串联重复序列在高粱基因组中的特征及分布

The Characteristics and Distribution of Tandem Repeats in Sorghum bicolor Genome

以高粱全基因组及基因中不同结构区域为研究对象,从Phytozome数据库中下载高粱基因组数据及基因注解数据,利用重复序列分析工具(Phobos v3.3.12),检测串联重复序列在不同区域的密度变化、模体类型及其在基因内与基因间的位置分布情况。结果表明,在高粱基因组中5'UTR、UI200、UI500中重复序列密度较高,分别为25 655 bp/Mb、16 761 bp/Mb、10 718 bp/Mb,其余区域密度差别不大,约为6 000 bp/Mb。在基因内及基因间区域中,重复序列模体主要为二碱基和三碱基重复,占到总密度的30%以上;特别在基因编码区(CDS),重复序列模体主要为3的倍数(如三碱基、六碱基等)。并且串联重复序列在基因组中并非随机分布,在基因间隔区,串联重复序列的分布明显靠近基因,这样的分布特征可能与其基因转录调控有关;在内含子(Intron)区域,更多的重复序列分布偏向于内含子两端,这可能与内含子剪切有关。

The study was aimed to explore the characteristics and distribution of tandem repeats （TRs） in genome,genic and intergenic regions in Sorghum bicolor. Genome and gene annotation data of S. bicolor were downloaded from Phytozome （http-//www. phytozome, net/）, and then tandem repeat search tool （Phobos version 3.3.12） was utilized to detect the variation of TR density, motifs and their distribution （ 1-50 bp）. The results showed that 5＇UTR, UI200 and UI500 regions had high densities （25 655 bp/ Mb,16 761 bp/Mb and 10 718 bp/Mb, respectively）, and the densities were similar in other regions （about 6 000 bp/Mb）. TR motifs were mainly a multiple of 3 in CDS regions （e. g. , 3-bp and 6-bp motifs）. In intragenic and intergenic regions, the densities of 2 bp and 3 bp TRs were high, accounting for more than 30% of the whole densities. Moreover, the location of TRs was not randomly distributed, and in intergenic regions many TRs were detected to be close to the genes,indicating the relationship with gene transcription and regulation. In intron region TRs were mostly detected near the both ends, which may have potential roles in intron splicing.