系统发育基因组学方法研究进展
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摘要
系统发育基因组学是系统发育学与基因组学融合产生的一个交叉学科,主要通过分析基因组水平的大规模分子数据来解析生物之间的系统进化关系.本文简述了5种常用的基于高通量测序技术的系统发育基因组学数据获取方法:扩增子测序(targeted amplicon sequencing)、转录组测序(transcriptome sequencing)、简化基因组测序(reduced-representation sequencing)、目标序列捕获(target sequence capture)和低覆盖度的全基因组测序(low coverage whole-genome shotgun sequencing),归纳比较了每种方法的特点、适用范围、成本花费等.此外,本文还简述了系统发育基因组学数据分析中的5个基本步骤:数据预处理与组装、直系同源基因的鉴定、序列比对、数据质量控制和系统发育树的构建,并对这5个步骤的分析要点与常用软件的特点做了归纳.虽然系统发育基因组学分析是重建生命之树的一条必由之路,当前它也面临着一系列的问题:如大量数据的分析导致计算量与时间花费大幅增加、系统误差的影响会随着数据量增大而变得更为明显、不同数据集可能会给出高支持率但不一致的结果.最后,本文综合国内外学者的最新研究成果,对这些问题进行了讨论并给出了相应的建议.
Phylogenomics is the intersection of the fields of phylogenetics and genomics,aiming to use genome-scale molecular data to resolve the phylogenetic relationships among organisms.In this review,we briefly introduced five methods of data collection in phylogenomics by high-throughput sequencing:targeted amplicon sequencing,transcriptome sequencing,reduced-genomerepresentation sequencing,target sequence capture,and low coverage whole-genome shotgun sequencing.We summarized and compared the characteristics,applications and costs of each method.In addition,we reviewed the current work flow of data processing of a typical phylogenomic analysis,including five steps:data preprocessing and assembly,orthologous sequences identification,sequence alignment,data quality control and phylogenetic tree reconstruction.We also summarized the key points of each step and introduced software that are used in these steps.Phylogenomics is a promising way to reconstruct the Tree of Life.However,it also faces a series of problems at present.For example,the analysis of genome-scale data will lead to a significant increase in computation time,the impact of systematic error will become more serious when the data size increases and different data sets may yield strongly supported but inconsistent results.In the end of this review,we summarized and discussed the latest studies concerning these issues and made some suggestions to deal with these problems in the future.
Phylogenomics is the intersection of the fields of phylogenetics and genomics,aiming to use genome-scale molecular data to resolve the phylogenetic relationships among organisms.In this review,we briefly introduced five methods of data collection in phylogenomics by high-throughput sequencing:targeted amplicon sequencing,transcriptome sequencing,reduced-genomerepresentation sequencing,target sequence capture,and low coverage whole-genome shotgun sequencing.We summarized and compared the characteristics,applications and costs of each method.In addition,we reviewed the current work flow of data processing of a typical phylogenomic analysis,including five steps:data preprocessing and assembly,orthologous sequences identification,sequence alignment,data quality control and phylogenetic tree reconstruction.We also summarized the key points of each step and introduced software that are used in these steps.Phylogenomics is a promising way to reconstruct the Tree of Life.However,it also faces a series of problems at present.For example,the analysis of genome-scale data will lead to a significant increase in computation time,the impact of systematic error will become more serious when the data size increases and different data sets may yield strongly supported but inconsistent results.In the end of this review,we summarized and discussed the latest studies concerning these issues and made some suggestions to deal with these problems in the future.
引文
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