%0 Journal Article %J Nature %D 2010 %T Complete Khoisan and Bantu genomes from southern Africa. %A Schuster, Stephan C %A Miller, Webb %A Ratan, Aakrosh %A Tomsho, Lynn P %A Giardine, Belinda %A Kasson, Lindsay R %A Harris, Robert S %A Petersen, Desiree C %A Zhao, Fangqing %A Qi, Ji %A Alkan, Can %A Kidd, Jeffrey M %A Sun, Yazhou %A Drautz, Daniela I %A Bouffard, Pascal %A Muzny, Donna M %A Reid, Jeffrey G %A Nazareth, Lynne V %A Wang, Qingyu %A Burhans, Richard %A Riemer, Cathy %A Wittekindt, Nicola E %A Moorjani, Priya %A Tindall, Elizabeth A %A Danko, Charles G %A Teo, Wee Siang %A Buboltz, Anne M %A Zhang, Zhenhai %A Ma, Qianyi %A Oosthuysen, Arno %A Steenkamp, Abraham W %A Oostuisen, Hermann %A Venter, Philippus %A Gajewski, John %A Zhang, Yu %A Pugh, B Franklin %A Makova, Kateryna D %A Nekrutenko, Anton %A Mardis, Elaine R %A Patterson, Nick %A Pringle, Tom H %A Chiaromonte, Francesca %A Mullikin, James C %A Eichler, Evan E %A Hardison, Ross C %A Gibbs, Richard A %A Harkins, Timothy T %A Hayes, Vanessa M %K Asian People %K Black People %K Ethnicity %K Exons %K Genetics, Medical %K Genome, Human %K Humans %K Phylogeny %K Polymorphism, Single Nucleotide %K South Africa %K White People %X

The genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is important for understanding human diversity. Studies based on mitochondrial and small sets of nuclear markers have shown that these hunter-gatherers, known as Khoisan, San, or Bushmen, are genetically divergent from other humans. However, until now, fully sequenced human genomes have been limited to recently diverged populations. Here we present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants. In terms of nucleotide substitutions, the Bushmen seem to be, on average, more different from each other than, for example, a European and an Asian. Observed genomic differences between the hunter-gatherers and others may help to pinpoint genetic adaptations to an agricultural lifestyle. Adding the described variants to current databases will facilitate inclusion of southern Africans in medical research efforts, particularly when family and medical histories can be correlated with genome-wide data.

%B Nature %V 463 %P 943-7 %8 2010 Feb 18 %G eng %N 7283 %1 https://www.ncbi.nlm.nih.gov/pubmed/20164927?dopt=Abstract %R 10.1038/nature08795 %0 Journal Article %J Genome Res %D 2007 %T 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. %A Miller, Webb %A Rosenbloom, Kate %A Hardison, Ross C %A Hou, Minmei %A Taylor, James %A Raney, Brian %A Burhans, Richard %A King, David C %A Baertsch, Robert %A Blankenberg, Daniel %A Kosakovsky Pond, Sergei L %A Nekrutenko, Anton %A Giardine, Belinda %A Harris, Robert S %A Tyekucheva, Svitlana %A Diekhans, Mark %A Pringle, Thomas H %A Murphy, William J %A Lesk, Arthur %A Weinstock, George M %A Lindblad-Toh, Kerstin %A Gibbs, Richard A %A Lander, Eric S %A Siepel, Adam %A Haussler, David %A Kent, W James %K Animals %K Base Sequence %K Cats %K Cattle %K Codon, Initiator %K Codon, Terminator %K Conserved Sequence %K Databases, Genetic %K Dogs %K Genome, Human %K Guinea Pigs %K Humans %K Mice %K Molecular Sequence Data %K Mutagenesis, Insertional %K Rabbits %K Rats %K Sequence Alignment %K Sequence Deletion %X

This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006 assembly) at http://genome.ucsc.edu, downloaded in bulk by anonymous FTP from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way, or analyzed with the Galaxy server at http://g2.bx.psu.edu. This article illustrates the power of this resource for exploring vertebrate and mammalian evolution, using three examples. First, we present several vignettes involving insertions and deletions within protein-coding regions, including a look at some human-specific indels. Then we study the extent to which start codons and stop codons in the human sequence are conserved in other species, showing that start codons are in general more poorly conserved than stop codons. Finally, an investigation of the phylogenetic depth of conservation for several classes of functional elements in the human genome reveals striking differences in the rates and modes of decay in alignability. Each functional class has a distinctive period of stringent constraint, followed by decays that allow (for the case of regulatory regions) or reject (for coding regions and ultraconserved elements) insertions and deletions.

%B Genome Res %V 17 %P 1797-808 %8 2007 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/17984227?dopt=Abstract %R 10.1101/gr.6761107 %0 Journal Article %J Nature %D 2004 %T Genome sequence of the Brown Norway rat yields insights into mammalian evolution. %A Gibbs, Richard A %A Weinstock, George M %A Metzker, Michael L %A Muzny, Donna M %A Sodergren, Erica J %A Scherer, Steven %A Scott, Graham %A Steffen, David %A Worley, Kim C %A Burch, Paula E %A Okwuonu, Geoffrey %A Hines, Sandra %A Lewis, Lora %A DeRamo, Christine %A Delgado, Oliver %A Dugan-Rocha, Shannon %A Miner, George %A Morgan, Margaret %A Hawes, Alicia %A Gill, Rachel %A Holt, Robert A %A Adams, Mark D %A Amanatides, Peter G %A Baden-Tillson, Holly %A Barnstead, Mary %A Chin, Soo %A Evans, Cheryl A %A Ferriera, Steve %A Fosler, Carl %A Glodek, Anna %A Gu, Zhiping %A Jennings, Don %A Kraft, Cheryl L %A Nguyen, Trixie %A Pfannkoch, Cynthia M %A Sitter, Cynthia %A Sutton, Granger G %A Venter, J Craig %A Woodage, Trevor %A Smith, Douglas %A Lee, Hong-Mei %A Gustafson, Erik %A Cahill, Patrick %A Kana, Arnold %A Doucette-Stamm, Lynn %A Weinstock, Keith %A Fechtel, Kim %A Weiss, Robert B %A Dunn, Diane M %A Green, Eric D %A Blakesley, Robert W %A Bouffard, Gerard G %A De Jong, Pieter J %A Osoegawa, Kazutoyo %A Zhu, Baoli %A Marra, Marco %A Schein, Jacqueline %A Bosdet, Ian %A Fjell, Chris %A Jones, Steven %A Krzywinski, Martin %A Mathewson, Carrie %A Siddiqui, Asim %A Wye, Natasja %A McPherson, John %A Zhao, Shaying %A Fraser, Claire M %A Shetty, Jyoti %A Shatsman, Sofiya %A Geer, Keita %A Chen, Yixin %A Abramzon, Sofyia %A Nierman, William C %A Havlak, Paul H %A Chen, Rui %A Durbin, K James %A Simons, Rain %A Ren, Yanru %A Song, Xing-Zhi %A Li, Bingshan %A Liu, Yue %A Qin, Xiang %A Cawley, Simon %A Worley, Kim C %A Cooney, A J %A D'Souza, Lisa M %A Martin, Kirt %A Wu, Jia Qian %A Gonzalez-Garay, Manuel L %A Jackson, Andrew R %A Kalafus, Kenneth J %A McLeod, Michael P %A Milosavljevic, Aleksandar %A Virk, Davinder %A Volkov, Andrei %A Wheeler, David A %A Zhang, Zhengdong %A Bailey, Jeffrey A %A Eichler, Evan E %A Tuzun, Eray %A Birney, Ewan %A Mongin, Emmanuel %A Ureta-Vidal, Abel %A Woodwark, Cara %A Zdobnov, Evgeny %A Bork, Peer %A Suyama, Mikita %A Torrents, David %A Alexandersson, Marina %A Trask, Barbara J %A Young, Janet M %A Huang, Hui %A Wang, Huajun %A Xing, Heming %A Daniels, Sue %A Gietzen, Darryl %A Schmidt, Jeanette %A Stevens, Kristian %A Vitt, Ursula %A Wingrove, Jim %A Camara, Francisco %A Mar Albà, M %A Abril, Josep F %A Guigó, Roderic %A Smit, Arian %A Dubchak, Inna %A Rubin, Edward M %A Couronne, Olivier %A Poliakov, Alexander %A Hübner, Norbert %A Ganten, Detlev %A Goesele, Claudia %A Hummel, Oliver %A Kreitler, Thomas %A Lee, Young-Ae %A Monti, Jan %A Schulz, Herbert %A Zimdahl, Heike %A Himmelbauer, Heinz %A Lehrach, Hans %A Jacob, Howard J %A Bromberg, Susan %A Gullings-Handley, Jo %A Jensen-Seaman, Michael I %A Kwitek, Anne E %A Lazar, Jozef %A Pasko, Dean %A Tonellato, Peter J %A Twigger, Simon %A Ponting, Chris P %A Duarte, Jose M %A Rice, Stephen %A Goodstadt, Leo %A Beatson, Scott A %A Emes, Richard D %A Winter, Eitan E %A Webber, Caleb %A Brandt, Petra %A Nyakatura, Gerald %A Adetobi, Margaret %A Chiaromonte, Francesca %A Elnitski, Laura %A Eswara, Pallavi %A Hardison, Ross C %A Hou, Minmei %A Kolbe, Diana %A Makova, Kateryna %A Miller, Webb %A Nekrutenko, Anton %A Riemer, Cathy %A Schwartz, Scott %A Taylor, James %A Yang, Shan %A Zhang, Yi %A Lindpaintner, Klaus %A Andrews, T Dan %A Caccamo, Mario %A Clamp, Michele %A Clarke, Laura %A Curwen, Valerie %A Durbin, Richard %A Eyras, Eduardo %A Searle, Stephen M %A Cooper, Gregory M %A Batzoglou, Serafim %A Brudno, Michael %A Sidow, Arend %A Stone, Eric A %A Venter, J Craig %A Payseur, Bret A %A Bourque, Guillaume %A López-Otín, Carlos %A Puente, Xose S %A Chakrabarti, Kushal %A Chatterji, Sourav %A Dewey, Colin %A Pachter, Lior %A Bray, Nicolas %A Yap, Von Bing %A Caspi, Anat %A Tesler, Glenn %A Pevzner, Pavel A %A Haussler, David %A Roskin, Krishna M %A Baertsch, Robert %A Clawson, Hiram %A Furey, Terrence S %A Hinrichs, Angie S %A Karolchik, Donna %A Kent, William J %A Rosenbloom, Kate R %A Trumbower, Heather %A Weirauch, Matt %A Cooper, David N %A Stenson, Peter D %A Ma, Bin %A Brent, Michael %A Arumugam, Manimozhiyan %A Shteynberg, David %A Copley, Richard R %A Taylor, Martin S %A Riethman, Harold %A Mudunuri, Uma %A Peterson, Jane %A Guyer, Mark %A Felsenfeld, Adam %A Old, Susan %A Mockrin, Stephen %A Collins, Francis %K Animals %K Base Composition %K Centromere %K Chromosomes, Mammalian %K CpG Islands %K DNA Transposable Elements %K DNA, Mitochondrial %K Evolution, Molecular %K Gene Duplication %K Genome %K Genomics %K Humans %K Introns %K Male %K Mice %K Models, Molecular %K Mutagenesis %K Polymorphism, Single Nucleotide %K Rats %K Rats, Inbred BN %K Regulatory Sequences, Nucleic Acid %K Retroelements %K RNA Splice Sites %K RNA, Untranslated %K Sequence Analysis, DNA %K Telomere %X

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

%B Nature %V 428 %P 493-521 %8 2004 Apr 01 %G eng %N 6982 %1 https://www.ncbi.nlm.nih.gov/pubmed/15057822?dopt=Abstract %R 10.1038/nature02426