The study of neighboring nucleotide composition and transition/transversion bias

作     者：ZHAO Hui LI Qizhai LI Jun ZENG Changqing HU Songnian YU Jun 

作者机构：Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100030China Academy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100080China Graduate University of Chinese Academy of SciencesBeijing 100039China 

出 版 物：《Science China(Life Sciences)》 (中国科学(生命科学英文版))

年 卷 期：2006年第49卷第4期

页      面：395-402页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 071008[理学-发育生物学] 

基　　金：supported partly by the National 863 Project(Grant No.2003AA231050) National Natural Science Foundation of China(Grant No.10371126) Mega-projects of Science Research for the 10th Five-year Plan(Grant No.2002BA711A09) 

主　　题：Base substitution SNP Transition bias Transition Transversion 

摘      要：Base substitution is one of the raw fuels that produce genetic variation; drive evolution. Recent studies have shown that the genome components affect mutation patterns to some extent. In order to infer the correlation between the Transition/Transversion ratio (Ts/Tv); the number of immediately adjacent A&T nucleotides, we investigated 3611007 Oryza sativa SNPs (including 45462 coding SNPs,; 242811 intronic SNPs); 32019 Arabidopsis SNPs. The results show that Ts/Tv is negatively correlated with the number of immediately adjacent A&T in O. Sativa; Arabidopsis. We further calculated AT2 (the number of SNPs whose immediately adjacent nucleotides are either A or T); AT0 (the number of SNPs whose immediately adjacent nucleotides are either C or G) for all 6 types of SNPs. C/G SNP of O. sativa; Arabidopsis has the highest AT2/AT0, which denotes C/G SNP may be influenced by the adjacent A&T nucleotides mostly. For SNPs in O. sativa, the neighboring effect of A&T nucleotides is limited to 2 nucleotides on both sides; for SNPs in Arabidopsis, the effect extends no more than 4 nucleotides on both sides.