Table 2. References for 20 abstracts analyzed in our study.
Countries (based on affiliations of all authors) and model organisms are included to display the diversity of the abstracts.
| Papers | Countries | Model Organisms |
|---|---|---|
| Keese, P. K., and Gibbs, A. (1992). Origins of genes: ‘big bang’ or continuous creation? PNAS 89:9489–9493. | Australia | Cellular life, Viruses |
| Kastenmayer, J. P., Ni, L., Chu, A., Kitchen, L. E., Au, W. C., Yang, H.,. .. and Basrai, M. A. (2006). Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Research 16:365–373. |
USA | S. cerevisiae |
| Levine, M. T., Jones, C. D., Kern, A. D., Lindfors, H. A., and Begun, D. J. (2006). Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. PNAS 103:9935–9939. |
USA | D. melanogaster |
| Stepanov, V. G., and Fox, G. E. (2007). Stress-driven in vivo selection of a functional mini-gene from a randomized DNA library expressing combinatorial peptides in Escherichia coli. Molecular Biology and Evolution 24:1480–1491. |
USA | E. coli |
| Cai, J., Zhao, R., Jiang, H., and Wang, W. (2008). De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics 179:487–496. | China | S. cerevisiae |
| Zhou, Q., Zhang, G., Zhang, Y., Xu, S., Zhao, R., Zhan, Z.,. .. and Wang, W. (2008). On the origin of new genes in Drosophila. Genome Research 18:1446–1455. | China | Drosophila |
| Xiao, W., Liu, H., Li, Y., Li, X., Xu, C., Long, M., and Wang, S. (2009). A rice gene of de novo origin negatively regulates pathogen-induced defense response. PLoS One 4:e4603. |
China, USA | rice |
| Carvunis, A. R., Rolland, T., Wapinski, I., Calderwood, M. A., Yildirim, M. A., Simonis, N.,. ..and Vidal M. (2012). Proto-genes and de novo gene birth. Nature 487:370–374. |
Belgium, France, USA | S. cerevisiae |
| Ding, Y., Zhou, Q., and Wang, W. (2012). Origins of new genes and evolution of their novel functions. Annual Review of Ecology, Evolution, and Systematics 43:345–363. |
China, USA | |
| Tautz, D., Neme, R., and Domazet-Lošo, T. (2013). Evolutionary Origin of Orphan Genes. In: Encyclopedia of Life Sciences. John Wiley & Sons. DOI: https://doi.org/10.1002/9780470015902.a0024601 | Croatia, Germany | |
| Reinhardt, J. A., Wanjiru, B. M., Brant, A. T., Saelao, P., Begun, D. J., and Jones, C. D. (2013). De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences. PLoS Genetics 9:e1003860. |
USA | D. melanogaster |
| Wissler, L., Gadau, J., Simola, D. F., Helmkampf, M., and Bornberg-Bauer, E. (2013). Mechanisms and dynamics of orphan gene emergence in insect genomes. Genome Biology and Evolution 5:439–455. |
Germany, USA | Insects |
| Brylinski, M. (2013). Exploring the ‘dark matter’ of a mammalian proteome by protein structure and function modeling. Proteome Science 11:47. | USA | M. musculus |
| Li, D., Yan, Z., Lu, L., Jiang, H., and Wang, W. (2014). Pleiotropy of the de novo-originated gene MDF1. Scientific Reports 4:7280. |
China | S. cerevisiae |
| Wirthlin, M., Lovell, P. V., Jarvis, E. D., and Mello, C. V. (2014). Comparative genomics reveals molecular features unique to the songbird lineage. BMC Genomics 15:1082. |
USA | Songbirds |
| Suenaga, Y., Islam, S. R., Alagu, J., Kaneko, Y., Kato, M., Tanaka, Y.,. .. and Nakagawara, A.(2014). NCYM, a Cis-antisense gene of MYCN, encodes a de novo evolved protein that inhibits GSK3β resulting in the stabilization of MYCN in human neuroblastomas. PLoS Genetics 10:e1003996. |
Japan | Human |
| Arendsee, Z. W., Li, L., and Wurtele, E. S. (2014). Coming of age: Orphan genes in plants. Trends in Plant Science 19:698–708. |
USA | A. thaliana |
| Ruiz-Orera, J., Hernandez-Rodriguez, J., Chiva, C., Sabidó, E., Kondova, I., Bontrop, R.,. .. and Albà, M. M. (2015). Origins of de novo genes in human and chimpanzee. PLoS Genetics 11:e1005721. |
Spain, The Netherlands | Human, Chimpanzee |
| Couso, J. P., and Patraquim, P. (2017). Classification and function of small open reading frames.Nature Reviews Molecular Cell Biology 18:575–589. | Spain, UK | D. melanogaster |
| Luis Villanueva-Cañas, J., Ruiz-Orera, J., Agea, M. I., Gallo, M., Andreu, D., and Albà, M. M. (2017). New genes and functional innovation in mammals. Genome Biology and Evolution 9:1886–1900. | Spain | Mammals |