tailieunhanh - Báo cáo y học: "Systematic overestimation of gene gain through false diagnosis of gene absenc"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Minireview cung cấp cho các bạn kiến thức về ngành y đề tài: Systematic overestimation of gene gain through false diagnosis of gene absence. | Correspondence Systematic overestimation of gene gain through false diagnosis of gene absence Olga Zhaxybayeva Camilla L Nesb0 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@ Published 26 February 2007 Genome Biology 2007 8 402 doi gb-2007-8-2-402 The electronic version of this article is the complete one and can be found online at http 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 same bacterial species often differ substantially up to 30 in gene content 1-6 . There are two general ways to account for such gene content variability patchy distribution among closely related genomes strain-specific loss of genes after divergence from a common species ancestor that contained the genes and strain-specific gain of genes after divergence from an ancestor that lacked them. Gain might be effected through lateral gene transfer LGT duplication paralog creation or much less likely de novo creation. Several recent publications have attempted to assess rates of within-species gain and loss using parsimonybased approaches applied to gene presence absence data in the context of a reference strain phylogeny 7-11 . Similar parsimony-based approaches have also been taken for inferences of gene gain loss at larger phylogenetic distances 12-14 . In such analyses a pattern like that shown in Figure 1a would be interpreted to indicate a single event of gain of a gene X not present in the species ancestor after the separation of taxa 4 and 5. Explaining this distribution as the result of loss of a gene X initially present in the ancestor would in contrast require a minimum of four separate events a seemingly less parsimonious