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章祎胤,徐福意,戚礼兴,李凯,周宇荀,肖君华.2015.贝叶斯一致性分析法在全基因组系统发生树分析上的应用.动物学杂志,50(3):470-476.
贝叶斯一致性分析法在全基因组系统发生树分析上的应用
Phylogenetic Analysis across Whole Genome Using the Method of Bayesian Concordance Analysis
投稿时间:2014-08-28  修订日期:2015-04-21
DOI:DOI: 10.13859/j.cjz.201503019
中文关键词:  贝叶斯一致性分析法  系统发生树  小鼠基因组  生物信息学
英文关键词:Bayesian Concordance Analysis  Phylogenetic analysis  Mouse genome  Bioinformatics
基金项目:国家自然科学基金项目(面上项目,重点项目,重大项目)
作者单位E-mail
章祎胤 东华大学 dreamchaserzyy@sina.com 
徐福意 东华大学  
戚礼兴 东华大学  
李凯 东华大学 likai@dhu.edu.cn 
周宇荀 东华大学  
肖君华 东华大学  
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中文摘要:
      构建系统发生树时,其拓扑结构会在不同的基因组区域产生不一致性。对此问题,贝叶斯一致性分析法(Bayesian Concordance Analysis, BCA)可在全基因组规模上进行系统发生树分析,并进而对不一致性信息进行量化统计。该法以基因组序列文件作为输入,调用若干生物信息学软件(如VCFtools, RepeatMasker, PAUP*4.0, MrModelTest, Mr.Bayes等)对其进行屏蔽重复序列、序列比对等处理,辅以Perl语言脚本,最终得到全基因组范围上不同区段系统发生树不一致信息。系统发生树的不一致性信息有助于进行进一步研究对于基因组的不同区段的进化历史。最后,本文利用此方法,对由C3H/Hu小鼠和129/Sv小鼠回交多代产生的129S1小鼠进行系统发生树分析,在基因组层面上证明了C3H/Hu小鼠对129S1小鼠基因组的贡献程度较小。
英文摘要:
      When we construct phylogenetic trees, there might be discordance of topologies in different genomic regions. In order to address this issue, Bayesian Concordance Analysis (BCA) can be utilized to perform a phylogenetic analysis across whole genome and statistically quantification of the discordance. Supplemented some Perl scripts, the pipeline takes the genomic sequence files as input and calls several bioinformatics software (e.g. VCFtools, RepeatMasker, PAUP*4.0, MrModelTest, Mr.Bayes and so on) to mask their repeat sequences, align sequences and so on, and whereby we can obtain the phylogenetic discordance information of various locus across whole genome, which can contribute to the further research about the evolutionary history of different genome regions. At last, we applied this method into 129S1 mouse which is originated from the backcross of several generation between C3H/Hu mouse and 129/Sv mouse, finding that the contribution of C3H/Hu mouse to the mosaic genome of 129S1 mouse is less than that of 129/Sv.
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