systematic overestimation of gene gain through false diagnosis of gene absence系统性偏高的基因获得通过虚假的诊断基因缺失.pdf

Correspondence Systematic overestimation of gene gain through false diagnosis of gene absence Olga Zhaxybayeva, Camilla L Nesbø and W Ford Doolittle Address: Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS, B3H 1X5 Canada. Correspondence: Olga Zhaxybayeva. Email: olgazh@dal.ca Published: 26 February 2007 Genome Biology 2007, 8:402 (doi:10.1186/gb-2007-8-2-402) The electronic version of this article is the complete one and can be found online at /2007/8/2/402 © 2007 BioMed Central Ltd Abstract The usual BLAST-based methods for assessing gene presence and absence lead to systematic overestimation of within-species gene gain by lateral transfer. Genomes from different strains of the and 5. Explaining this distribution as the species’ ancestor has deteriorated in all same bacterial species often differ result of loss of a gene X initially present lineages but one) for the situation in substantially (up to 30%) in gene in the ancestor would, in contrast, Figure 1a (in which a gene absent from content [1-6]. There are two general require a minimum of four separate the ancestor has been gained in a single ways to account for such gene content events, a seemingly less parsimonious lineage). Our goal in the present analysis variability (‘patchy distribution’) among scenario. However, reasoning by was to assess how often such mistakes closely related genomes: strain-specific parsimony in such a situation requires might be made. loss of genes after divergence from a difficult-to-test assumptions about the common species ancestor that