龙眼全基因组和转录本序列SSR位点的鉴定

SSR loci analysis in genome and transcriptome of longan

基于龙眼基因组和转录本数据,共鉴定了260 204个SSR位点,平均每1 Mb含有538.24个SSR位点.在全基因组中,二核苷酸重复基序所占比例最大,为36%;在转录本中,三核苷酸重复基序所占比例最大,达50%.在基因组序列和转录本中,发现不同长度基序的SSR重复次数的分布规律基本相似,均表现为基序越短,重复次数越多,出现频率越高.在全基因组中,共有20 761个基因含有SSR位点,16 381个基因不含SSR位点,SSR位点多分布于基因的内含子区域.此外,龙眼及其近缘种全基因组SSR分布规律比较分析表明,龙眼SSR的分布规律与荔枝最为相似,龙眼与荔枝的近缘关系也高于其他物种;在本研究所有物种的SSR序列中,A+T含量均显著高于G+C含量,表明含有A/T核苷酸的SSR位点在无患子科植物中的含量尤为丰富.

A total of 260 204 simple sequence repeat(SSR) loci with an average density of 538.24 SSRs per Mb were identified based on longan genome sequences and transcript data. At the genome level, dinucleotide repeats accounted for the largest proportion(36%), while the proportion of trinucleotide repeats was the largest(50%) at the transcriptome level. SSRs under different length classes showed similar distribution pattern, the shorter motifs got, the higher repetition rate and occurrence frequency they were. In the whole genome, 20 761 genes containing SSR loci were detected, with SSRs mainly distributed in the intron region;while another 16 381 genes did not contain SSR. In addition, comparative analysis of SSR distribution patterns between longan and the related species revealed predominant AT-rich motifs in the genomic SSRs among Sapindaceae species.