狗牙根转录组微卫星序列统计及其比较分析

Statistics and Comparative Analysis of Microsatellite Sequence in the Transcriptome of Cynodon dactylon

微卫星(simple sequence repeats, SSRs)广泛分布于生物基因组的编码区和非编码区,是最常用的分子标记。本研究利用生物信息学方法搜索和统计了狗牙根匍匐茎和根状茎转录组中完整型SSRs序列,并对其生物信息学特征进行比较分析。狗牙根匍匐茎和根状茎转录组中SSRs总数量分别为21800个和27431个,占其转录组长度的比例分别为0.118%和0.152%。狗牙根匍匐茎和根状茎转录组SSRs平均丰度(185.25 vs191.22个/Mb)和密度(3 437.47 vs 3 523.07 bp/Mb)基本一致。狗牙根匍匐茎和根状茎转录组SSRs丰富度具有明显的分布模式。在狗牙根匍匐茎和根状茎转录组SSRs序列中,单碱基SSRs重复拷贝数变异最大,其次是二碱基SSRs重复拷贝数,从三碱基SSRs开始,重复拷贝数明显下降。狗牙根匍匐茎和根状茎转录组中单碱基至六碱基各重复类型优势SSRs序列基本一致。

SSRs are widely distributed throughout the coding and non-coding regions of organism genomes, which have become the most popular source of genetic markers. The perfect SRRs sequences were searched and computed in the stolon and rhizome transcriptomes of Cynodon dactylon by using bio-informatics methods, and their bioinformatic traits were comparatively analyzed in the study. The total SSRs number detected in the stolon and rhizome transcriptomes of Cynodon dactylon were 21 800 and 27 431 loci, respectively, which accounted for 0.118% and0.152% of its transcriptome length, respectively. The average abundance and density showed great similarity in the stolon and rhizome transcriptomes of C. dactylon, of which average frequency were 185.25 and 191.22 No./Mb and average density were 3 437.47 and 3 523.07 bp/Mb, respectively. The SSRs frequency in the stolon and rhizome transcriptomes of C. dactylon showed obvious distribution pattern. In the SSRs sequences, peat copy number of mononucleotide SSRs had the biggest changes, followed by the repeat copy number of di-nucleotide SSRs. From the start of the tri-nucleotide SSRs, the repeat copy number decreased significantly. The SSRssequences of different dominant repeat types from mono-to hexa-nucleotide SSRs showed great similarity in the stolon and rhizome transcriptomes of Cynodon dactylon.