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      Genes from scratch – the evolutionary fate of de novo genes

      review-article
      Trends in Genetics
      Elsevier Trends Journals
      orphans, de novo genes, transcription, population genetics

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          Highlights

          • De novo genes frequently arise from noncoding DNA.

          • While most of the de novo genes are lost, a fraction of them becomes essential.

          • De novo genes are most likely involved in the response to a rapidly changing environment.

          Abstract

          Although considered an extremely unlikely event, many genes emerge from previously noncoding genomic regions. This review covers the entire life cycle of such de novo genes. Two competing hypotheses about the process of de novo gene birth are discussed as well as the high death rate of de novo genes. Despite the high death rate, some de novo genes are retained and remain functional, even in distantly related species, through their integration into gene networks. Further studies combining gene expression with ribosome profiling in multiple populations across different species will be instrumental for an improved understanding of the evolutionary processes operating on de novo genes.

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          Most cited references44

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          Selection on codon bias.

          In a wide variety of organisms, synonymous codons are used with different frequencies, a phenomenon known as codon bias. Population genetic studies have shown that synonymous sites are under weak selection and that codon bias is maintained by a balance between selection, mutation, and genetic drift. It appears that the major cause for selection on codon bias is that certain preferred codons are translated more accurately and/or efficiently. However, additional and sometimes maybe even contradictory selective forces appear to affect codon usage as well. In this review, we discuss the current understanding of the ways in which natural selection participates in the creation and maintenance of codon bias. We also raise several open questions: (i) Is natural selection weak independently of the level of codon bias? It is possible that selection for preferred codons is weak only when codon bias approaches equilibrium and may be quite strong on genes with codon bias levels that are much lower and/or above equilibrium. (ii) What determines the identity of the major codons? (iii) How do shifts in codon bias occur? (iv) What is the exact nature of selection on codon bias? We discuss these questions in depth and offer some ideas on how they can be addressed using a combination of computational and experimental analyses.
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            Evolution and tinkering.

            F Jacob (1977)
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              RNA-based gene duplication: mechanistic and evolutionary insights.

              Gene copies that stem from the mRNAs of parental source genes have long been viewed as evolutionary dead-ends with little biological relevance. Here we review a range of recent studies that have unveiled a significant number of functional retroposed gene copies in both mammalian and some non-mammalian genomes. These studies have not only revealed previously unknown mechanisms for the emergence of new genes and their functions but have also provided fascinating general insights into molecular and evolutionary processes that have shaped genomes. For example, analyses of chromosomal gene movement patterns via RNA-based gene duplication have shed fresh light on the evolutionary origin and biology of our sex chromosomes.
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                Author and article information

                Contributors
                Journal
                Trends Genet
                Trends Genet
                Trends in Genetics
                Elsevier Trends Journals
                0168-9525
                1 April 2015
                April 2015
                : 31
                : 4
                : 215-219
                Affiliations
                [0005]Institut für Populationsgenetik, Vetmeduni, Veterinärplatz 1, 1210 Wien, Austria
                Article
                S0168-9525(15)00034-7
                10.1016/j.tig.2015.02.007
                4383367
                25773713
                2981cd21-f237-415a-93d3-7814cfd04a9f
                © 2015 The Author

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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                Categories
                Review

                Genetics
                orphans,de novo genes,transcription,population genetics
                Genetics
                orphans, de novo genes, transcription, population genetics

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