%0 Journal Article %J Microbiol Spectr %D 2021 %T Primary Infection May Be an Underlying Factor Contributing to Lethal Hemorrhagic Disease Caused by Elephant Endotheliotropic Herpesvirus 3 in African Elephants (). %A Pursell, Taylor %A Spencer Clinton, Jennifer L %A Tan, Jie %A Peng, Rongsheng %A Xiang Qin %A Harshavardhan Doddapaneni %A Menon, Vipin %A Momin, Zeineen %A Kottapalli, Kavya %A Howard, Lauren %A Latimer, Erin %A Heaggans, Sarah %A Hayward, Gary S %A Ling, Paul D %K Animals %K Animals, Zoo %K Antibodies, Viral %K Elephants %K Female %K Hemorrhagic Disorders %K Herpesvirus 3, Equid %K Male %K Serologic Tests %K Viral Zoonoses %X

Distinct but related species of elephant endotheliotropic herpesviruses (EEHVs) circulate within Asian and African elephant populations. Primary infection with EEHVs endemic among Asian elephants can cause clinical illness and lethal EEHV hemorrhagic disease (EEHV-HD). The degree to which this occurs among African elephants has not been fully established. Recent cases of EEHV-HD caused by the EEHV3 species in African elephants housed in North American zoos has heightened concern about the susceptibility of this elephant species to EEHV-HD. In this study, we utilize the luciferase immunoprecipitation system (LIPS) to generate a serological assay specific for EEHV3 in African elephants by detecting antibodies against the EEHV3 E34 protein. The results showed that the majority of tested elephants from four separate and genetically unrelated herds, including five elephants that survived clinical illness associated with EEHV3, were positive for prior infection with EEHV3. However, African elephants who succumbed to EEHV3-HD were seronegative for EEHV3 prior to lethal infection. This supports the hypothesis that fatal EEHV-HD caused by EEHV3 is associated with primary infection rather than reactivation of latent virus. Lastly, we observed that African elephants, like Asian elephants, acquire abundant anti-EEHV antibodies prenatally and that anti-EEHV3 specific antibodies were either never detected or declined to undetectable levels in those animals that died from lethal disease following EEHV3 infection. Prior to 2019, only five cases of clinical disease from EEHV infection among African elephants had been documented. Since 2019, there have been at least seven EEHV-HD cases in North American zoos, resulting in three fatalities, all associated with EEHV3. Evidence is accumulating to suggest that EEHV-associated clinical illness and death among Asian elephants is due to primary infection and may be associated with waning anti-EEHV antibody levels in young elephants. The development of the EEHV3 serological test described in this study enabled us to confirm that similar dynamics may be contributing to EEHV-HD in African elephants. The ability to screen for EEHV immune status in African elephant calves will have a major impact on managing captive African elephant herds and will provide new tools for investigating and understanding EEHV in wild populations.

%B Microbiol Spectr %V 9 %P e0098321 %8 2021 Oct 31 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/34668724?dopt=Abstract %R 10.1128/Spectrum.00983-21 %0 Journal Article %J Int J Epidemiol %D 2020 %T Cohort Profile: The Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment Protocol (RIGHT Protocol). %A Bielinski, Suzette J %A St Sauver, Jennifer L %A Olson, Janet E %A Larson, Nicholas B %A Black, John L %A Steven E Scherer %A Bernard, Matthew E %A Eric Boerwinkle %A Borah, Bijan J %A Caraballo, Pedro J %A Curry, Timothy B %A Harshavardhan Doddapaneni %A Formea, Christine M %A Freimuth, Robert R %A Richard A Gibbs %A Giri, Jyothsna %A Hathcock, Matthew A %A Jianhong Hu %A Jacobson, Debra J %A Jones, Leila A %A Sara E Kalla %A Koep, Tyler H %A Korchina, Viktoriya %A Kovar, Christie L %A Lee, Sandra %A Liu, Hongfang %A Matey, Eric T %A McGree, Michaela E %A McAllister, Tammy M %A Moyer, Ann M %A Donna M Muzny %A Nicholson, Wayne T %A Oyen, Lance J %A Xiang Qin %A Raj, Ritika %A Roger, Véronique L %A Rohrer Vitek, Carolyn R %A Ross, Jason L %A Sharp, Richard R %A Takahashi, Paul Y %A Eric Venner %A Kimberly Walker %A Wang, Liwei %A Wang, Qiaoyan %A Wright, Jessica A %A Wu, Tsung-Jung %A Wang, Liewei %A Weinshilboum, Richard M %K Clinical Protocols %K Cohort Studies %K Female %K Genomics %K Humans %K Male %K Pharmacogenetics %K Precision Medicine %B Int J Epidemiol %V 49 %P 23-24k %8 2020 Feb 01 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31378813?dopt=Abstract %R 10.1093/ije/dyz123 %0 Journal Article %J PLoS One %D 2013 %T Metagenomic analyses of alcohol induced pathogenic alterations in the intestinal microbiome and the effect of Lactobacillus rhamnosus GG treatment. %A Bull-Otterson, Lara %A Feng, Wenke %A Kirpich, Irina %A Wang, Yuhua %A Qin, Xiang %A Liu, Yanlong %A Gobejishvili, Leila %A Joshi-Barve, Swati %A Ayvaz, Tulin %A Petrosino, Joseph %A Kong, Maiying %A Barker, David %A McClain, Craig %A Barve, Shirish %K Animals %K Anti-Infective Agents, Local %K Bacteria %K Biodiversity %K Claudin-1 %K Ethanol %K Feces %K Gene Expression %K Genetic Variation %K Hydrogen-Ion Concentration %K Intestinal Mucosa %K Intestines %K Lacticaseibacillus rhamnosus %K Liver Diseases, Alcoholic %K Male %K Metagenome %K Metagenomics %K Mice %K Mice, Inbred C57BL %K Probiotics %K Reverse Transcriptase Polymerase Chain Reaction %K RNA, Ribosomal, 16S %K Sequence Analysis, DNA %K Species Specificity %K Zonula Occludens-1 Protein %X

Enteric dysbiosis plays an essential role in the pathogenesis of alcoholic liver disease (ALD). Detailed characterization of the alterations in the gut microbiome is needed for understanding their pathogenic role in ALD and developing effective therapeutic approaches using probiotic supplementation. Mice were fed liquid Lieber-DeCarli diet without or with alcohol (5% v/v) for 6 weeks. A subset of mice were administered the probiotic Lactobacillus rhamnosus GG (LGG) from 6 to 8 weeks. Indicators of intestinal permeability, hepatic steatosis, inflammation and injury were evaluated. Metagenomic analysis of the gut microbiome was performed by analyzing the fecal DNA by amplification of the V3-V5 regions of the 16S rRNA gene and large-scale parallel pyrosequencing on the 454 FLX Titanium platform. Chronic ethanol feeding caused a decline in the abundance of both Bacteriodetes and Firmicutes phyla, with a proportional increase in the gram negative Proteobacteria and gram positive Actinobacteria phyla; the bacterial genera that showed the biggest expansion were the gram negative alkaline tolerant Alcaligenes and gram positive Corynebacterium. Commensurate with the qualitative and quantitative alterations in the microbiome, ethanol caused an increase in plasma endotoxin, fecal pH, hepatic inflammation and injury. Notably, the ethanol-induced pathogenic changes in the microbiome and the liver were prevented by LGG supplementation. Overall, significant alterations in the gut microbiome over time occur in response to chronic alcohol exposure and correspond to increases in intestinal barrier dysfunction and development of ALD. Moreover, the altered bacterial communities of the gut may serve as significant therapeutic target for the prevention/treatment of chronic alcohol intake induced intestinal barrier dysfunction and liver disease.

%B PLoS One %V 8 %P e53028 %8 2013 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/23326376?dopt=Abstract %R 10.1371/journal.pone.0053028 %0 Journal Article %J PLoS Negl Trop Dis %D 2012 %T Whole genome sequence of Treponema pallidum ssp. pallidum, strain Mexico A, suggests recombination between yaws and syphilis strains. %A Pětrošová, Helena %A Zobaníková, Marie %A Čejková, Darina %A Mikalová, Lenka %A Pospíšilová, Petra %A Strouhal, Michal %A Chen, Lei %A Qin, Xiang %A Muzny, Donna M %A Weinstock, George M %A Smajs, David %K DNA, Bacterial %K Genome, Bacterial %K Humans %K Male %K Mexico %K Molecular Sequence Data %K Open Reading Frames %K Recombination, Genetic %K Sequence Analysis, DNA %K Synteny %K Syphilis %K Treponema pallidum %K Yaws %X

BACKGROUND: Treponema pallidum ssp. pallidum (TPA), the causative agent of syphilis, and Treponema pallidum ssp. pertenue (TPE), the causative agent of yaws, are closely related spirochetes causing diseases with distinct clinical manifestations. The TPA Mexico A strain was isolated in 1953 from male, with primary syphilis, living in Mexico. Attempts to cultivate TPA Mexico A strain under in vitro conditions have revealed lower growth potential compared to other tested TPA strains.

METHODOLOGY/PRINCIPAL FINDINGS: The complete genome sequence of the TPA Mexico A strain was determined using the Illumina sequencing technique. The genome sequence assembly was verified using the whole genome fingerprinting technique and the final sequence was annotated. The genome size of the Mexico A strain was determined to be 1,140,038 bp with 1,035 predicted ORFs. The Mexico A genome sequence was compared to the whole genome sequences of three TPA (Nichols, SS14 and Chicago) and three TPE (CDC-2, Samoa D and Gauthier) strains. No large rearrangements in the Mexico A genome were found and the identified nucleotide changes occurred most frequently in genes encoding putative virulence factors. Nevertheless, the genome of the Mexico A strain, revealed two genes (TPAMA_0326 (tp92) and TPAMA_0488 (mcp2-1)) which combine TPA- and TPE- specific nucleotide sequences. Both genes were found to be under positive selection within TPA strains and also between TPA and TPE strains.

CONCLUSIONS/SIGNIFICANCE: The observed mosaic character of the TPAMA_0326 and TPAMA_0488 loci is likely a result of inter-strain recombination between TPA and TPE strains during simultaneous infection of a single host suggesting horizontal gene transfer between treponemal subspecies.

%B PLoS Negl Trop Dis %V 6 %P e1832 %8 2012 %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/23029591?dopt=Abstract %R 10.1371/journal.pntd.0001832 %0 Journal Article %J Gastroenterology %D 2011 %T Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. %A Saulnier, Delphine M %A Riehle, Kevin %A Mistretta, Toni-Ann %A Diaz, Maria-Alejandra %A Mandal, Debasmita %A Raza, Sabeen %A Weidler, Erica M %A Qin, Xiang %A Coarfa, Cristian %A Milosavljevic, Aleksandar %A Petrosino, Joseph F %A Highlander, Sarah %A Gibbs, Richard %A Lynch, Susan V %A Shulman, Robert J %A Versalovic, James %K Abdominal Pain %K Case-Control Studies %K Child %K DNA Probes %K Female %K Gastrointestinal Tract %K Haemophilus parainfluenzae %K Humans %K Incidence %K Irritable Bowel Syndrome %K Male %K Metagenome %K Phenotype %K Phylogeny %K RNA, Ribosomal, 16S %K Ruminococcus %X

BACKGROUND & AIMS: The intestinal microbiomes of healthy children and pediatric patients with irritable bowel syndrome (IBS) are not well defined. Studies in adults have indicated that the gastrointestinal microbiota could be involved in IBS.

METHODS: We analyzed 71 samples from 22 children with IBS (pediatric Rome III criteria) and 22 healthy children, ages 7-12 years, by 16S ribosomal RNA gene sequencing, with an average of 54,287 reads/stool sample (average 454 read length = 503 bases). Data were analyzed using phylogenetic-based clustering (Unifrac), or an operational taxonomic unit (OTU) approach using a supervised machine learning tool (randomForest). Most samples were also hybridized to a microarray that can detect 8741 bacterial taxa (16S rRNA PhyloChip).

RESULTS: Microbiomes associated with pediatric IBS were characterized by a significantly greater percentage of the class γ-proteobacteria (0.07% vs 0.89% of total bacteria, respectively; P < .05); 1 prominent component of this group was Haemophilus parainfluenzae. Differences highlighted by 454 sequencing were confirmed by high-resolution PhyloChip analysis. Using supervised learning techniques, we were able to classify different subtypes of IBS with a success rate of 98.5%, using limited sets of discriminant bacterial species. A novel Ruminococcus-like microbe was associated with IBS, indicating the potential utility of microbe discovery for gastrointestinal disorders. A greater frequency of pain correlated with an increased abundance of several bacterial taxa from the genus Alistipes.

CONCLUSIONS: Using 16S metagenomics by PhyloChip DNA hybridization and deep 454 pyrosequencing, we associated specific microbiome signatures with pediatric IBS. These findings indicate the important association between gastrointestinal microbes and IBS in children; these approaches might be used in diagnosis of functional bowel disorders in pediatric patients.

%B Gastroenterology %V 141 %P 1782-91 %8 2011 Nov %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/21741921?dopt=Abstract %R 10.1053/j.gastro.2011.06.072 %0 Journal Article %J PLoS One %D 2010 %T Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential. %A Yeoman, Carl J %A Yildirim, Suleyman %A Thomas, Susan M %A Durkin, A Scott %A Torralba, Manolito %A Sutton, Granger %A Buhay, Christian J %A Ding, Yan %A Dugan-Rocha, Shannon P %A Muzny, Donna M %A Qin, Xiang %A Gibbs, Richard A %A Leigh, Steven R %A Stumpf, Rebecca %A White, Bryan A %A Highlander, Sarah K %A Nelson, Karen E %A Wilson, Brenda A %K Bacterial Proteins %K Female %K Gardnerella vaginalis %K Genomics %K Humans %K Male %K Molecular Sequence Data %K Phylogeny %K Vagina %K Vaginosis, Bacterial %K Virulence %X

BACKGROUND: Gardnerella vaginalis is described as a common vaginal bacterial species whose presence correlates strongly with bacterial vaginosis (BV). Here we report the genome sequencing and comparative analyses of three strains of G. vaginalis. Strains 317 (ATCC 14019) and 594 (ATCC 14018) were isolated from the vaginal tracts of women with symptomatic BV, while Strain 409-05 was isolated from a healthy, asymptomatic individual with a Nugent score of 9.

PRINCIPAL FINDINGS: Substantial genomic rearrangement and heterogeneity were observed that appeared to have resulted from both mobile elements and substantial lateral gene transfer. These genomic differences translated to differences in metabolic potential. All strains are equipped with significant virulence potential, including genes encoding the previously described vaginolysin, pili for cytoadhesion, EPS biosynthetic genes for biofilm formation, and antimicrobial resistance systems, We also observed systems promoting multi-drug and lantibiotic extrusion. All G. vaginalis strains possess a large number of genes that may enhance their ability to compete with and exclude other vaginal colonists. These include up to six toxin-antitoxin systems and up to nine additional antitoxins lacking cognate toxins, several of which are clustered within each genome. All strains encode bacteriocidal toxins, including two lysozyme-like toxins produced uniquely by strain 409-05. Interestingly, the BV isolates encode numerous proteins not found in strain 409-05 that likely increase their pathogenic potential. These include enzymes enabling mucin degradation, a trait previously described to strongly correlate with BV, although commonly attributed to non-G. vaginalis species.

CONCLUSIONS: Collectively, our results indicate that all three strains are able to thrive in vaginal environments, and therein the BV isolates are capable of occupying a niche that is unique from 409-05. Each strain has significant virulence potential, although genomic and metabolic differences, such as the ability to degrade mucin, indicate that the detection of G. vaginalis in the vaginal tract provides only partial information on the physiological potential of the organism.

%B PLoS One %V 5 %P e12411 %8 2010 Aug 26 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/20865041?dopt=Abstract %R 10.1371/journal.pone.0012411 %0 Journal Article %J Science %D 2009 %T The genome sequence of taurine cattle: a window to ruminant biology and evolution. %A Elsik, Christine G %A Tellam, Ross L %A Worley, Kim C %A Gibbs, Richard A %A Muzny, Donna M %A Weinstock, George M %A Adelson, David L %A Eichler, Evan E %A Elnitski, Laura %A Guigó, Roderic %A Hamernik, Debora L %A Kappes, Steve M %A Lewin, Harris A %A Lynn, David J %A Nicholas, Frank W %A Reymond, Alexandre %A Rijnkels, Monique %A Skow, Loren C %A Zdobnov, Evgeny M %A Schook, Lawrence %A Womack, James %A Alioto, Tyler %A Antonarakis, Stylianos E %A Astashyn, Alex %A Chapple, Charles E %A Chen, Hsiu-Chuan %A Chrast, Jacqueline %A Camara, Francisco %A Ermolaeva, Olga %A Henrichsen, Charlotte N %A Hlavina, Wratko %A Kapustin, Yuri %A Kiryutin, Boris %A Kitts, Paul %A Kokocinski, Felix %A Landrum, Melissa %A Maglott, Donna %A Pruitt, Kim %A Sapojnikov, Victor %A Searle, Stephen M %A Solovyev, Victor %A Souvorov, Alexandre %A Ucla, Catherine %A Wyss, Carine %A Anzola, Juan M %A Gerlach, Daniel %A Elhaik, Eran %A Graur, Dan %A Reese, Justin T %A Edgar, Robert C %A McEwan, John C %A Payne, Gemma M %A Raison, Joy M %A Junier, Thomas %A Kriventseva, Evgenia V %A Eyras, Eduardo %A Plass, Mireya %A Donthu, Ravikiran %A Larkin, Denis M %A Reecy, James %A Yang, Mary Q %A Chen, Lin %A Cheng, Ze %A Chitko-McKown, Carol G %A Liu, George E %A Matukumalli, Lakshmi K %A Song, Jiuzhou %A Zhu, Bin %A Bradley, Daniel G %A Brinkman, Fiona S L %A Lau, Lilian P L %A Whiteside, Matthew D %A Walker, Angela %A Wheeler, Thomas T %A Casey, Theresa %A German, J Bruce %A Lemay, Danielle G %A Maqbool, Nauman J %A Molenaar, Adrian J %A Seo, Seongwon %A Stothard, Paul %A Baldwin, Cynthia L %A Baxter, Rebecca %A Brinkmeyer-Langford, Candice L %A Brown, Wendy C %A Childers, Christopher P %A Connelley, Timothy %A Ellis, Shirley A %A Fritz, Krista %A Glass, Elizabeth J %A Herzig, Carolyn T A %A Iivanainen, Antti %A Lahmers, Kevin K %A Bennett, Anna K %A Dickens, C Michael %A Gilbert, James G R %A Hagen, Darren E %A Salih, Hanni %A Aerts, Jan %A Caetano, Alexandre R %A Dalrymple, Brian %A Garcia, Jose Fernando %A Gill, Clare A %A Hiendleder, Stefan G %A Memili, Erdogan %A Spurlock, Diane %A Williams, John L %A Alexander, Lee %A Brownstein, Michael J %A Guan, Leluo %A Holt, Robert A %A Jones, Steven J M %A Marra, Marco A %A Moore, Richard %A Moore, Stephen S %A Roberts, Andy %A Taniguchi, Masaaki %A Waterman, Richard C %A Chacko, Joseph %A Chandrabose, Mimi M %A Cree, Andy %A Dao, Marvin Diep %A Dinh, Huyen H %A Gabisi, Ramatu Ayiesha %A Hines, Sandra %A Hume, Jennifer %A Jhangiani, Shalini N %A Joshi, Vandita %A Kovar, Christie L %A Lewis, Lora R %A Liu, Yih-Shin %A Lopez, John %A Morgan, Margaret B %A Nguyen, Ngoc Bich %A Okwuonu, Geoffrey O %A Ruiz, San Juana %A Santibanez, Jireh %A Wright, Rita A %A Buhay, Christian %A Ding, Yan %A Dugan-Rocha, Shannon %A Herdandez, Judith %A Holder, Michael %A Sabo, Aniko %A Egan, Amy %A Goodell, Jason %A Wilczek-Boney, Katarzyna %A Fowler, Gerald R %A Hitchens, Matthew Edward %A Lozado, Ryan J %A Moen, Charles %A Steffen, David %A Warren, James T %A Zhang, Jingkun %A Chiu, Readman %A Schein, Jacqueline E %A Durbin, K James %A Havlak, Paul %A Jiang, Huaiyang %A Liu, Yue %A Qin, Xiang %A Ren, Yanru %A Shen, Yufeng %A Song, Henry %A Bell, Stephanie Nicole %A Davis, Clay %A Johnson, Angela Jolivet %A Lee, Sandra %A Nazareth, Lynne V %A Patel, Bella Mayurkumar %A Pu, Ling-Ling %A Vattathil, Selina %A Williams, Rex Lee %A Curry, Stacey %A Hamilton, Cerissa %A Sodergren, Erica %A Wheeler, David A %A Barris, Wes %A Bennett, Gary L %A Eggen, André %A Green, Ronnie D %A Harhay, Gregory P %A Hobbs, Matthew %A Jann, Oliver %A Keele, John W %A Kent, Matthew P %A Lien, Sigbjørn %A McKay, Stephanie D %A McWilliam, Sean %A Ratnakumar, Abhirami %A Schnabel, Robert D %A Smith, Timothy %A Snelling, Warren M %A Sonstegard, Tad S %A Stone, Roger T %A Sugimoto, Yoshikazu %A Takasuga, Akiko %A Taylor, Jeremy F %A Van Tassell, Curtis P %A Macneil, Michael D %A Abatepaulo, Antonio R R %A Abbey, Colette A %A Ahola, Virpi %A Almeida, Iassudara G %A Amadio, Ariel F %A Anatriello, Elen %A Bahadue, Suria M %A Biase, Fernando H %A Boldt, Clayton R %A Carroll, Jeffery A %A Carvalho, Wanessa A %A Cervelatti, Eliane P %A Chacko, Elsa %A Chapin, Jennifer E %A Cheng, Ye %A Choi, Jungwoo %A Colley, Adam J %A de Campos, Tatiana A %A De Donato, Marcos %A Santos, Isabel K F de Miranda %A de Oliveira, Carlo J F %A Deobald, Heather %A Devinoy, Eve %A Donohue, Kaitlin E %A Dovc, Peter %A Eberlein, Annett %A Fitzsimmons, Carolyn J %A Franzin, Alessandra M %A Garcia, Gustavo R %A Genini, Sem %A Gladney, Cody J %A Grant, Jason R %A Greaser, Marion L %A Green, Jonathan A %A Hadsell, Darryl L %A Hakimov, Hatam A %A Halgren, Rob %A Harrow, Jennifer L %A Hart, Elizabeth A %A Hastings, Nicola %A Hernandez, Marta %A Hu, Zhi-Liang %A Ingham, Aaron %A Iso-Touru, Terhi %A Jamis, Catherine %A Jensen, Kirsty %A Kapetis, Dimos %A Kerr, Tovah %A Khalil, Sari S %A Khatib, Hasan %A Kolbehdari, Davood %A Kumar, Charu G %A Kumar, Dinesh %A Leach, Richard %A Lee, Justin C-M %A Li, Changxi %A Logan, Krystin M %A Malinverni, Roberto %A Marques, Elisa %A Martin, William F %A Martins, Natalia F %A Maruyama, Sandra R %A Mazza, Raffaele %A McLean, Kim L %A Medrano, Juan F %A Moreno, Barbara T %A Moré, Daniela D %A Muntean, Carl T %A Nandakumar, Hari P %A Nogueira, Marcelo F G %A Olsaker, Ingrid %A Pant, Sameer D %A Panzitta, Francesca %A Pastor, Rosemeire C P %A Poli, Mario A %A Poslusny, Nathan %A Rachagani, Satyanarayana %A Ranganathan, Shoba %A Razpet, Andrej %A Riggs, Penny K %A Rincon, Gonzalo %A Rodriguez-Osorio, Nelida %A Rodriguez-Zas, Sandra L %A Romero, Natasha E %A Rosenwald, Anne %A Sando, Lillian %A Schmutz, Sheila M %A Shen, Libing %A Sherman, Laura %A Southey, Bruce R %A Lutzow, Ylva Strandberg %A Sweedler, Jonathan V %A Tammen, Imke %A Telugu, Bhanu Prakash V L %A Urbanski, Jennifer M %A Utsunomiya, Yuri T %A Verschoor, Chris P %A Waardenberg, Ashley J %A Wang, Zhiquan %A Ward, Robert %A Weikard, Rosemarie %A Welsh, Thomas H %A White, Stephen N %A Wilming, Laurens G %A Wunderlich, Kris R %A Yang, Jianqi %A Zhao, Feng-Qi %K Alternative Splicing %K Animals %K Animals, Domestic %K Biological Evolution %K Cattle %K Evolution, Molecular %K Female %K Genetic Variation %K Genome %K Humans %K Male %K MicroRNAs %K Molecular Sequence Data %K Proteins %K Sequence Analysis, DNA %K Species Specificity %K Synteny %X

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

%B Science %V 324 %P 522-8 %8 2009 Apr 24 %G eng %N 5926 %1 https://www.ncbi.nlm.nih.gov/pubmed/19390049?dopt=Abstract %R 10.1126/science.1169588 %0 Journal Article %J Science %D 2009 %T Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. %A Gibbs, Richard A %A Taylor, Jeremy F %A Van Tassell, Curtis P %A Barendse, William %A Eversole, Kellye A %A Gill, Clare A %A Green, Ronnie D %A Hamernik, Debora L %A Kappes, Steven M %A Lien, Sigbjørn %A Matukumalli, Lakshmi K %A McEwan, John C %A Nazareth, Lynne V %A Schnabel, Robert D %A Weinstock, George M %A Wheeler, David A %A Ajmone-Marsan, Paolo %A Boettcher, Paul J %A Caetano, Alexandre R %A Garcia, Jose Fernando %A Hanotte, Olivier %A Mariani, Paola %A Skow, Loren C %A Sonstegard, Tad S %A Williams, John L %A Diallo, Boubacar %A Hailemariam, Lemecha %A Martinez, Mario L %A Morris, Chris A %A Silva, Luiz O C %A Spelman, Richard J %A Mulatu, Woudyalew %A Zhao, Keyan %A Abbey, Colette A %A Agaba, Morris %A Araujo, Flábio R %A Bunch, Rowan J %A Burton, James %A Gorni, Chiara %A Olivier, Hanotte %A Harrison, Blair E %A Luff, Bill %A Machado, Marco A %A Mwakaya, Joel %A Plastow, Graham %A Sim, Warren %A Smith, Timothy %A Thomas, Merle B %A Valentini, Alessio %A Williams, Paul %A Womack, James %A Woolliams, John A %A Liu, Yue %A Qin, Xiang %A Worley, Kim C %A Gao, Chuan %A Jiang, Huaiyang %A Moore, Stephen S %A Ren, Yanru %A Song, Xing-Zhi %A Bustamante, Carlos D %A Hernandez, Ryan D %A Muzny, Donna M %A Patil, Shobha %A San Lucas, Anthony %A Fu, Qing %A Kent, Matthew P %A Vega, Richard %A Matukumalli, Aruna %A McWilliam, Sean %A Sclep, Gert %A Bryc, Katarzyna %A Choi, Jungwoo %A Gao, Hong %A Grefenstette, John J %A Murdoch, Brenda %A Stella, Alessandra %A Villa-Angulo, Rafael %A Wright, Mark %A Aerts, Jan %A Jann, Oliver %A Negrini, Riccardo %A Goddard, Mike E %A Hayes, Ben J %A Bradley, Daniel G %A Barbosa da Silva, Marcos %A Lau, Lilian P L %A Liu, George E %A Lynn, David J %A Panzitta, Francesca %A Dodds, Ken G %K Animals %K Breeding %K Cattle %K Female %K Gene Frequency %K Genetic Variation %K Genome %K Male %K Molecular Sequence Data %K Mutation %K Polymorphism, Single Nucleotide %K Population Density %X

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.

%B Science %V 324 %P 528-32 %8 2009 Apr 24 %G eng %N 5926 %1 https://www.ncbi.nlm.nih.gov/pubmed/19390050?dopt=Abstract %R 10.1126/science.1167936 %0 Journal Article %J Nature %D 2008 %T The complete genome of an individual by massively parallel DNA sequencing. %A Wheeler, David A %A Srinivasan, Maithreyan %A Egholm, Michael %A Shen, Yufeng %A Chen, Lei %A McGuire, Amy %A He, Wen %A Chen, Yi-Ju %A Makhijani, Vinod %A Roth, G Thomas %A Gomes, Xavier %A Tartaro, Karrie %A Niazi, Faheem %A Turcotte, Cynthia L %A Irzyk, Gerard P %A Lupski, James R %A Chinault, Craig %A Song, Xing-Zhi %A Liu, Yue %A Yuan, Ye %A Nazareth, Lynne %A Xiang Qin %A Donna M Muzny %A Margulies, Marcel %A Weinstock, George M %A Richard A Gibbs %A Rothberg, Jonathan M %K Alleles %K Computational Biology %K Genetic Predisposition to Disease %K Genetic Variation %K Genome, Human %K Genomics %K Genotype %K Humans %K Individuality %K Male %K Oligonucleotide Array Sequence Analysis %K Polymorphism, Single Nucleotide %K Reproducibility of Results %K Sensitivity and Specificity %K Sequence Alignment %K Sequence Analysis, DNA %K Software %X

The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2-40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'.

%B Nature %V 452 %P 872-6 %8 2008 Apr 17 %G eng %N 7189 %1 https://www.ncbi.nlm.nih.gov/pubmed/18421352?dopt=Abstract %R 10.1038/nature06884 %0 Journal Article %J Science %D 2007 %T Evolutionary and biomedical insights from the rhesus macaque genome. %A Richard A Gibbs %A Jeffrey Rogers %A Katze, Michael G %A Bumgarner, Roger %A Weinstock, George M %A Mardis, Elaine R %A Remington, Karin A %A Strausberg, Robert L %A Venter, J Craig %A Wilson, Richard K %A Batzer, Mark A %A Bustamante, Carlos D %A Eichler, Evan E %A Hahn, Matthew W %A Hardison, Ross C %A Makova, Kateryna D %A Miller, Webb %A Milosavljevic, Aleksandar %A Palermo, Robert E %A Siepel, Adam %A Sikela, James M %A Attaway, Tony %A Bell, Stephanie %A Bernard, Kelly E %A Buhay, Christian J %A Chandrabose, Mimi N %A Dao, Marvin %A Davis, Clay %A Delehaunty, Kimberly D %A Ding, Yan %A Dinh, Huyen H %A Dugan-Rocha, Shannon %A Fulton, Lucinda A %A Gabisi, Ramatu Ayiesha %A Garner, Toni T %A Godfrey, Jennifer %A Hawes, Alicia C %A Hernandez, Judith %A Hines, Sandra %A Holder, Michael %A Hume, Jennifer %A Jhangiani, Shalini N %A Joshi, Vandita %A Ziad Khan %A Kirkness, Ewen F %A Cree, Andrew %A Fowler, R Gerald %A Lee, Sandra %A Lewis, Lora R %A Li, Zhangwan %A Liu, Yih-Shin %A Moore, Stephanie M %A Donna M Muzny %A Nazareth, Lynne V %A Ngo, Dinh Ngoc %A Okwuonu, Geoffrey O %A Pai, Grace %A Parker, David %A Paul, Heidie A %A Pfannkoch, Cynthia %A Pohl, Craig S %A Rogers, Yu-Hui %A Ruiz, San Juana %A Aniko Sabo %A Santibanez, Jireh %A Schneider, Brian W %A Smith, Scott M %A Sodergren, Erica %A Svatek, Amanda F %A Utterback, Teresa R %A Vattathil, Selina %A Warren, Wesley %A White, Courtney Sherell %A Chinwalla, Asif T %A Feng, Yucheng %A Halpern, Aaron L %A Hillier, LaDeana W %A Huang, Xiaoqiu %A Minx, Pat %A Nelson, Joanne O %A Pepin, Kymberlie H %A Xiang Qin %A Sutton, Granger G %A Venter, Eli %A Walenz, Brian P %A Wallis, John W %A Kim C Worley %A Yang, Shiaw-Pyng %A Jones, Steven M %A Marra, Marco A %A Rocchi, Mariano %A Schein, Jacqueline E %A Baertsch, Robert %A Clarke, Laura %A Csuros, Miklos %A Glasscock, Jarret %A R. Alan Harris %A Havlak, Paul %A Jackson, Andrew R %A Jiang, Huaiyang %A Liu, Yue %A Messina, David N %A Shen, Yufeng %A Song, Henry Xing-Zhi %A Wylie, Todd %A Zhang, Lan %A Birney, Ewan %A Han, Kyudong %A Konkel, Miriam K %A Lee, Jungnam %A Smit, Arian F A %A Ullmer, Brygg %A Wang, Hui %A Xing, Jinchuan %A Burhans, Richard %A Cheng, Ze %A Karro, John E %A Ma, Jian %A Raney, Brian %A She, Xinwei %A Cox, Michael J %A Demuth, Jeffery P %A Dumas, Laura J %A Han, Sang-Gook %A Hopkins, Janet %A Karimpour-Fard, Anis %A Kim, Young H %A Pollack, Jonathan R %A Vinar, Tomas %A Addo-Quaye, Charles %A Degenhardt, Jeremiah %A Denby, Alexandra %A Hubisz, Melissa J %A Indap, Amit %A Kosiol, Carolin %A Lahn, Bruce T %A Lawson, Heather A %A Marklein, Alison %A Nielsen, Rasmus %A Vallender, Eric J %A Clark, Andrew G %A Ferguson, Betsy %A Hernandez, Ryan D %A Hirani, Kashif %A Kehrer-Sawatzki, Hildegard %A Kolb, Jessica %A Patil, Shobha %A Pu, Ling-Ling %A Ren, Yanru %A Smith, David Glenn %A David A Wheeler %A Schenck, Ian %A Ball, Edward V %A Rui Chen %A Cooper, David N %A Giardine, Belinda %A Hsu, Fan %A Kent, W James %A Lesk, Arthur %A Nelson, David L %A O'brien, William E %A Prüfer, Kay %A Stenson, Peter D %A Wallace, James C %A Ke, Hui %A Liu, Xiao-Ming %A Wang, Peng %A Xiang, Andy Peng %A Yang, Fan %A Barber, Galt P %A Haussler, David %A Karolchik, Donna %A Kern, Andy D %A Kuhn, Robert M %A Smith, Kayla E %A Zwieg, Ann S %K Animals %K Biomedical Research %K Evolution, Molecular %K Female %K Gene Duplication %K Gene Rearrangement %K Genetic Diseases, Inborn %K Genetic Variation %K Genome %K Humans %K Macaca mulatta %K Male %K Multigene Family %K Mutation %K Pan troglodytes %K Sequence Analysis, DNA %K Species Specificity %X

The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.

%B Science %V 316 %P 222-34 %8 2007 Apr 13 %G eng %N 5822 %1 https://www.ncbi.nlm.nih.gov/pubmed/17431167?dopt=Abstract %R 10.1126/science.1139247 %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