鸟类基因组进化树的构建与分析

Abstract

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。 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.