基于Solexa高通量测序的唐古特红景天(Rhodiola algida)微卫星信息分析

Analysis on Microsatellites in Rhodiola algida Based on Solexa Sequencing

利用所获得的Solexa高通量唐古特红景天转录组拼接EST序列进行微卫星位点的挖掘分析,期望为红景天属SSR标记的开发提供生物信息学依据。在得到的6552条EST序列中,三碱基最多,占总EST序列的41.50%;单核苷酸和二核苷酸重复类型的SSR含量相似,分别为27.76%和24.76%;二至六碱基微卫星分布密度与其对应的SSR含量成正比。在单核苷酸重复类型中,T和A重复类型最多,分别为总SSR的14.91%、12.70%,而G和C重复类型则很少;在二核苷酸重复类型中,AG重复类型最多,占总SSR的5.60%,GA和TC重复类型次之,分别为4.75%、4.72%;在三核苷酸重复类型中,GAA重复类型最多,为总SSR的1.85%,GAT次之,为1.79%,TTC、TCT、TCA、GGA、GCT、GAG重复类型间的SSR数相差不大;四、五、六核苷酸重复类型则很少。除五、六核苷酸重复类型外,其长度变化与其对应的重复类型碱基长度成反比;同种重复类型中,微卫星的长度与其对应的SSR数成反比。

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 with5.60%,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.