串联重复序列在克莱门柚基因组中的特征研究

Characteristics of Tandem Repeats in Citrus clementina Genome

【目的】串联重复序列存在于大多数真核生物基因组中,对于生物基因表达调控具有重要意义。本研究从基因组角度探究串联重复序列在克莱门柚基因不同区域的模体特征,为重复序列在基因调控中的作用提供提供参考。【方法】从Phytozome数据库下载克莱门柚全基因组序列和基因注解(gene annotation)数据,然后使用Phobos version 3.3.12软件抓取1~50 bp的重复单元,检测分析串联重复序列在基因内和基因间的密度及模体类型特征。【结果】克莱门柚基因组串联重复序列高密度的主要为短序列重复单元(1~7 bp),主要重复类别是单碱基、二碱基、六碱基、三碱基、七碱基、四碱基和22碱基等,且以A和T重复为主。克莱门柚基因组中最高和次高的串联重复序列密度在5'UTR和它的直接上游区域,即UI500和UI200;CDS中密度最低,且以3n模体(如3、9、12 bp等)为主要的重复单元。【结论】串联重复序列在克莱门柚基因组中的特征,与基因转录、翻译等功能有密切的关系,本研究对串联重复序列在植物基因组中的特征及作用有借鉴作用。

【Objective】Tandem repeat sequences(TRs)exist in the most of the eukaryotic genomes and they play key roles in the regulation of gene expression.The paper explorered the characteristics of TRs in Citrus clementina genome,which would provide reference of TRs in gene regulations.【Method】Genome and gene annotation data of C.clementina were downloaded from Phytozome(http://www.phytozome.net/),and then tandem repeat search tool(Phobos version 3.3.12)was utilized to grab 1-50 bp repeat units for TR density and motif analysis in intragenic and intergenic regions.【Result】High densities of TRs mainly were short repeat units(1-7 bp)in C.clementina genome,and the primary repeat units were 1,2,6,3,7,4 and 22 bp based on the densities.Moreover,A and T nucleotides dominated exclusively in 1 bp repeat unit.TR densities in 5′UTR and upstream intergenic regions(UI500 and UI200)were the first and second high in the whole genome;yet the lowest density was in CDS,and 3n were the primary repeat units,e.g.3,9,12 bp.【Conclusion】The characteristics of TRs in C.clementina genome have close relationships with gene expression and regulation.The study would help our understanding on TR characteristics and functions in plant genomes.