用实时定量PCR解决基因组序列组装中的重复序列问题  

Using Real-Time PCR to Resolve RepetitiveDNA Issue in de novo Genome Assembly

作　　者：徐晓蒙[1,2] 康怀兴[2] 张志毅[2] 童贻刚[1,2] 

机构地区：[1]安徽医科大学,安徽合肥230032 [2]军事医学科学院微生物流行病研究所,北京100071

出　　处：《生物技术通讯》2015年第3期408-410,共3页Letters in Biotechnology

基　　金：国家科技重大专项(2011ZX10004001;2013ZX10004607-004;2013ZX10004217-002-003);国家高技术研究发展计划(2012AA022003;2014AA021402)

摘　　要：目的:探寻一种简单、经济的方法,解决基因组序列拼接中的重复序列问题。方法:选取序列拼接中遇到重复序列问题的质粒NDM-BTR,在其与重复序列相关的contigs两端设计引物,进行实时定量PCR,通过观察临界循环数来判断contig之间的位置关系。结果:成功判断出质粒contig之间的位置关系,得到了质粒基因组完成图。结论:实时定量PCR法可用于解决基因组序列拼接中的重复序列问题,相比较传统建立大片段文库更加简单、快速、经济。Objective： To explore a simple,quick and economical method to resolve repetitiveDNA issue in de novo genome assembly.Methods： We designed primers anchored in both ends of the contigs of plasmid NDM-BTR which have problems caused by repetitive sequences in de novo assembly for real-time PCR amplification.Through the cross point（CP） that PCR products massively appeared,we deduced the relationship of contigs that re-flects the initial templates.Results： We successfully figured out the relationship of contigs and obtain the com-plete genome of plasmid NDM-BTR.Conclusion： The real-time PCR method can be used to resolve the issuethat caused by repeats in de novo genome assembly,meanwhile,it is more simple and economical than the tradi-tional way that constructs opposite ends of a long fragment ofDNA library containing mata-pair information.

关 键 词：高通量测序 重复序列 基因组序列组装 实时定量PCR 

分 类 号：Q78[生物学—分子生物学]