay a solid foundation for the development of EST-SSR markers in this species.Methods ESTs of S.henryi were downloaded from GenBank and used to perform the contig assembly using Sequencher 4.8.Uni-ESTs were obtained and screened for SSR-containing unigenes using SciRoKo 3.4.The distributing frequency of the EST-SSRs and the basic characteristics of motifs were analyzed.Results A total of 10 274 ESTs of S.henryi were retrieved and were assembled into 6 643 non-redundant Uni-ESTs with a total length of 5.11?106 bp.In all,the data mining yielded 1 408 SSR loci,which corresponded to 1 232 Uni-ESTs(18.55%).On average,EST-SSRs spanned 22.30 bp,and occurred every 3.63 kb in length.In S.henryi,mononucleotide repeats predominated with an occurrence frequency of 12.24%.Dinucleotide repeats followed with a frequency of 5.01%.The most frequent one was A/T among all the repeat motifs,then followed by AG/CT.Conclusion SSRs in ESTs of S.henryi display a relatively high level of occurrence frequency and show abundance of types.