In silico mining of SSR markers from expressed sequence tags of Clematis chinensis

Abstract Clematis chinensis (family: Ranunculaceae) is a deciduous climbing plant having multipurpose use in traditional Chinese medicine, but the use of molecular markers in Clematis chinensis is yet to gain momentum. Recently EST-SSRs are the free by-product of the currently growing EST databases. SSRs (microsatellites) have been extensively used as molecular marker in several genetic studies. The present study reports the frequency of SSRs and appropriate primers for the C. chinensis EST sequences. The EST sequences of C. chinensis were obtained from NCBI database and screened for the presence of SSRs. MISA tool was used to predict the microsatellites and Primer3 plus software was used for designing the primers. By using the MISA tool a total of 155 SSRs were identified in contigs and 275 SSRs were identified in singletones. Occurrence of trinucleotide repeats were most abundant both in contigs (52.3%) and singletones (41.5%) followed by dinucleotides. Maximum trinucleotide motifs code for Leucine (CTT) followed by glutamic acid (GAA) and Serine (TCT) i.e., whereas in singleton sequences glutamic acid (GAA) is dominated followed by glutamine (CAA) and asparagine (AAC). AG/CT was the most recurrent repeat of dinucleotide. We also In silico designed 60 primers flanking the SSR repeats. The identified SSRs and their related markers can be used in future studies of linkage mapping, comparative genomics study, genetic diversity analysis and different breeding programs in Clematis chinensis.