兽类学报

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应用非序列联配方法对哺乳动物系统发育关系的探讨

吴蔚 张梦洁 朱立峰 吴琦   

  1. 南京师范大学生命科学学院
  • 出版日期:2018-03-30 发布日期:2018-06-19
  • 通讯作者: 朱立峰 E-mail: zhulf@ioz.ac.cn; 吴琦 E-mail: ribozyme@ioz.ac.cn

Construction and discussion of whole-genome phylogeny of mammals by alignment-free method

WU Wei, ZHANG Mengjie, ZHU Lifeng,WU Qi   

  1. College of Life Sciences,Nanjing Normal University
  • Online:2018-03-30 Published:2018-06-19

摘要: 非序列联配的序列分析方法,将序列中特定寡聚核苷酸的kmer统计频率作为特征,在序列间按特征进行比较和分析。这种方法综合考虑了所有变异类型对序列整体特征的影响,因而在组学数据分析上有独特的优势。但是,这类方法在复杂多细胞生物基因组系统发育中的适用性仍然有待检验。在本文中,我们使用基于非序列联配方法的CVTree软件,以45种哺乳动物的蛋白质组数据建立了系统发育关系NJ树,并据此探讨了哺乳动物系统发育的若干问题。在广受关注的真兽下纲四个总目的关系问题上,CVTree支持形态学的普遍结论即上兽类(Epitheria)假说。这与基于序列联配方法支持的外非洲胎盘类(Exafro-placentalia )假说不同。在哺乳动物内部目的层次上,CVTree树的结论与分子和形态所普遍接受的系统发育关系基本一致。但是在目的内部,CVTree树会有较多的差异。研究结果初步显示非序列联配方法在使用复杂多细胞生物的组学数据进行系统发育关系分析中的可行性。对非序列联配方法自身的改进及其与传统基于取代的序列联配方法之间的比较仍有待深入研究。

关键词: 非序列联配, 哺乳动物, 组学数据, 上兽类假说, 系统发育关系

Abstract: Alignment-free methods have been used to analyze genomic or proteomic sequences by characterizing and comparing statistical features of sequences, or the frequencies of certain kmer within sequences. These methods have unique advantages for summarizing the overall features of -omic data since it takes into account the influence of all of the variation types on the whole sequence. In this work, a phylogenetic relationships of NJ trees were established using the CVTree software based on the alignment-free method, and includes the proteome data of 45 mammalian species. We discuss several issues on phylogenetic relationships of mammals according to these trees. On the relation of four superorders within Eutheira, our results provided evidence for the hypothesis of epistheria, which is in line with the morphological conclusion but different from the Exafro-Placentalia hypothesis mainly supported by sequence alignment methods. At the order level, the tree is primarily consistent with the phylogenetic relationships accepted by both morpholigical and molecular evidence. But within the order level there are more discrepancies. The results show that the alignment-free method is available in phylogenetic study using -omic data for complex multicellular creatures. The improvement of the alignment-free method itself and its comparison with traditional sequence alignment methods still need more in-depth studies.

Key words: Alignment-free method, Mammalian, Omics Data, Epitheria Hypothesis, Phylogenetic Relationship