The Distribution and Characteristics of SSR in Transcriptome of Psammosilene tunicoides

PurposeThe distribution and sequence characteristics of SSR loci information in Psammosilene tunicoides in Yunnan-Guizhou region were analyzed, which laid a foundation for the development of SSR primers.

MethodDe novo assembly was carried out by MISA software after transcriptome sequencing with the young leaves of P. tunicoides as material. Excel software was used to analyze and Primer 3 software was used to design primers.

ResultsA total of 6 660 microsatellite loci were detected from 77 942 Unigenes sequences, with a frequency of 8.54% and an average distribution distance of 401.64 kb. Trinucleotide and dinucleotide were major repeat types, accounting for 58.69% and 35.77%, respectively. Pentanucleotide was minimum (1.24%). AG/TC, GA/CT, CTT/GAA and ACC/TGG were respectively most frequent repeated motifs in di-nucleotide and tri-nucleotide repeated types, and accounting for 12.66%, 10.45%, 3.71% and 3.60%. SSR primers were designed based on these Unigenes. The SSR loci in the P. tunicoides transcriptome showed moderate frequency of distribution, close distribution distance, rich repeated types, high repeated times and significant potention of polymorphism. 20 primers were successfully amplified which were selected randomly from 82 primers.

ConclusionThe results indicated that the Unigenes obtained from transcriptome sequence in P. tunicoides can be used as an effective way for the development of SSR loci. The SSR primers will provide more markers for the research of genetic variation of P. tunicoides.