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      Ectopic Gene Conversions in the Genome of Ten Hemiascomycete Yeast Species

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      International Journal of Evolutionary Biology
      SAGE-Hindawi Access to Research

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          Abstract

          We characterized ectopic gene conversions in the genome of ten hemiascomycete yeast species. Of the ten species, three diverged prior to the whole genome duplication (WGD) event present in the yeast lineage and seven diverged after it. We analyzed gene conversions from three separate datasets: paralogs from the three pre-WGD species, paralogs from the seven post-WGD species, and common ohnologs from the seven post-WGD species. Gene conversions have similar lengths and frequency and occur between sequences having similar degrees of divergence, in paralogs from pre- and post-WGD species. However, the sequences of ohnologs are both more divergent and less frequently converted than those of paralogs. This likely reflects the fact that ohnologs are more often found on different chromosomes and are evolving under stronger selective pressures than paralogs. Our results also show that ectopic gene conversions tend to occur more frequently between closely linked genes. They also suggest that the mechanisms responsible for the loss of introns in S. cerevisiae are probably also involved in the gene 3′-end gene conversion bias observed between the paralogs of this species.

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          Most cited references29

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          GPOWER: A general power analysis program

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            Sequencing and comparison of yeast species to identify genes and regulatory elements.

            Identifying the functional elements encoded in a genome is one of the principal challenges in modern biology. Comparative genomics should offer a powerful, general approach. Here, we present a comparative analysis of the yeast Saccharomyces cerevisiae based on high-quality draft sequences of three related species (S. paradoxus, S. mikatae and S. bayanus). We first aligned the genomes and characterized their evolution, defining the regions and mechanisms of change. We then developed methods for direct identification of genes and regulatory motifs. The gene analysis yielded a major revision to the yeast gene catalogue, affecting approximately 15% of all genes and reducing the total count by about 500 genes. The motif analysis automatically identified 72 genome-wide elements, including most known regulatory motifs and numerous new motifs. We inferred a putative function for most of these motifs, and provided insights into their combinatorial interactions. The results have implications for genome analysis of diverse organisms, including the human.
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              Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.

              Q. Z. Yang (2000)
              Approximate methods for estimating the numbers of synonymous and nonsynonymous substitutions between two DNA sequences involve three steps: counting of synonymous and nonsynonymous sites in the two sequences, counting of synonymous and nonsynonymous differences between the two sequences, and correcting for multiple substitutions at the same site. We examine complexities involved in those steps and propose a new approximate method that takes into account two major features of DNA sequence evolution: transition/transversion rate bias and base/codon frequency bias. We compare the new method with maximum likelihood, as well as several other approximate methods, by examining infinitely long sequences, performing computer simulations, and analyzing a real data set. The results suggest that when there are transition/transversion rate biases and base/codon frequency biases, previously described approximate methods for estimating the nonsynonymous/synonymous rate ratio may involve serious biases, and the bias can be both positive and negative. The new method is, in general, superior to earlier approximate methods and may be useful for analyzing large data sets, although maximum likelihood appears to always be the method of choice.
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                Author and article information

                Journal
                Int J Evol Biol
                IJEB
                International Journal of Evolutionary Biology
                SAGE-Hindawi Access to Research
                2090-052X
                2011
                25 November 2010
                : 2011
                : 970768
                Affiliations
                Département de Biologie et Centre de Recherche Avancée en Génomique Environnementale, Université d'Ottawa, 30 Marie Curie, Ottawa, ON, Canada K1N 6N5
                Author notes

                Academic Editor: Hiromi Nishida

                Article
                10.4061/2011/970768
                3042673
                21350633
                10b82bbf-6193-4011-9b7d-80450be6482e
                Copyright © 2011 R. T. Morris and G. Drouin.

                This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 21 July 2010
                : 18 September 2010
                : 15 October 2010
                Categories
                Research Article

                Evolutionary Biology
                Evolutionary Biology

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