Analysis on Microsatellites in Rhodiola algida Based on Solexa Sequencing
LEI Shu-Yun1,2；GAO Qing-Bo1；FU Peng-Cheng1；YANG Hui-Ling1*；CHEN Shi-Long1；ZHANG Fa-Qi1,3
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Solexa sequencing was used to analyze microsatellites in Rhodiola algida based on EST-assembled sequences, expecting to find out the genetic diversity and to develop microsatellite markers for Rhodiola. A total of 6552 EST sequences were obtained in the current study, trinucleotide repeats were the most with 41.5%, mononucleotide and dinucleotide repeats were almost similar with 27.76% and 24.76%, respectively. The distribution densities of dinucleotides repeats to hexanucleotides were directly proportional to the number of SSR number. In mononucleotides repeats, thymine(T) and adenine(A) accounted for 14.91% and 12.70%, respectively, while with less G and C repeats. In dinucleotide repeats, AG repeats were the dominated with 5.60%, followed by GA(4.75%) and TC(4.72%). In trinucleotides repeats, GAA were the most frequent, accounted for 1.85%, followed by GAT(1.79%), while TTC, TCT, TCA, GGA, GCT, GAG with similar composition. The tetranucleotide, pentanucleotide and hexanucleotide repeats were very few. Except for pentanucleotide and hexanucleotide repeats, the variation of repeats are inversely proportional to the length of repeated nucleotide, while on one type, the variation of repeats is in negative correlation.