基于高通量测序的怒江红山茶微卫星位点特征分析
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摘要
以怒江红山茶叶片为材料,采用Illumina Hiseq 2000平台测序,共获得140 996条无冗余的序列,进行SSR位点搜索后,得到32 696个SSR位点,出现频率为23.2%。所搜索的SSR以二核苷酸重复类型最多,三核苷酸和单核苷酸次之,四、五、六核苷酸重复类型较少(<1%)。单核苷酸重复类型中以A/T基元较丰富(10.92%);二核苷酸中AG/CT基元出现频率最大,达到49.72%,AT/AT基元和AC/GT基元所占比例相差不多,而CG/CG基元所占比例最少,为0.07%;三核苷酸重复类型中AAG/CTT最多,ACC/GGT、ATC/ATG和AGG/CCT基元次之,CCG/GGC、ACT/AGT和ACG/CGT基元较低,都小于1%;四、五、六核苷酸类型中各重复基元均较少。在怒江红山茶转录组中,微卫星的数量随着对应的重复类型、重复次数的增加而降低,也随重复区段碱基长度的增加而降低。
Leaves sample of Camellia saluenensis Stapf ex Bean was sequenced with high-throughput sequencing technology(Illumina Hiseq 2000).In total 140 996 transcripts of C.saluenensis were screened using MISA software.The 32 696 SSRs were identified,and the frequency of SSR was 23.2% and mean distribution density was dinucleotide 32.02 kB.The di-nucleotide repeats were the highest,followed by tri-nucleotide and mononucleotide repeat types.The tetra-nucleotide,penta-nucleotide and hexa-nucleotide were all less than 1%.Among the mononucleotide repeats,the A/T repeats motifs were the highest frequency(10.92%).AG/CT was the most frequent repeat motifs in di-nucleotide repeats(49.72%),followed by AT/AT and AC/GT.CG/CG were minimum.AAG/CTT repeats motifs was the highest in tri-nucleotide followed by ACC/GGT,ATC/ATG and AGG/CCT,while CCG/GGC,ACT/AGT and ACG/CGT were lowest(<1%).The repeat motifs were very few in tetra-nucleotide,petra-nucleotide and hexa-nucleotide and had no obvious differences.The microsatellite number in C.saluenensis decreased with the increased number of repeats and length of repeats.
Leaves sample of Camellia saluenensis Stapf ex Bean was sequenced with high-throughput sequencing technology(Illumina Hiseq 2000).In total 140 996 transcripts of C.saluenensis were screened using MISA software.The 32 696 SSRs were identified,and the frequency of SSR was 23.2% and mean distribution density was dinucleotide 32.02 kB.The di-nucleotide repeats were the highest,followed by tri-nucleotide and mononucleotide repeat types.The tetra-nucleotide,penta-nucleotide and hexa-nucleotide were all less than 1%.Among the mononucleotide repeats,the A/T repeats motifs were the highest frequency(10.92%).AG/CT was the most frequent repeat motifs in di-nucleotide repeats(49.72%),followed by AT/AT and AC/GT.CG/CG were minimum.AAG/CTT repeats motifs was the highest in tri-nucleotide followed by ACC/GGT,ATC/ATG and AGG/CCT,while CCG/GGC,ACT/AGT and ACG/CGT were lowest(<1%).The repeat motifs were very few in tetra-nucleotide,petra-nucleotide and hexa-nucleotide and had no obvious differences.The microsatellite number in C.saluenensis decreased with the increased number of repeats and length of repeats.
引文
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