%0 Journal Article %J Nature %D 2005 %T Generation and annotation of the DNA sequences of human chromosomes 2 and 4. %A Hillier, LaDeana W %A Graves, Tina A %A Fulton, Robert S %A Fulton, Lucinda A %A Pepin, Kymberlie H %A Minx, Patrick %A Wagner-McPherson, Caryn %A Layman, Dan %A Wylie, Kristine %A Sekhon, Mandeep %A Becker, Michael C %A Fewell, Ginger A %A Delehaunty, Kimberly D %A Miner, Tracie L %A Nash, William E %A Kremitzki, Colin %A Oddy, Lachlan %A Du, Hui %A Sun, Hui %A Bradshaw-Cordum, Holland %A Ali, Johar %A Carter, Jason %A Cordes, Matt %A Harris, Anthony %A Isak, Amber %A van Brunt, Andrew %A Nguyen, Christine %A Du, Feiyu %A Courtney, Laura %A Kalicki, Joelle %A Ozersky, Philip %A Abbott, Scott %A Armstrong, Jon %A Belter, Edward A %A Caruso, Lauren %A Cedroni, Maria %A Cotton, Marc %A Davidson, Teresa %A Desai, Anu %A Elliott, Glendoria %A Erb, Thomas %A Fronick, Catrina %A Gaige, Tony %A Haakenson, William %A Haglund, Krista %A Holmes, Andrea %A Harkins, Richard %A Kim, Kyung %A Kruchowski, Scott S %A Strong, Cynthia Madsen %A Grewal, Neenu %A Goyea, Ernest %A Hou, Shunfang %A Levy, Andrew %A Martinka, Scott %A Mead, Kelly %A McLellan, Michael D %A Meyer, Rick %A Randall-Maher, Jennifer %A Tomlinson, Chad %A Dauphin-Kohlberg, Sara %A Kozlowicz-Reilly, Amy %A Shah, Neha %A Swearengen-Shahid, Sharhonda %A Snider, Jacqueline %A Strong, Joseph T %A Thompson, Johanna %A Yoakum, Martin %A Leonard, Shawn %A Pearman, Charlene %A Trani, Lee %A Radionenko, Maxim %A Waligorski, Jason E %A Wang, Chunyan %A Rock, Susan M %A Tin-Wollam, Aye-Mon %A Maupin, Rachel %A Latreille, Phil %A Wendl, Michael C %A Yang, Shiaw-Pyng %A Pohl, Craig %A Wallis, John W %A Spieth, John %A Bieri, Tamberlyn A %A Berkowicz, Nicolas %A Nelson, Joanne O %A Osborne, John %A Ding, Li %A Meyer, Rekha %A Aniko Sabo %A Shotland, Yoram %A Sinha, Prashant %A Wohldmann, Patricia E %A Cook, Lisa L %A Hickenbotham, Matthew T %A Eldred, James %A Williams, Donald %A Jones, Thomas A %A She, Xinwei %A Ciccarelli, Francesca D %A Izaurralde, Elisa %A Taylor, James %A Schmutz, Jeremy %A Myers, Richard M %A Cox, David R %A Huang, Xiaoqiu %A McPherson, John D %A Mardis, Elaine R %A Clifton, Sandra W %A Warren, Wesley C %A Chinwalla, Asif T %A Eddy, Sean R %A Marra, Marco A %A Ovcharenko, Ivan %A Furey, Terrence S %A Miller, Webb %A Eichler, Evan E %A Bork, Peer %A Suyama, Mikita %A Torrents, David %A Waterston, Robert H %A Wilson, Richard K %K Animals %K Base Composition %K Base Sequence %K Centromere %K Chromosomes, Human, Pair 2 %K Chromosomes, Human, Pair 4 %K Conserved Sequence %K CpG Islands %K Euchromatin %K Expressed Sequence Tags %K Gene Duplication %K Genetic Variation %K Genomics %K Humans %K Molecular Sequence Data %K Physical Chromosome Mapping %K Polymorphism, Genetic %K Primates %K Proteins %K Pseudogenes %K Recombination, Genetic %K RNA, Messenger %K RNA, Untranslated %K Sequence Analysis, DNA %X

Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.

%B Nature %V 434 %P 724-31 %8 2005 Apr 07 %G eng %N 7034 %1 https://www.ncbi.nlm.nih.gov/pubmed/15815621?dopt=Abstract %R 10.1038/nature03466 %0 Journal Article %J Nat Genet %D 2004 %T Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. %A McClelland, Michael %A Sanderson, Kenneth E %A Clifton, Sandra W %A Latreille, Phil %A Porwollik, Steffen %A Aniko Sabo %A Meyer, Rekha %A Bieri, Tamberlyn %A Ozersky, Phil %A McLellan, Michael %A Harkins, C Richard %A Wang, Chunyan %A Nguyen, Christine %A Berghoff, Amy %A Elliott, Glendoria %A Kohlberg, Sara %A Strong, Cindy %A Du, Feiyu %A Carter, Jason %A Kremizki, Colin %A Layman, Dan %A Leonard, Shawn %A Sun, Hui %A Fulton, Lucinda %A Nash, William %A Miner, Tracie %A Minx, Patrick %A Delehaunty, Kim %A Fronick, Catrina %A Magrini, Vincent %A Nhan, Michael %A Warren, Wesley %A Florea, Liliana %A Spieth, John %A Wilson, Richard K %K Base Sequence %K Evolution, Molecular %K Gene Library %K Genetic Variation %K Genome Components %K Genome, Bacterial %K Humans %K Microarray Analysis %K Molecular Sequence Data %K Mutation %K Pseudogenes %K Salmonella paratyphi A %K Salmonella typhi %K Sequence Analysis, DNA %K Species Specificity %X

Salmonella enterica serovars often have a broad host range, and some cause both gastrointestinal and systemic disease. But the serovars Paratyphi A and Typhi are restricted to humans and cause only systemic disease. It has been estimated that Typhi arose in the last few thousand years. The sequence and microarray analysis of the Paratyphi A genome indicates that it is similar to the Typhi genome but suggests that it has a more recent evolutionary origin. Both genomes have independently accumulated many pseudogenes among their approximately 4,400 protein coding sequences: 173 in Paratyphi A and approximately 210 in Typhi. The recent convergence of these two similar genomes on a similar phenotype is subtly reflected in their genotypes: only 30 genes are degraded in both serovars. Nevertheless, these 30 genes include three known to be important in gastroenteritis, which does not occur in these serovars, and four for Salmonella-translocated effectors, which are normally secreted into host cells to subvert host functions. Loss of function also occurs by mutation in different genes in the same pathway (e.g., in chemotaxis and in the production of fimbriae).

%B Nat Genet %V 36 %P 1268-74 %8 2004 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/15531882?dopt=Abstract %R 10.1038/ng1470