http://precedings.nature.com/tags/genome%20evolution Recently posted documents tagged with 'genome evolution' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2008.1376.2 Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are probabilities of duplication, innovation, and loss of domains. However, no one so far has addressed the issue that these distributions follow definite trends depending on protein-coding genome size only. We present a stochastic duplication/innovation model, falling in the class of so-called Chinese Restaurant Processes, able to explain this feature of the data. Using only two universal parameters, related to a minimal number of domains and to the relative weight of innovation to duplication, the model reproduces two important aspects: (a) the populations of domain classes (the sets, related to homology classes, containing realizations of the same domain in different proteins) follow common power-laws whose cutoff is dictated by genome size, and (b) the number of domain families is universal and markedly sublinear in genome size. An important ingredient of the model is that the innovation probability decreases with genome size. We propose the possibility to interpret this as a global constraint given by the cost of expanding an increasingly complex interactome. Finally, we introduce a variant of the model where the choice of a new domain relates to its occurrence in genomic data, and thus accounts for fold specificity. Both models have general quantitative agreement with data from hundreds of genomes, which indicates the coexistence of the well-known specificity of proteomes with robust self-organizing phenomena related to the basic evolutionary ``moves’’ of duplication and innovation. http://dx.doi.org/10.1038/npre.2008.1376.2 Wed, 16 Jul 2008 16:28:36 UTC Universal Features in the Genome-level Evolution of Protein Domains doi:10.1038/npre.2008.1376.2 2008-07-16 Marco Cosentino Lagomarsino Nature Precedings 2008-07-16T16:28:36Z Manuscript Genetics & Genomics Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1988/version/1 The natural genetics of an organism is determined by the distribution of sequences of its genome. Here we present one- to four-fold, with some deeper, coverage of the genome sequences of over seventy isolates of the domesticated baker’s yeast, Saccharomyces cerevisiae, and its closest relative, the wild S. paradoxus, which has never been associated with human activity. These were collected from numerous geographic locations and sources (including wild, clinical, baking, wine, laboratory and food spoilage). These sequences provide an unprecedented view of the population structure, natural (and artificial) selection and genome evolution in these species. Variation in gene content, SNPs, indels, copy numbers and transposable elements provide insights into the evolution of different lineages. Phenotypic variation broadly correlates with global genome-wide phylogenetic relationships however there is no correlation with source. S. paradoxus populations are well delineated along geographic boundaries while the variation among worldwide S. cerevisiae isolates show less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker’s yeasts, the population structure of S. cerevisiae shows a few well defined geographically isolated lineages and many different mosaics of these lineages, supporting the notion that human influence provided the opportunity for outbreeding and production of new combinations of pre-existing variation. http://precedings.nature.com/documents/1988/version/1 Fri, 20 Jun 2008 15:24:32 UTC Population genomics of domestic and wild yeasts hdl:10101/npre.2008.1988.1 2008-06-20 Edward Louis Nature Precedings 2008-06-20T15:24:32Z Manuscript Ecology Genetics & Genomics Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1376/version/1 The availability of many genome sequences gives us abundant information, which is, however, very difficult to decode. As a consequence, in order to advance our understanding of biological processes at the whole-cell scale, it becomes very important to develop higher-level, synthetic descriptions of the contents of a genome. At the protein level, an effective scale of description is provided by protein domains. Domains are independent unit-shapes (or “folds”) forming proteins. They are structurally stable and have thermodynamic origin. A domain determines a set of potential functions and interactions for the protein that carries it, for example DNA- or protein-binding capability or catalytic sites. Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. A stochastic growth model with two universal parameters, related to a minimal number of domains and to the relative time-scale of innovation to duplication reproduces two important features of these distributions: (i) the populations of domain classes (the sets, related to homology classes, containing realizations of the same domain in different proteins) follow common power-laws whose diversity is related to genome size measured by the total number of proteins or protein domains and (ii) the number of domain families is sublinear in genome size. In this evolutionary process, selective pressure can enter both as a global constraint on the innovation time-scale, and as a regulator of the population of specific domain classes, related to their modularity: some shapes are common to all genomes, some are contextual. These two features are sufficient to obtain general quantitative agreement with data from hundreds of genomes, and show that robust self-organizing phenomena encase specific selective pressures during evolution. http://precedings.nature.com/documents/1376/version/1 Fri, 30 Nov 2007 21:30:43 UTC Evolution of the Protein Universe. Time Scales and Selection hdl:10101/npre.2007.1376.1 2007-11-30 Marco Cosentino Lagomarsino Nature Precedings 2007-11-30T21:30:43Z Manuscript Ecology Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/