基于编码序列、基因间序列和氨基酸序列构建的系统发生关系比较  

Comparison of Phylogenetic Relationships Constructed by Using Protein-Coding Sequences,Intergenic Sequences and Amino Acid Sequences

作　　者：杨林源[1] 李宏 赵小庆[1] 刘国庆[2] 

机构地区：[1]内蒙古大学物理科学与技术学院,呼和浩特010021 [2]内蒙古科技大学数理与生物工程学院,包头014010

出　　处：《生物物理学报》2012年第2期157-168,共12页Acta Biophysica Sinica

基　　金：国家自然科学基金项目(30660044)

摘　　要：以7种古菌、46种细菌和10种真核生物的基因组为样本,考虑碱基间的短程关联和长程关联作用,得到编码序列的密码对和基因间序列的三联体对中不同位点的二核苷酸频率,据此构建了基于编码序列和基因间序列的系统发生关系。无论是基于编码序列还是基因间序列对信息进行聚类,古菌或真核均被聚在一支上,表明聚类参数的选择是合适的;与基于氨基酸序列构建的系统发生关系进行两两比较,发现大部分硬壁菌的编码序列与基因间序列之间,以及编码序列与氨基酸序列之间的进化都存在较大差异。通过分析认为,只有综合考虑这三类序列的进化信息,才可能得到更自然的系统发生关系。Considering the effect of short and long range correlation of base pairs,dinucleotide frequencies in different sites either of codon pairs of protein coding sequences or triplet pairs of intergenic sequences were calculated for 7 archaea,46 bacteria and 10 eukaryote genomes.Phylogenetic relationships were constructed respectively for protein coding sequences and intergenic sequences.Archaea or eukaryotes were clustered one independent branch by the two kinds of sequences.It shows that the selected parameters are suitable.Compared with the phylogenetic relationship which was constructed by amino acid sequences,it was found that the evolutions of protein coding,intergenic and amino acid sequences have distinct differences for most firmicutes.We propose that the evolution information of three kinds of sequences should be combined together so that a more natural phylogenetic relationship can be obtained.

关 键 词：系统发生关系 二核苷酸频率 碱基长程关联 编码序列 基因间序列 

分 类 号：Q61[生物学—生物物理学]