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。
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-omie data since it takes into account the influence of all of the variation types on the whole sequence. In this work, a pbylogenetic relationship of NJ trees were established using the CVTree soft- ware based on the alignment-free method, and includes the proteome data of 45 mammalian species. We discuss several is- sues 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 differ- ent 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 morpholigieal and molecular evidence. But within the order level there are more discrepancies. The results show that the alignment-free method is available in pbylogenetic study using-omic data for complex multieellular creatures. The improvement of the alignment-free method itself and its comparison with traditional sequence alignment methods still need more in-depth studies.
作者
吴蔚
张梦洁
朱立峰
吴琦
WU Wei;ZHANG Mengjie;ZHU Lifeng;WU Qi(College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;Institute of Zoology, Chinese Academy of Science, Beijing 100101, China)
出处
《兽类学报》
CAS
CSCD
北大核心
2018年第2期174-182,共9页
Acta Theriologica Sinica
基金
江苏高校优势学科建设工程资助项目
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
Alignment-free method
Epitberia hypothesis
Mammalian
Omics data
Phylogenetic relationship
