New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Aoife McLysaght, Daniele Guerzoni

Abstract

The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages. There is now evidence that this mechanism has contributed a significant number of genes to genomes of organisms as diverse as Saccharomyces, Drosophila, Plasmodium, Arabidopisis and human. From simple beginnings, these genes have in some instances acquired complex structure, regulated expression and important functional roles. New genes are often thought of as dispensable late additions; however, some recent de novo genes in human can play a role in disease. Rather than an extremely rare occurrence, it is now evident that there is a relatively constant trickle of proto-genes released into the testing ground of natural selection. It is currently unknown whether de novo genes arise primarily through an 'RNA-first' or 'ORF-first' pathway. Either way, evolutionary tinkering with this pool of genetic potential may have been a significant player in the origins of lineage-specific traits and adaptations.

References

Jun 10, 1977·Science·F Jacob
Oct 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·P K Keese, A Gibbs
Dec 7, 1990·Science·R L DoritW Gilbert
Apr 15, 1997·Proceedings of the National Academy of Sciences of the United States of America·L ChenC H Cheng
Feb 8, 2003·Journal of Molecular Evolution·Yuuki HayashiTetsuya Yomo
Nov 25, 2003·Science·Michael Lynch, John S Conery
Nov 25, 2003·Nature Reviews. Genetics·Manyuan LongWen Wang
Nov 10, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jianming ZhangManyuan Long
Feb 1, 2005·Computational Biology and Chemistry·Izabela MakalowskaWojciech Makalowski
Jun 17, 2006·Proceedings of the National Academy of Sciences of the United States of America·Mia T LevineDavid J Begun
Jul 20, 2007·Nature Reviews. Genetics·Adam Eyre-Walker, Peter D Keightley
Dec 26, 2007·Molecular Biology and Evolution·Martin J Lercher, Csaba Pál
May 7, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ben-Yang Liao, Jianzhi Zhang
Jun 14, 2008·Genome Research·Qi ZhouWen Wang
Jul 3, 2008·Nature·David L Des Marais, Mark D Rausher
Dec 10, 2008·Molecular Biology and Evolution·Macarena Toll-RieraM Mar Albà
Jan 22, 2009·The Plant Journal : for Cell and Molecular Biology·Ling LiEve Syrkin Wurtele
Sep 1, 2009·Trends in Genetics : TIG·Konstantin KhalturinThomas C G Bosch
Sep 4, 2009·Genome Research·David G Knowles, Aoife McLysaght
Sep 8, 2009·Current Biology : CB·Tobias J A J HeinenDiethard Tautz
Oct 3, 2009·Genome Research·Adam Siepel
Apr 9, 2010·PLoS Computational Biology·Chuan-Yun LiLiping Wei
Jul 17, 2010·Nature Reviews. Genetics·Misha Soskine, Dan S Tawfik
Jul 24, 2010·Genome Research·Henrik Kaessmann
Dec 18, 2010·Science·Sidi ChenManyuan Long
Jan 19, 2011·FEBS Letters·Zefeng Yang, Jinling Huang
Feb 22, 2011·BMC Evolutionary Biology·Mark Ta DonoghueCharles Spillane
Sep 1, 2011·Nature Reviews. Genetics·Diethard Tautz, Tomislav Domazet-Lošo
Sep 29, 2011·Genome Biology and Evolution·Benjamin A Wilson, Joanna Masel
Nov 22, 2011·PLoS Genetics·Dong-Dong WuYa-Ping Zhang
Nov 22, 2011·PLoS Genetics·Daniele Guerzoni, Aoife McLysaght
Dec 24, 2011·Science·Gloria A BrarJonathan S Weissman
Mar 31, 2012·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·José M Ranz, John Parsch
Jun 23, 2012·Nature·Anne-Ruxandra CarvunisMarc Vidal
Jul 24, 2012·Molecular Biology and Evolution·Niv SabathDavid Karlin
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Nov 28, 2012·PloS One·Daniel N Murphy, Aoife McLysaght

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Citations

Sep 2, 2015·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Tom A Williams, T Martin Embley
Jul 28, 2016·Nature Reviews. Genetics·Aoife McLysaght, Laurence D Hurst
Oct 30, 2016·Trends in Biochemical Sciences·Rita Pancsa, Peter Tompa
Jan 1, 2016·PLoS Genetics·Jorge Ruiz-OreraM Mar Albà
Mar 24, 2017·Molecular Biology and Evolution·Achala S JayasenaJoshua S Mylne
May 19, 2017·Journal of Experimental Botany·Jillian M Hagel, Peter J Facchini
Oct 6, 2017·Molecular Biology and Evolution·Fanny E Hartmann, Daniel Croll
Dec 9, 2017·Molecular Biology and Evolution·Nikolaos VakirlisIngrid Lafontaine
Dec 8, 2017·Molecular Biology and Evolution·Helle Tessand BaalsrudSissel Jentoft
Nov 2, 2017·Molecular Biology and Evolution·Jananan Sylvestre PathmanathanEric Bapteste
Apr 20, 2018·Molecular Biology and Evolution·Leon HilgersThomas von Rintelen
Apr 21, 2018·Nature Communications·Yanlong GuanJinling Huang
May 24, 2019·PLoS Genetics·Stephen Branden Van Oss, Anne-Ruxandra Carvunis
Jul 13, 2017·Nature Reviews. Molecular Cell Biology·Juan-Pablo Couso, Pedro Patraquim
Aug 8, 2019·Genome Research·Igor FesenkoVadim Govorun
Dec 17, 2019·Molecular Biology and Evolution·Liam Abrahams, Laurence D Hurst
Feb 27, 2020·Molecular Biology and Evolution·Luke J Kosinski, Joanna Masel
Sep 30, 2019·Cellular and Molecular Life Sciences : CMLS·Adrián Cárdenas, Víctor Borrell
Jun 14, 2020·Integrative and Comparative Biology·C Darrin HulseyGareth J Fraser
Jul 13, 2016·Genome Biology and Evolution·Zi-Wen LiYa-Long Guo
Sep 11, 2019·Genome Biology and Evolution·Gavin M Douglas, Morgan G I Langille
Jun 25, 2020·Japanese Journal of Clinical Oncology·Yusuke SuenagaAkira Nakagawara
Mar 15, 2018·BMC Biology·Raphaël MéheustEric Bapteste
Aug 2, 2018·MBio·Baojun Wu, Alicia Knudson
Apr 8, 2020·Journal of Molecular Evolution·Brennen HeamesErich Bornberg-Bauer
Jun 24, 2017·Nature Ecology & Evolution·Benjamin A WilsonJoanna Masel
Feb 16, 2019·Proceedings of the National Academy of Sciences of the United States of America·Xuan ZhuangC-H Christina Cheng
Jun 27, 2019·The New Phytologist·James C Schnable
Aug 5, 2018·BMC Evolutionary Biology·Cemalettin BekpenDiethard Tautz
Nov 20, 2020·Genome Biology and Evolution·Daniel DowlingErich Bornberg-Bauer

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Methods Mentioned

BETA
RNA-seq

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