Daubin Vincent, Gouy Manolo, Perrière Guy
Laboratoire de Biométrie et Biologie Evolutive, Unité Mixte de Recherche Centre National de la Recherche Scientifique, Université Claude Bernard - Lyon 1, 69622 Villeurbanne Cedex, France.
Genome Res. 2002 Jul;12(7):1080-90. doi: 10.1101/gr.187002.
It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms, but up to now, no satisfying approach has been proposed to use efficiently these data. For instance, if the coding of presence or absence of genes in complete genomes gives interesting results, it does not take into account the phylogenetic information contained in sequences and ignores hidden paralogies by using a BLAST reciprocal best hit definition of orthology. In addition, concatenation of sequences of different genes as well as building of consensus trees only consider the few genes that are shared among all organisms. Here we present an attempt to use a supertree method to build the phylogenetic tree of 45 organisms, with special focus on bacterial phylogeny. This led us to perform a phylogenetic study of congruence of tree topologies, which allows the identification of a core of genes supporting similar species phylogeny. We then used this core of genes to infer a tree. This phylogeny presents several differences with the rRNA phylogeny, notably for the position of hyperthermophilic bacteria.
有人声称完整的基因组序列将阐明生物体之间的系统发育关系，但到目前为止，尚未提出一种令人满意的方法来有效利用这些数据。例如，虽然完整基因组中基因存在与否的编码能给出有趣的结果，但它没有考虑序列中包含的系统发育信息，并且通过使用BLAST双向最佳比对同源性定义忽略了隐藏的旁系同源性。此外，不同基因序列的拼接以及构建一致树只考虑了所有生物体中都共有的少数基因。在这里，我们尝试使用超级树方法构建45种生物体的系统发育树，特别关注细菌的系统发育。这使我们对树拓扑结构的一致性进行了系统发育研究，从而能够识别出支持相似物种系统发育的核心基因。然后我们使用这个核心基因来推断一棵树。这个系统发育与rRNA系统发育存在一些差异，特别是对于嗜热细菌的位置。
