ALBERT

Description: The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence times. We show that the A and B genomes diverged from a common ancestor ~7 million years ago and that these genomes gave rise to the D genome through homoploid hybrid speciation 1 to 2 million years later. Our findings imply that the present-day bread wheat genome is a product of multiple rounds of hybrid speciation (homoploid and polyploid) and lay the foundation for a new framework for understanding the wheat genome as a multilevel phylogenetic mosaic.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marcussen, Thomas -- Sandve, Simen R -- Heier, Lise -- Spannagl, Manuel -- Pfeifer, Matthias -- International Wheat Genome Sequencing Consortium -- Jakobsen, Kjetill S -- Wulff, Brande B H -- Steuernagel, Burkhard -- Mayer, Klaus F X -- Olsen, Odd-Arne -- New York, N.Y. -- Science. 2014 Jul 18;345(6194):1250092. doi: 10.1126/science.1250092.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Sciences, Norwegian University of Life Sciences, 1432 As, Norway. ; Department of Plant Sciences, Norwegian University of Life Sciences, 1432 As, Norway. simen.sandve@nmbu.no. ; Stromsveien 78 B, 0663 Oslo, Norway. ; Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany. ; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway. ; The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25035499" target="_blank"〉PubMed〈/a〉

Description: Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type-specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type- and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pfeifer, Matthias -- Kugler, Karl G -- Sandve, Simen R -- Zhan, Bujie -- Rudi, Heidi -- Hvidsten, Torgeir R -- International Wheat Genome Sequencing Consortium -- Mayer, Klaus F X -- Olsen, Odd-Arne -- New York, N.Y. -- Science. 2014 Jul 18;345(6194):1250091. doi: 10.1126/science.1250091.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany. ; Department of Plant Sciences/Centre for Integrative Genetics, The Norwegian University of Life Sciences (NMBU), 1432 Aas, Norway. ; Department of Chemistry, Biotechnology and Food Science, NMBU, 1432 Aas, Norway. ; Department of Plant Sciences/Centre for Integrative Genetics, The Norwegian University of Life Sciences (NMBU), 1432 Aas, Norway. odd-arne.olsen@nmbu.no.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25035498" target="_blank"〉PubMed〈/a〉

Description: 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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lien, Sigbjorn -- Koop, Ben F -- Sandve, Simen R -- Miller, Jason R -- Kent, Matthew P -- Nome, Torfinn -- Hvidsten, Torgeir R -- Leong, Jong S -- Minkley, David R -- Zimin, Aleksey -- Grammes, Fabian -- Grove, Harald -- Gjuvsland, Arne -- Walenz, Brian -- Hermansen, Russell A -- von Schalburg, Kris -- Rondeau, Eric B -- Di Genova, Alex -- Samy, Jeevan K A -- Olav Vik, Jon -- Vigeland, Magnus D -- Caler, Lis -- Grimholt, Unni -- Jentoft, Sissel -- Inge Vage, Dag -- de Jong, Pieter -- Moen, Thomas -- Baranski, Matthew -- Palti, Yniv -- Smith, Douglas R -- Yorke, James A -- Nederbragt, Alexander J -- Tooming-Klunderud, Ave -- Jakobsen, Kjetill S -- Jiang, Xuanting -- Fan, Dingding -- Hu, Yan -- Liberles, David A -- Vidal, Rodrigo -- Iturra, Patricia -- Jones, Steven J M -- Jonassen, Inge -- Maass, Alejandro -- Omholt, Stig W -- Davidson, William S -- England -- Nature. 2016 Apr 18;533(7602):200-5. doi: 10.1038/nature17164.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, As NO-1432, Norway. ; Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada. ; J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, USA. ; Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, As NO-1432 Norway. ; Department of Plant Physiology, Umea Plant Science Centre, Umea University, Umea 90187, Sweden. ; Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742-2431, USA. ; Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA. ; Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania 19122-6078, USA. ; Department of Biology, Temple University, Philadelphia, Pennsylvania 19122-6078, USA. ; Center for Mathematical Modeling, University of Chile, Santiago 8370456, Chile. ; Center for Genome Regulation, University of Chile, Santiago 8370415, Chile. ; Medical Genetics, Oslo University Hospital and University of Oslo, Oslo NO-0424, Norway. ; Department of Virology, Norwegian Veterinary Institute, Oslo NO-0454, Norway. ; Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo NO-0316, Norway. ; CHORI, Oakland, California 94609, USA. ; AquaGen, Trondheim NO-7462, Norway. ; Nofima, Tromso NO-9291, Norway. ; National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, West Virginia 25430, USA. ; Beckman Genomics, Danvers, Massachusetts 01923, USA. ; Courtagen Life Sciences, Woburn, Massachusetts 01801, USA. ; BGI-Shenzhen, Shenzhen 518083, China. ; Laboratory of Molecular Ecology, Genomics, and Evolutionary Studies, Department of Biology, University of Santiago, Santiago 9170022, Chile. ; Faculty of Medicine, University of Chile, Santiago 8380453, Chile. ; Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada. ; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada. ; Department of Informatics, University of Bergen, Bergen NO-6020, Norway. ; Centre for Biodiversity Dynamics, Department of Biology, NTNU - Norwegian University of Science and Technology, Trondheim NO-7491, Norway.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27088604" target="_blank"〉PubMed〈/a〉