Analysis of SSR distribution and sequence characteristics of Bupleurum chinense DC. Transcriptome

【Objective】 The SSR locus information and sequence characteristics in the transcriptome of Bupleurum chinense DC. were analyzed,so as to provide the basis for the development of functional gene-related SSR markers with good polymorphism.【Method】The processed seeds of B. chinense were used as materials to perform high-throughput transcriptome sequencing. Trinity was used to assemble the sequencing results for De Novo assembly. The unigenes obtained were searched for the presence of SSR sites by MISA software and then the SSR data was statistically analyzed.【Result】244194 unigenes were assembled from B. chinense DC. The transcriptome data had an N50 value of 1036 bp,an average length of 791 bp and a total length of 193138105 bp. A total of 50303 SSR loci were identified from the unigene sequences,among which 20405 were complex SSR loci and 29898 SSR loci were actually analyzed. The frequency of SSR accounted for 12.24% of all unigenes with an average distribution distance of 6.46 kb. The major repeat motifs were dinucleotide(17105),accounting for 57.21% of all SSRs, followed by trinucleotide and mononucleotide(20.75% and 20.46%, respectively). The proportion of tetranucleotide repeat units to hexanucleotide repeat units was low. 97 kinds of repeat motifs were found in the B. chinense DC. transcriptome. The main repeat motif types in dinucleotide were AT/AT and in trinucleotide were ATC/GAT, which accounted for 33.33% and 3.98% of the total SSR,respectively. The types of SSR repeat units with 5 to 10 repeats had the highest proportion,with a total of 27942,accounting for 93.46% of the total SSRs. The sequence length ranged from 12 bp to 76 bp,with an average length of 15.28 bp.【Conclusion】The SSR loci in the B. chinense transcriptome have high frequency and diversity,and it is possible to develop SSR primers with high polymorphism,which can be used in the analysis of B. chinense genetic diversity,germplasm resource evaluation and molecular marker-assisted breeding.