Data mining of simple sequence repeats in Codonopsis pilosula transcriptome / 中草药

ABSTRACT

Objective: To rapidly and largely identify the functional simple sequence repeat (SSR) in transcriptome dataset of Codonopsis pilosula based on bioinformatics analysis. Methods: MicroSAtellite (MISA) sofeware was used to analyze the distributing frequency of high-flux transcriptome SSR and the basic characteristics of repeat motifs. Primers were designed using Primer3, and SSRFinder was used to check SSR and screen the SSR primers. Results: SSR loci (7 327) were obtained from 45 511 unigenes, distributed in 6 017 unigenes (12.22%). There are 415 kinds of repeat motifs existing in C. pilosula transcriptome. On average, SSRs occurred every 4 520 bp in length. Dinucleotid repeats predominated with an occurrence frequency of 58.67%, and AG/CT was the most frequent one among all the repeat types. A total of 4 329 primer pairs were designed for marker development. Conclusion: The large number of SSR genetic markers developed in the present study should contribute greatly to research into genetic diversity and germplasm characterization in C. pilosula.