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SCIENTIA SINICA Vitae, Volume 49 , Issue 4 : 456-471(2019) https://doi.org/10.1360/N052018-00222

Recent progress in phylogenomic methods

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  • ReceivedDec 20, 2018
  • AcceptedJan 31, 2019
  • PublishedApr 15, 2019

Abstract


References

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  • Figure 1

    The bioinformatic pipeline for analyzing high-throughput phylogenetic data. Beginning with high-throughput data, Fillet square boxes and arrows represent the order and steps of data analysis. Gray dotted lines and square boxes represent common used software and methods (color online)

  • Table 1   Comparison of five RAD-seq technologies

    方法

    标准RAD

    2bRAD

    ezRAD

    ddRAD

    Rapture

    限制性内切酶数目

    1

    1

    ≥1

    2

    1

    限制性内切酶种类

    稀有酶

    ⅡB型限制性内切酶

    同裂酶

    稀有酶和常见酶

    稀有酶

    DNA降解对实验的影响

    起始DNA量

    100 ng~1 μg

    低至1 ng

    50 ng~1 μg

    50 ng~100 ng

    50 ng

    基因组二次打断

    需要

    不需要

    不需要

    不需要

    需要

    插入片段大小

    ≤300 bp

    33~36 bp

    ≤300 bp

    ≤300 bp

    ≤300 bp

    文库制备时间

    ~24 h

    ~4 h

    ~6 h

    ~8 h

    ~30 h

    实验操作流程

    复杂

    简单

    简单

    简单

    复杂

    剪切位点选择

    改变限制性内切酶

    改变限制性内切酶

    改变限制性内切酶和片段大小选择

    改变限制性内切酶和片段大小选择

    设计不同区域的捕获探针和改变限制性内切酶

    实验成本

    中等

    很低

    中等

  • Table 2   Comparison of four target sequence capture approaches

    方法

    代表文献

    研究对象

    基因组捕获区域

    串联数据集大小

    探针来源

    杂交方式

    锚定序列捕获

    [61]

    动物

    核基因序列

    ~123 KB

    商业合成

    液相

    超保守序列元件捕获

    [62]

    动物

    核基因序列

    ~352 KB

    商业合成

    液相

    外显子捕获

    [63]

    动物

    核基因序列

    ~25.3 MB

    商业合成

    液相

    [64]

    动物

    核基因序列、线粒体基因

    ~4 MB

    商业合成

    固相

    [65]

    动物

    核基因序列

    ~400 KB

    商业合成

    液相

    基于PCR产物制备探针的捕获

    [66]

    动物

    线粒体基因组

    ~17 KB

    实验室自制

    液相

    [67]

    植物

    叶绿体基因组

    ~146 KB

    实验室自制

    液相

    [68]

    动物

    核基因序列

    ~52 KB

    实验室自制

    液相

  • Table 3   Comparison of five methods of data collection in phylogenomics based on high-throughput sequencing

    方法

    扩增子测序

    转录组测序

    简化基因组测序

    目标序列捕获

    低覆盖度的全基因组测序

    适用的分类阶元范围

    种级至目级水平

    种级至纲级水平或更高

    种下、种间及属内

    种级至纲级水平或更高

    种级至纲级水平或更高

    获得标记的长度

    中等

    短到中等

    中等

    数据集缺失率

    中等

    中等

    中等

    数据集信息量

    (串联数据集大小或SNPs数目)

    50~200 KB

    1~20 MB

    几万~几十万SNPs

    1.5~26 KB

    100 KB以上

    核酸质量要求

    DNA片段>5 KB

    需新鲜样品提RNA

    DNA片段>20 KB

    DNA片段>200 bp

    DNA片段>200 bp

    实验操作难度

    简单

    简单

    简单

    中等

    简单

    数据分析难度

    简单

    中等

    简单

    中等

    简单

    实验成本

    中等

    中等

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