ALBERT

Description: The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering approximately 4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for approximately 60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lindblad-Toh, Kerstin -- Garber, Manuel -- Zuk, Or -- Lin, Michael F -- Parker, Brian J -- Washietl, Stefan -- Kheradpour, Pouya -- Ernst, Jason -- Jordan, Gregory -- Mauceli, Evan -- Ward, Lucas D -- Lowe, Craig B -- Holloway, Alisha K -- Clamp, Michele -- Gnerre, Sante -- Alfoldi, Jessica -- Beal, Kathryn -- Chang, Jean -- Clawson, Hiram -- Cuff, James -- Di Palma, Federica -- Fitzgerald, Stephen -- Flicek, Paul -- Guttman, Mitchell -- Hubisz, Melissa J -- Jaffe, David B -- Jungreis, Irwin -- Kent, W James -- Kostka, Dennis -- Lara, Marcia -- Martins, Andre L -- Massingham, Tim -- Moltke, Ida -- Raney, Brian J -- Rasmussen, Matthew D -- Robinson, Jim -- Stark, Alexander -- Vilella, Albert J -- Wen, Jiayu -- Xie, Xiaohui -- Zody, Michael C -- Broad Institute Sequencing Platform and Whole Genome Assembly Team -- Baldwin, Jen -- Bloom, Toby -- Chin, Chee Whye -- Heiman, Dave -- Nicol, Robert -- Nusbaum, Chad -- Young, Sarah -- Wilkinson, Jane -- Worley, Kim C -- Kovar, Christie L -- Muzny, Donna M -- Gibbs, Richard A -- Baylor College of Medicine Human Genome Sequencing Center Sequencing Team -- Cree, Andrew -- Dihn, Huyen H -- Fowler, Gerald -- Jhangiani, Shalili -- Joshi, Vandita -- Lee, Sandra -- Lewis, Lora R -- Nazareth, Lynne V -- Okwuonu, Geoffrey -- Santibanez, Jireh -- Warren, Wesley C -- Mardis, Elaine R -- Weinstock, George M -- Wilson, Richard K -- Genome Institute at Washington University -- Delehaunty, Kim -- Dooling, David -- Fronik, Catrina -- Fulton, Lucinda -- Fulton, Bob -- Graves, Tina -- Minx, Patrick -- Sodergren, Erica -- Birney, Ewan -- Margulies, Elliott H -- Herrero, Javier -- Green, Eric D -- Haussler, David -- Siepel, Adam -- Goldman, Nick -- Pollard, Katherine S -- Pedersen, Jakob S -- Lander, Eric S -- Kellis, Manolis -- 095908/Wellcome Trust/United Kingdom -- GM82901/GM/NIGMS NIH HHS/ -- R01 HG003474/HG/NHGRI NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-09/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA. kersli@broadinstitute.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21993624" target="_blank"〉PubMed〈/a〉

Description: The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633110/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633110/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Amemiya, Chris T -- Alfoldi, Jessica -- Lee, Alison P -- Fan, Shaohua -- Philippe, Herve -- Maccallum, Iain -- Braasch, Ingo -- Manousaki, Tereza -- Schneider, Igor -- Rohner, Nicolas -- Organ, Chris -- Chalopin, Domitille -- Smith, Jeramiah J -- Robinson, Mark -- Dorrington, Rosemary A -- Gerdol, Marco -- Aken, Bronwen -- Biscotti, Maria Assunta -- Barucca, Marco -- Baurain, Denis -- Berlin, Aaron M -- Blatch, Gregory L -- Buonocore, Francesco -- Burmester, Thorsten -- Campbell, Michael S -- Canapa, Adriana -- Cannon, John P -- Christoffels, Alan -- De Moro, Gianluca -- Edkins, Adrienne L -- Fan, Lin -- Fausto, Anna Maria -- Feiner, Nathalie -- Forconi, Mariko -- Gamieldien, Junaid -- Gnerre, Sante -- Gnirke, Andreas -- Goldstone, Jared V -- Haerty, Wilfried -- Hahn, Mark E -- Hesse, Uljana -- Hoffmann, Steve -- Johnson, Jeremy -- Karchner, Sibel I -- Kuraku, Shigehiro -- Lara, Marcia -- Levin, Joshua Z -- Litman, Gary W -- Mauceli, Evan -- Miyake, Tsutomu -- Mueller, M Gail -- Nelson, David R -- Nitsche, Anne -- Olmo, Ettore -- Ota, Tatsuya -- Pallavicini, Alberto -- Panji, Sumir -- Picone, Barbara -- Ponting, Chris P -- Prohaska, Sonja J -- Przybylski, Dariusz -- Saha, Nil Ratan -- Ravi, Vydianathan -- Ribeiro, Filipe J -- Sauka-Spengler, Tatjana -- Scapigliati, Giuseppe -- Searle, Stephen M J -- Sharpe, Ted -- Simakov, Oleg -- Stadler, Peter F -- Stegeman, John J -- Sumiyama, Kenta -- Tabbaa, Diana -- Tafer, Hakim -- Turner-Maier, Jason -- van Heusden, Peter -- White, Simon -- Williams, Louise -- Yandell, Mark -- Brinkmann, Henner -- Volff, Jean-Nicolas -- Tabin, Clifford J -- Shubin, Neil -- Schartl, Manfred -- Jaffe, David B -- Postlethwait, John H -- Venkatesh, Byrappa -- Di Palma, Federica -- Lander, Eric S -- Meyer, Axel -- Lindblad-Toh, Kerstin -- 095908/Wellcome Trust/United Kingdom -- MC_U137761446/Medical Research Council/United Kingdom -- P42 ES007381/ES/NIEHS NIH HHS/ -- R01 ES006272/ES/NIEHS NIH HHS/ -- R01 HG003474/HG/NHGRI NIH HHS/ -- R01 OD011116/OD/NIH HHS/ -- R24 OD011199/OD/NIH HHS/ -- R24 RR032670/RR/NCRR NIH HHS/ -- R37 HD032443/HD/NICHD NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- England -- Nature. 2013 Apr 18;496(7445):311-6. doi: 10.1038/nature12027.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington 98101, USA. camemiya@benaroyaresearch.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23598338" target="_blank"〉PubMed〈/a〉

Description: Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353498/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353498/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brawand, David -- Wagner, Catherine E -- Li, Yang I -- Malinsky, Milan -- Keller, Irene -- Fan, Shaohua -- Simakov, Oleg -- Ng, Alvin Y -- Lim, Zhi Wei -- Bezault, Etienne -- Turner-Maier, Jason -- Johnson, Jeremy -- Alcazar, Rosa -- Noh, Hyun Ji -- Russell, Pamela -- Aken, Bronwen -- Alfoldi, Jessica -- Amemiya, Chris -- Azzouzi, Naoual -- Baroiller, Jean-Francois -- Barloy-Hubler, Frederique -- Berlin, Aaron -- Bloomquist, Ryan -- Carleton, Karen L -- Conte, Matthew A -- D'Cotta, Helena -- Eshel, Orly -- Gaffney, Leslie -- Galibert, Francis -- Gante, Hugo F -- Gnerre, Sante -- Greuter, Lucie -- Guyon, Richard -- Haddad, Natalie S -- Haerty, Wilfried -- Harris, Rayna M -- Hofmann, Hans A -- Hourlier, Thibaut -- Hulata, Gideon -- Jaffe, David B -- Lara, Marcia -- Lee, Alison P -- MacCallum, Iain -- Mwaiko, Salome -- Nikaido, Masato -- Nishihara, Hidenori -- Ozouf-Costaz, Catherine -- Penman, David J -- Przybylski, Dariusz -- Rakotomanga, Michaelle -- Renn, Suzy C P -- Ribeiro, Filipe J -- Ron, Micha -- Salzburger, Walter -- Sanchez-Pulido, Luis -- Santos, M Emilia -- Searle, Steve -- Sharpe, Ted -- Swofford, Ross -- Tan, Frederick J -- Williams, Louise -- Young, Sarah -- Yin, Shuangye -- Okada, Norihiro -- Kocher, Thomas D -- Miska, Eric A -- Lander, Eric S -- Venkatesh, Byrappa -- Fernald, Russell D -- Meyer, Axel -- Ponting, Chris P -- Streelman, J Todd -- Lindblad-Toh, Kerstin -- Seehausen, Ole -- Di Palma, Federica -- 2R01DE019637-04/DE/NIDCR NIH HHS/ -- F30 DE023013/DE/NIDCR NIH HHS/ -- MC_U137761446/Medical Research Council/United Kingdom -- R01 DE019637/DE/NIDCR NIH HHS/ -- R01 NS034950/NS/NINDS NIH HHS/ -- U54 HG002045/HG/NHGRI NIH HHS/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2014 Sep 18;513(7518):375-81. doi: 10.1038/nature13726. Epub 2014 Sep 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK [3]. ; 1] Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution &Biogeochemistry, CH-6047 Kastanienbaum, Switzerland [2] Division of Aquatic Ecology, Institute of Ecology &Evolution, University of Bern, CH-3012 Bern, Switzerland [3]. ; 1] MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK [2]. ; 1] Gurdon Institute, Cambridge CB2 1QN, UK [2] Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK. ; Division of Aquatic Ecology, Institute of Ecology &Evolution, University of Bern, CH-3012 Bern, Switzerland. ; Department of Biology, University of Konstanz, D-78457 Konstanz, Germany. ; 1] Department of Biology, University of Konstanz, D-78457 Konstanz, Germany [2] European Molecular Biology Laboratory, 69117 Heidelberg, Germany. ; Institute of Molecular and Cell Biology, A*STAR, 138673 Singapore. ; Department of Biology, Reed College, Portland, Oregon 97202, USA. ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. ; Biology Department, Stanford University, Stanford, California 94305-5020, USA. ; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA. ; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK. ; Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA. ; Institut Genetique et Developpement, CNRS/University of Rennes, 35043 Rennes, France. ; CIRAD, Campus International de Baillarguet, TA B-110/A, 34398 Montpellier cedex 5, France. ; School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA. ; Department of Biology, University of Maryland, College Park, Maryland 20742, USA. ; Animal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel. ; Zoological Institute, University of Basel, CH-4051 Basel, Switzerland. ; 1] Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution &Biogeochemistry, CH-6047 Kastanienbaum, Switzerland [2] Division of Aquatic Ecology, Institute of Ecology &Evolution, University of Bern, CH-3012 Bern, Switzerland. ; MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK. ; Department of Integrative Biology, Center for Computational Biology and Bioinformatics; The University of Texas at Austin, Austin, Texas 78712, USA. ; Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution &Biogeochemistry, CH-6047 Kastanienbaum, Switzerland. ; Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan. ; Systematique, Adaptation, Evolution, National Museum of Natural History, 75005 Paris, France. ; Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK. ; Carnegie Institution of Washington, Department of Embryology, 3520 San Martin Drive Baltimore, Maryland 21218, USA. ; 1] Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan [2] National Cheng Kung University, Tainan City, 704 Taiwan. ; Gurdon Institute, Cambridge CB2 1QN, UK. ; 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden. ; 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Vertebrate and Health Genomics, The Genome Analysis Centre, Norwich NR18 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25186727" target="_blank"〉PubMed〈/a〉

Description: We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cuomo, Christina A -- Guldener, Ulrich -- Xu, Jin-Rong -- Trail, Frances -- Turgeon, B Gillian -- Di Pietro, Antonio -- Walton, Jonathan D -- Ma, Li-Jun -- Baker, Scott E -- Rep, Martijn -- Adam, Gerhard -- Antoniw, John -- Baldwin, Thomas -- Calvo, Sarah -- Chang, Yueh-Long -- Decaprio, David -- Gale, Liane R -- Gnerre, Sante -- Goswami, Rubella S -- Hammond-Kosack, Kim -- Harris, Linda J -- Hilburn, Karen -- Kennell, John C -- Kroken, Scott -- Magnuson, Jon K -- Mannhaupt, Gertrud -- Mauceli, Evan -- Mewes, Hans-Werner -- Mitterbauer, Rudolf -- Muehlbauer, Gary -- Munsterkotter, Martin -- Nelson, David -- O'donnell, Kerry -- Ouellet, Therese -- Qi, Weihong -- Quesneville, Hadi -- Roncero, M Isabel G -- Seong, Kye-Yong -- Tetko, Igor V -- Urban, Martin -- Waalwijk, Cees -- Ward, Todd J -- Yao, Jiqiang -- Birren, Bruce W -- Kistler, H Corby -- U54 HG003067/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1400-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17823352" target="_blank"〉PubMed〈/a〉

Description: We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785132/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785132/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wade, C M -- Giulotto, E -- Sigurdsson, S -- Zoli, M -- Gnerre, S -- Imsland, F -- Lear, T L -- Adelson, D L -- Bailey, E -- Bellone, R R -- Blocker, H -- Distl, O -- Edgar, R C -- Garber, M -- Leeb, T -- Mauceli, E -- MacLeod, J N -- Penedo, M C T -- Raison, J M -- Sharpe, T -- Vogel, J -- Andersson, L -- Antczak, D F -- Biagi, T -- Binns, M M -- Chowdhary, B P -- Coleman, S J -- Della Valle, G -- Fryc, S -- Guerin, G -- Hasegawa, T -- Hill, E W -- Jurka, J -- Kiialainen, A -- Lindgren, G -- Liu, J -- Magnani, E -- Mickelson, J R -- Murray, J -- Nergadze, S G -- Onofrio, R -- Pedroni, S -- Piras, M F -- Raudsepp, T -- Rocchi, M -- Roed, K H -- Ryder, O A -- Searle, S -- Skow, L -- Swinburne, J E -- Syvanen, A C -- Tozaki, T -- Valberg, S J -- Vaudin, M -- White, J R -- Zody, M C -- Broad Institute Genome Sequencing Platform -- Broad Institute Whole Genome Assembly Team -- Lander, E S -- Lindblad-Toh, K -- 098051/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Nov 6;326(5954):865-7. doi: 10.1126/science.1178158.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA. c.wade@usyd.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19892987" target="_blank"〉PubMed〈/a〉