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Schlötterer, C. Genes from scratch—the evolutionary fate of de novo genes. Trends Genet. 31, 215–219 (2015).
- 2.
McLysaght, A. & Hurst, L. D. Open questions in the study of de novo genes: what, how and why. Nat. Rev. Genet. 17, 567–578 (2016).
- 3.
Schmitz, J. F. & Bornberg-Bauer, E. Fact or fiction: Updates on how protein-coding genes might emerge de novo from previously non-coding DNA. F1000Research 6, 57 (2017).
- 4.
Van Oss, S. B. V. & Carvunis, A.-R. De novo gene birth. PLoS Genet. 15, e1008160 (2019).
- 5.
Liberles, D. A., Kolesov, G. & Dittmar, K. Understanding gene duplication through biochemistry and population genetics. in Evolution after Gene Duplication, (eds Dittmar, K. & Liberles, D.) 1–21 (John Wiley & Sons, Ltd, 2011).
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Begun, D. J., Lindfors, H. A., Thompson, M. E. & Holloway, A. K. Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. Genetics 172, 1675–1681 (2006).
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Cai, J., Zhao, R., Jiang, H. & Wang, W. De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics 179, 487–496 (2008).
- 9.
Neme, R. & Tautz, D. Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. BMC Genomics 14, 117 (2013).
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McLysaght, A. & Guerzoni, D. New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation. Philos. Trans. R. Soc. B Biol. Sci. 370, 20140332 (2015).
- 11.
Schmitz, J. F., Ullrich, K. K. & Bornberg-Bauer, E. Incipient de novo genes can evolve from frozen accidents that escaped rapid transcript turnover. Nat. Ecol. Evol. 2, 1626–1632 (2018).
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Vakirlis, N. et al. A molecular portrait of de novo genes in yeasts. Mol. Biol. Evol. 35, 631–645 (2018).
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Prabh, N. & Rödelsperger, C. De novo, divergence, and mixed origin contribute to the emergence of orphan genes in pristionchus nematodes. G3 Genes Genomes Genet. 9, 2277–2286 (2019).
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Zhang, L. et al. Rapid evolution of protein diversity by de novo origination in Oryza. Nat. Ecol. Evol. 3, 679 (2019).
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Zhou, Q. et al. On the origin of new genes in Drosophila. Genome Res. 18, 1446–1455 (2008).
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Carvunis, A.-R. et al. Proto-genes and de novo gene birth. Nature 487, 370–374 (2012).
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Klasberg, S., Bitard-Feildel, T., Callebaut, I. & Bornberg-Bauer, E. Origins and structural properties of novel and de novo protein domains during insect evolution. FEBS J. 285, 2605–2625 (2018).
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Zhao, L., Saelao, P., Jones, C. D. & Begun, D. J. Origin and spread of de novo genes in Drosophila melanogaster populations. Science 343, 769–772 (2014).
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Zhuang, X., Yang, C., Murphy, K. R. & Cheng, C.-H. C. Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids. Proc. Natl Acad. Sci. USA 116, 4400–4405 (2019).
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Kelly, S. M., Jess, T. J. & Price, N. C. How to study proteins by circular dichroism. Biochim. Biophys. Acta BBA - Proteins Proteomics 1751, 119–139 (2005).
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Greenfield, N. J. Using circular dichroism spectra to estimate protein secondary structure. Nat. Protoc. 1, 2876–2890 (2006).
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Louis-Jeune, C., Andrade-Navarro, M. A. & Perez-Iratxeta, C. Prediction of protein secondary structure from circular dichroism using theoretically derived spectra. Proteins 80, 374–381 (2012).
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Jinek, M. et al. RNA-Programmed genome editing in human cells. eLife 2, e00471 (2013).
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Source: https://www.nature.com/articles/s41467-021-21667-6
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Original Text (This is the original text for your reference.)
- 1.
Schlötterer, C. Genes from scratch—the evolutionary fate of de novo genes. Trends Genet. 31, 215–219 (2015).
- 2.
McLysaght, A. & Hurst, L. D. Open questions in the study of de novo genes: what, how and why. Nat. Rev. Genet. 17, 567–578 (2016).
- 3.
Schmitz, J. F. & Bornberg-Bauer, E. Fact or fiction: Updates on how protein-coding genes might emerge de novo from previously non-coding DNA. F1000Research 6, 57 (2017).
- 4.
Van Oss, S. B. V. & Carvunis, A.-R. De novo gene birth. PLoS Genet. 15, e1008160 (2019).
- 5.
Liberles, D. A., Kolesov, G. & Dittmar, K. Understanding gene duplication through biochemistry and population genetics. in Evolution after Gene Duplication, (eds Dittmar, K. & Liberles, D.) 1–21 (John Wiley & Sons, Ltd, 2011).
- 6.
Bornberg-Bauer, E. & Albà, M. M. Dynamics and adaptive benefits of modular protein evolution. Curr. Opin. Struct. Biol. 23, 459–466 (2013).
- 7.
Begun, D. J., Lindfors, H. A., Thompson, M. E. & Holloway, A. K. Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. Genetics 172, 1675–1681 (2006).
- 8.
Cai, J., Zhao, R., Jiang, H. & Wang, W. De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics 179, 487–496 (2008).
- 9.
Neme, R. & Tautz, D. Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. BMC Genomics 14, 117 (2013).
- 10.
McLysaght, A. & Guerzoni, D. New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation. Philos. Trans. R. Soc. B Biol. Sci. 370, 20140332 (2015).
- 11.
Schmitz, J. F., Ullrich, K. K. & Bornberg-Bauer, E. Incipient de novo genes can evolve from frozen accidents that escaped rapid transcript turnover. Nat. Ecol. Evol. 2, 1626–1632 (2018).
- 12.
Vakirlis, N. et al. A molecular portrait of de novo genes in yeasts. Mol. Biol. Evol. 35, 631–645 (2018).
- 13.
Prabh, N. & Rödelsperger, C. De novo, divergence, and mixed origin contribute to the emergence of orphan genes in pristionchus nematodes. G3 Genes Genomes Genet. 9, 2277–2286 (2019).
- 14.
Zhang, L. et al. Rapid evolution of protein diversity by de novo origination in Oryza. Nat. Ecol. Evol. 3, 679 (2019).
- 15.
Zhou, Q. et al. On the origin of new genes in Drosophila. Genome Res. 18, 1446–1455 (2008).
- 16.
Carvunis, A.-R. et al. Proto-genes and de novo gene birth. Nature 487, 370–374 (2012).
- 17.
Klasberg, S., Bitard-Feildel, T., Callebaut, I. & Bornberg-Bauer, E. Origins and structural properties of novel and de novo protein domains during insect evolution. FEBS J. 285, 2605–2625 (2018).
- 18.
Zhao, L., Saelao, P., Jones, C. D. & Begun, D. J. Origin and spread of de novo genes in Drosophila melanogaster populations. Science 343, 769–772 (2014).
- 19.
Ruiz-Orera, J., Messeguer, X., Subirana, J. A. & Albà, M. M. Long non-coding RNAs as a source of new peptides. eLife 3, e03523 (2014).
- 20.
Palmieri, N., Kosiol, C. & Schlötterer, C. The life cycle of Drosophila orphan genes. eLife 3, e01311 (2014).
- 21.
Levy, A. How evolution builds genes from scratch. Nature 574, 314–316 (2019).
- 22.
Khalturin, K., Hemmrich, G., Fraune, S., Augustin, R. & Bosch, T. C. More than just orphans: are taxonomically-restricted genes important in evolution? Trends Genet. 25, 404–413 (2009).
- 23.
Baalsrud, H. T. et al. De novo gene evolution of antifreeze glycoproteins in codfishes revealed by whole genome sequence data. Mol. Biol. Evol. 35, 593–606 (2018).
- 24.
Zhuang, X., Yang, C., Murphy, K. R. & Cheng, C.-H. C. Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids. Proc. Natl Acad. Sci. USA 116, 4400–4405 (2019).
- 25.
Chen, L., DeVries, A. L. & Cheng, C.-H. C. Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod. PNAS 94, 3817–3822 (1997).
- 26.
Brockhausen, I., Schachter, H. & Stanley, P. O-GalNAc Glycans. in Essentials of Glycobiology, second edn. (eds Varki, A. et al.) (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2009).
- 27.
Pan, X. et al. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 124, 1069–1081 (2006).
- 28.
Bungard, D. et al. Foldability of a natural de novo evolved protein. Structure 25, 1687–1696.e4 (2017).
- 29.
Vakirlis, N. et al. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat. Commun. 11, 781 (2020).
- 30.
Gubala, A. M. et al. The goddard and saturn genes are essential for Drosophila male fertility and may have arisen de novo. Mol. Biol. Evol. 34, 1066–1082 (2017).
- 31.
Keeling, D. M., Garza, P., Nartey, C. M. & Carvunis, A.-R. The meanings of ’function’ in biology and the problematic case of de novo gene emergence. eLife 8, e47014 (2019).
- 32.
Lupas, A., Van Dyke, M. & Stock, J. Predicting coiled coils from protein sequences. Science 252, 1162–1164 (1991).
- 33.
Truebestein L, Leonard TA. Coiled-coils: The long and short of it. Bioessays 38. 903–916 https://doi.org/10.1002/bies.201600062 (2016).
- 34.
Xu, D. & Zhang, Y. Toward optimal fragment generations for ab initio protein structure assembly. Proteins 81, 229–239 (2013).
- 35.
Reva, B. A., Finkelstein, A. V. & Skolnick, J. What is the probability of a chance prediction of a protein structure with an RMSD of 6 A? Fold Des. 3, 141–147 (1998).
- 36.
Berendsen, H. J. C., van der Spoel, D. & van Drunen, R. GROMACS: a message-passing parallel molecular dynamics implementation. Comput. Phys. Commu. 91, 43–56 (1995).
- 37.
Pronk, S. et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29, 845–854 (2013).
- 38.
Abraham, M. J. et al. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1-2, 19–25 (2015).
- 39.
Yang, J.-M. & Tung, C.-H. Protein structure database search and evolutionary classification. Nucleic Acids Res. 34, 3646–3659 (2006).
- 40.
Tung, C.-H., Huang, J.-W. & Yang, J.-M. Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. Genome Biol. 8, R31 (2007).
- 41.
Dong, R., Pan, S., Peng, Z., Zhang, Y. & Yang, J. mTM-align: a server for fast protein structure database search and multiple protein structure alignment. Nucleic Acids Res. 46, W380–W386 (2018).
- 42.
Kelly, S. M., Jess, T. J. & Price, N. C. How to study proteins by circular dichroism. Biochim. Biophys. Acta BBA - Proteins Proteomics 1751, 119–139 (2005).
- 43.
Greenfield, N. J. Using circular dichroism spectra to estimate protein secondary structure. Nat. Protoc. 1, 2876–2890 (2006).
- 44.
Louis-Jeune, C., Andrade-Navarro, M. A. & Perez-Iratxeta, C. Prediction of protein secondary structure from circular dichroism using theoretically derived spectra. Proteins 80, 374–381 (2012).
- 45.
Jinek, M. et al. RNA-Programmed genome editing in human cells. eLife 2, e00471 (2013).
- 46.
Fabian, L. & Brill, J. A. Drosophila spermiogenesis. Spermatogenesis 2, 197–212 (2012).
- 47.
Basiri, M. L. et al. A migrating ciliary gate compartmentalizes the site of axoneme assembly in Drosophila spermatids. Curr. Biol. 24, 2622–2631 (2014).
- 48.
Soulavie, F. et al. Hemingway is required for sperm flagella assembly and ciliary motility in Drosophila. MBoC 25, 1276–1286 (2014).
- 49.
Santel, A., Winhauer, T., Blümer, N. & Renkawitz-Pohl, R. The Drosophila don juan (dj) gene encodes a novel sperm specific protein component characterized by an unusual domain of a repetitive amino acid motif. Mech. Dev. 64, 19–30 (1997).
- 50.
Oliva, R. & Dixon, G. H. Vertebrate protamine genes and the histone-to-protamine replacement reaction. in Progress in Nucleic Acid Research and Molecular Biology, Vol. 40 (eds Cohn, W. E. & Moldave, K.) 25–94 (Academic Press, 1991).
- 51.
Jayaramaiah Raja, S. & Renkawitz-Pohl, R. Replacement by Drosophila melanogaster protamines and Mst77F of Histones during chromatin condensation in late spermatids and role of sesame in the removal of these proteins from the male pronucleus. Mol. Cell Biol. 25, 6165–6177 (2005).
- 52.
Tokuyasu, K. T. Dynamics of spermiogenesis in Drosophila melanogaster. 3. Relation between axoneme and mitochondrial derivatives. Exp. Cell Res. 84, 239–250 (1974).
- 53.
Begun, D. J., Lindfors, H. A., Kern, A. D. & Jones, C. D. Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics 176, 1131–1137 (2007).
- 54.
Moyers, B. A. & Zhang, J. Phylostratigraphic bias creates spurious patterns of genome evolution. Mol. Biol. Evol. 32, 258–267 (2015).
- 55.
Domazet-Lošo, T. et al. No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution. Mol. Biol. Evol. 34, 843–856 (2017).
- 56.
Weisman, C. M., Murray, A. W. & Eddy, S. R. Many, but not all, lineage-specific genes can be explained by homology detection failure. PLoS Biol. 18, e3000862 (2020).
- 57.
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