鸟类基因组进化树的构建与分析
Construction and Analysis of theAvian Phylogenetic Tree
DOI: 10.12677/HJCB.2017.71001, PDF, HTML, XML,  被引量 下载: 1,762  浏览: 4,123  国家自然科学基金支持
作者: 张永芬, 罗辽复*, 张利绒*:内蒙古大学物理科学与技术学院,内蒙古 呼和浩特
关键词: 鸟类DNA序列k联体进化树Avian DNA Sequence K-Mer Phylogenetic Tree
摘要: 本文选取了47种鸟类的基因组作为研究对象,根据靶定下一代DNA测序技术(targeted next-generation DNA sequencing)得到的394个保守片段的DNA序列数据,统计了从9联体到14联体的频数及其频率,基于k联体(k-mer)非联配算法得到了任意两种鸟类之间k联体的距离矩阵,并运用邻接(Neighbor-Joining)法构建了47种鸟类的进化树,发现当k = 12时达到稳定。最后,通过将该树与Prum和Jarvis构建的进化树进行了比较,分析了鸟类的进化和分类. 结果发现三个进化树基本一致, 只有部分姐妹分支有差别, 说明12联体的相对频数是能够较好描述基因组进化的动力学变量。
Abstract: Based on nucleotide sequences in 394 conserved regions of 47 avian DNA sequences obtained using targeted-next generation DNA sequencing, the k-mer frequency (from 9-mer to 14-mer) was counted. We calculated the distance matrix among 47 avians by k-mer Non-aligned Algorithm (KNA) and constructed the phylogenetic tree by the Neighbor-Joining method. The results showed that the phylogenetic tree is changed with increasing k and stabilized when k equals 12. Then, we compared 12-mer phylogenetic tree with two other trees constructed by Prum and Jarvis respectively and an-alyzed the evolution and classification of these birds. We found that the three phylogenetic trees are basically same apart from a small part of sister branches on the trees. The consistency revealed that the frequency of 12-mer is a better dynamic variable for measuring evolution of species.
文章引用:张永芬, 周勋, 罗辽复, 张利绒. 鸟类基因组进化树的构建与分析[J]. 计算生物学, 2017, 7(1): 1-11. https://doi.org/10.12677/HJCB.2017.71001

参考文献

[1] Zhang, G., Li, C., Li, Q., et al. (2014) Comparative Genomics Reveals Insights into Avian Genome Evolution and Adaptation. Science, 346, 1311-1320.
https://doi.org/10.1126/science.1251385
[2] 胡皓夫. 用基因组学解码鸟类进化史[J]. 科学, 2015, 67(2): 21-25.
[3] Jarvis, E.D., Mirarab, S., Aberer, A.J., et al. (2014) Whole-Genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds. Science, 346, 1320-1331.
https://doi.org/10.1126/science.1253451
[4] Hedges, S.B., Parker, P.H., Sibley, C.G., et al. (1996) Continental Breakup and the Ordinal Diversification of Birds and Mammals. Nature, 381, 226-229.
https://doi.org/10.1038/381226a0
[5] Cooper, A. and Penny, D. (1997) Mass Survival of Birds across the Cretaceous-Tertiary Boundary: Molecular Evidence. Science, 275, 1109-1113.
https://doi.org/10.1126/science.275.5303.1109
[6] Simon, Y.W.H. and Matthew, J.P. (2009) Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times. Sys-tematic Biology, 58, 367-380.
https://doi.org/10.1093/sysbio/syp035
[7] Prum, R.O., Berv, J.S., Dornburg, A., et al. (2015) A Comprehensive Phylogeny of Birds (Aves) Using Targeted Next-Generation DNA Sequencing. Nature, 526, 569-573.
https://doi.org/10.1038/nature15697
[8] Suh, A., Paus, M., Kiefmann, M., et al. (2011) Mesozoic Retroposons Reveal Parrots as the Closest Living Relatives of Passerine Birds. Nature Communications, 2, Article No. 443.
https://doi.org/10.1038/ncomms1448
[9] Matzke, A., Churakov, G., Berkes, P., et al. (2012) Retroposon Insertion Patterns of Neoavian Birds: Strong Evidence for an Extensive Incomplete Lineage Sorting Era. Molecular Biology and Evolution, 29, 1497-1501.
https://doi.org/10.1093/molbev/msr319
[10] 刘红梅, 刘国庆. 基于k-mer组分信息的系统发生树构建方法[J]. 生物信息学, 2013, 11(2): 100-104.
[11] Luo, L.F. (2004) Theoretic-Physical Approach to Molecular Biology. Shanghai Scientific & Technical Publishers, Shanghai, 388-402.
[12] Saitou, N. and Nei, M. (1987) The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees. Molecular Biology and Evolution, 4, 406-425.
[13] Slack, K.E., Janke, A., Penny, D., et al. (2003) Two New Avian Mitochondrial Genomes (Penguin and Goose) and a Summary of Bird and Reptile Mitogenomic Features. Gene, 302, 43-52.
[14] Luo, L.F. (2015) Quantum Theory on Genome Evolution.
https://doi.org/10.1101/034710