Whole-genome prokaryotic phylogeny
Whole-genome prokaryotic phylogeny
复制标题
DOI：
10.1093/bioinformatics/bth324
复制
发表时间：
2005-05-15
期刊：
影响因子：
5.8
通讯作者：
Schuster, SC
中科院分区：
文献类型：
--
作者：
Henz, SR;Huson, DH;Schuster, SC
目前对原核生物染色体发生的理解是基于高度保守的小Ssu-rRNA亚基和类似区域的比较。虽然这些分子已被证明是非常有用的系统发育标记，突变饱和是一个问题，由于其长度有限。现在，越来越多的完整的原核基因组是可用的。本文讨论了利用完整基因组比较确定原核生物同源性的问题。我们介绍了一种新的策略，GBDP，“基因组爆炸距离基因组”，并表明，这种方法的不同变体稳健地产生生物学上的声音，当应用于91个原核基因组。在这种方法中，首先使用Blast比较基因组，然后计算距离矩阵，最后应用树或网络重建方法，如UPGMA，Neighbor-Joining，BioNJ或Neighbor-Net。
Current understanding of the phylogeny of prokaryotes is based on the comparison of the highly conserved small ssu-rRNA subunit and similar regions. Although such molecules have proved to be very useful phylogenetic markers, mutational saturation is a problem, due to their restricted lengths. Now, a growing number of complete prokaryotic genomes are available. This paper addresses the problem of determining a prokaryotic phylogeny utilizing the comparison of complete genomes. We introduce a new strategy, GBDP, 'genome blast distance phylogeny', and show that different variants of this approach robustly produce phylogenies that are biologically sound, when applied to 91 prokaryotic genomes. In this approach, first Blast is used to compare genomes, then a distance matrix is computed, and finally a tree- or network-reconstruction method such as UPGMA, Neighbor-Joining, BioNJ or Neighbor-Net is applied.