The Atlantic salmon genome provides insights into rediploidization. Lien, S., Koop, B. F., Sandve, S. R., Miller, J. R., Kent, M. P., Nome, T., Hvidsten, T. R., Leong, J. S., Minkley, D. R., Zimin, A., Grammes, F., Grove, H., Gjuvsland, A., Walenz, B., Hermansen, R. A., von Schalburg, K., Rondeau, E. B., Di Genova, A., Samy, J. K. A., Olav Vik, J., Vigeland, M. D., Caler, L., Grimholt, U., Jentoft, S., Inge Våge, D., de Jong, P., Moen, T., Baranski, M., Palti, Y., Smith, D. R., Yorke, J. A., Nederbragt, A. J., Tooming-Klunderud, A., Jakobsen, K. S., Jiang, X., Fan, D., Hu, Y., Liberles, D. A., Vidal, R., Iturra, P., Jones, S. J. M., Jonassen, I., Maass, A., Omholt, S. W., & Davidson, W. S. Nature, 533(7602):200–205, May, 2016.
The Atlantic salmon genome provides insights into rediploidization [link]Paper  doi  abstract   bibtex   
Abstract The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon ( Salmo salar ), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.
@article{lien_atlantic_2016,
	title = {The {Atlantic} salmon genome provides insights into rediploidization},
	volume = {533},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature17164},
	doi = {10/f3rv45},
	abstract = {Abstract
            
              The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (
              Salmo salar
              ), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.},
	language = {en},
	number = {7602},
	urldate = {2021-06-07},
	journal = {Nature},
	author = {Lien, Sigbjørn and Koop, Ben F. and Sandve, Simen R. and Miller, Jason R. and Kent, Matthew P. and Nome, Torfinn and Hvidsten, Torgeir R. and Leong, Jong S. and Minkley, David R. and Zimin, Aleksey and Grammes, Fabian and Grove, Harald and Gjuvsland, Arne and Walenz, Brian and Hermansen, Russell A. and von Schalburg, Kris and Rondeau, Eric B. and Di Genova, Alex and Samy, Jeevan K. A. and Olav Vik, Jon and Vigeland, Magnus D. and Caler, Lis and Grimholt, Unni and Jentoft, Sissel and Inge Våge, Dag and de Jong, Pieter and Moen, Thomas and Baranski, Matthew and Palti, Yniv and Smith, Douglas R. and Yorke, James A. and Nederbragt, Alexander J. and Tooming-Klunderud, Ave and Jakobsen, Kjetill S. and Jiang, Xuanting and Fan, Dingding and Hu, Yan and Liberles, David A. and Vidal, Rodrigo and Iturra, Patricia and Jones, Steven J. M. and Jonassen, Inge and Maass, Alejandro and Omholt, Stig W. and Davidson, William S.},
	month = may,
	year = {2016},
	pages = {200--205},
}
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