tailieunhanh - Báo cáo y học: "2× genomes - depth does matter"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: 2× genomes - depth does matter. | Milinkovitch et al. Genome Biology 2010 11 R16 http 2010 11 2 R16 Genome Biology RESEARCH Open Access 2x genomes - depth does matter Michel C Milinkovitch1 Raphael Helaers2 Eric Depiereux2 Athanasia C Tzika1 3 Toni Gabaldón4 Abstract Background Given the availability of full genome sequences mapping gene gains duplications and losses during evolution should theoretically be straightforward. However this endeavor suffers from overemphasis on detecting conserved genome features which in turn has led to sequencing multiple eutherian genomes with low coverage rather than fewer genomes with high-coverage and more even distribution in the phylogeny. Although limitations associated with analysis of low coverage genomes are recognized they have not been quantified. Results Here using recently developed comparative genomic application systems we evaluate the impact of low-coverage genomes on inferences pertaining to gene gains and losses when analyzing eukaryote genome evolution through gene duplication. We demonstrate that when performing inference of genome content evolution low-coverage genomes generate not only a massive number of false gene losses but also striking artifacts in gene duplication inference especially at the most recent common ancestor of low-coverage genomes. We show that the artifactual gains are caused by the low coverage of genome sequence per se rather than by the increased taxon sampling in a biased portion of the species tree. Conclusions We argue that it will remain difficult to differentiate artifacts from true changes in modes and tempo of genome evolution until there is better homogeneity in both taxon sampling and high-coverage sequencing. This is important for broadening the utility of full genome data to the community of evolutionary biologists whose interests go well beyond widely conserved physiologies and developmental patterns as they seek to understand the generative mechanisms underlying biological diversity. .