Utterback TR

References (17)

Title : Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle - Kirkness_2010_Proc.Natl.Acad.Sci.U.S.A_107_12168
Author(s) : Kirkness EF , Haas BJ , Sun W , Braig HR , Perotti MA , Clark JM , Lee SH , Robertson HM , Kennedy RC , Elhaik E , Gerlach D , Kriventseva EV , Elsik CG , Graur D , Hill CA , Veenstra JA , Walenz B , Tubio JM , Ribeiro JM , Rozas J , Johnston JS , Reese JT , Popadic A , Tojo M , Raoult D , Reed DL , Tomoyasu Y , Kraus E , Mittapalli O , Margam VM , Li HM , Meyer JM , Johnson RM , Romero-Severson J , Vanzee JP , Alvarez-Ponce D , Vieira FG , Aguade M , Guirao-Rico S , Anzola JM , Yoon KS , Strycharz JP , Unger MF , Christley S , Lobo NF , Seufferheld MJ , Wang N , Dasch GA , Struchiner CJ , Madey G , Hannick LI , Bidwell S , Joardar V , Caler E , Shao R , Barker SC , Cameron S , Bruggner RV , Regier A , Johnson J , Viswanathan L , Utterback TR , Sutton GG , Lawson D , Waterhouse RM , Venter JC , Strausberg RL , Berenbaum MR , Collins FH , Zdobnov EM , Pittendrigh BR
Ref : Proc Natl Acad Sci U S A , 107 :12168 , 2010
Abstract : As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is an important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences of the body louse and its primary bacterial endosymbiont Candidatus Riesia pediculicola. The body louse has the smallest known insect genome, spanning 108 Mb. Despite its status as an obligate parasite, it retains a remarkably complete basal insect repertoire of 10,773 protein-coding genes and 57 microRNAs. Representing hemimetabolous insects, the genome of the body louse thus provides a reference for studies of holometabolous insects. Compared with other insect genomes, the body louse genome contains significantly fewer genes associated with environmental sensing and response, including odorant and gustatory receptors and detoxifying enzymes. The unique architecture of the 18 minicircular mitochondrial chromosomes of the body louse may be linked to the loss of the gene encoding the mitochondrial single-stranded DNA binding protein. The genome of the obligatory louse endosymbiont Candidatus Riesia pediculicola encodes less than 600 genes on a short, linear chromosome and a circular plasmid. The plasmid harbors a unique arrangement of genes required for the synthesis of pantothenate, an essential vitamin deficient in the louse diet. The human body louse, its primary endosymbiont, and the bacterial pathogens that it vectors all possess genomes reduced in size compared with their free-living close relatives. Thus, the body louse genome project offers unique information and tools to use in advancing understanding of coevolution among vectors, symbionts, and pathogens.
ESTHER : Kirkness_2010_Proc.Natl.Acad.Sci.U.S.A_107_12168
PubMedSearch : Kirkness_2010_Proc.Natl.Acad.Sci.U.S.A_107_12168
PubMedID: 20566863
Gene_locus related to this paper: pedhb-ACHE1 , pedhb-ACHE2 , pedhc-e0v9b5 , pedhc-e0v9b6 , pedhc-e0v9b7 , pedhc-e0vbv5 , pedhc-e0vcd0 , pedhc-e0vcl7 , pedhc-e0vd69 , pedhc-e0ve50 , pedhc-e0vel6 , pedhc-e0vel7 , pedhc-e0vf98 , pedhc-e0vfs8 , pedhc-e0vfv0 , pedhc-e0vg01 , pedhc-e0vha2 , pedhc-e0vha4 , pedhc-e0vi52 , pedhc-e0vp42 , pedhc-e0vqu6 , pedhc-e0vuj9 , pedhc-e0vup6 , pedhc-e0vv55 , pedhc-e0vwv3 , pedhc-e0vxf7 , pedhc-e0vxg1 , pedhc-e0w4a6 , pedhc-e0w4c8 , pedhc-e0w271 , pedhc-e0w444 , pedhc-e0vym0 , pedhc-e0vdk9 , pedhc-e0vk10 , pedhc-e0vgw4 , pedhc-e0vgw7 , pedhc-e0vga1 , pedhc-e0w3s1 , pedhc-e0vzt2

Title : Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis - Carlton_2007_Science_315_207
Author(s) : Carlton JM , Hirt RP , Silva JC , Delcher AL , Schatz M , Zhao Q , Wortman JR , Bidwell SL , Alsmark UC , Besteiro S , Sicheritz-Ponten T , Noel CJ , Dacks JB , Foster PG , Simillion C , Van de Peer Y , Miranda-Saavedra D , Barton GJ , Westrop GD , Muller S , Dessi D , Fiori PL , Ren Q , Paulsen I , Zhang H , Bastida-Corcuera FD , Simoes-Barbosa A , Brown MT , Hayes RD , Mukherjee M , Okumura CY , Schneider R , Smith AJ , Vanacova S , Villalvazo M , Haas BJ , Pertea M , Feldblyum TV , Utterback TR , Shu CL , Osoegawa K , de Jong PJ , Hrdy I , Horvathova L , Zubacova Z , Dolezal P , Malik SB , Logsdon JM, Jr. , Henze K , Gupta A , Wang CC , Dunne RL , Upcroft JA , Upcroft P , White O , Salzberg SL , Tang P , Chiu CH , Lee YS , Embley TM , Coombs GH , Mottram JC , Tachezy J , Fraser-Liggett CM , Johnson PJ
Ref : Science , 315 :207 , 2007
Abstract : We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.
ESTHER : Carlton_2007_Science_315_207
PubMedSearch : Carlton_2007_Science_315_207
PubMedID: 17218520
Gene_locus related to this paper: triva-a2d7i4 , triva-a2d9w5 , triva-a2d766 , triva-a2dah5 , triva-a2dlx9 , triva-a2dul1 , triva-a2dy49 , triva-a2e6h5 , triva-a2e7p9 , triva-a2e9l3 , triva-a2e414 , triva-a2e613 , triva-a2e983 , triva-a2eau8 , triva-a2ekb9 , triva-a2en58 , triva-a2erp5 , triva-a2et59 , triva-a2f7u4 , triva-a2f801 , triva-a2fa76 , triva-a2fbq3 , triva-a2fe47 , triva-a2fgl0 , triva-a2fhp7 , triva-a2fie6 , triva-a2fk22 , triva-a2fla2 , triva-a2fqm0 , triva-a2fqq2 , triva-a2frq0 , triva-a2frr3 , triva-a2fsq9 , triva-a2fsz5 , triva-a2fux4 , triva-a2fz57 , triva-a2g2h0 , triva-a2g9x0 , triva-a2fqi4

Title : Evolutionary and biomedical insights from the rhesus macaque genome - Gibbs_2007_Science_316_222
Author(s) : Gibbs RA , Rogers J , Katze MG , Bumgarner R , Weinstock GM , Mardis ER , Remington KA , Strausberg RL , Venter JC , Wilson RK , Batzer MA , Bustamante CD , Eichler EE , Hahn MW , Hardison RC , Makova KD , Miller W , Milosavljevic A , Palermo RE , Siepel A , Sikela JM , Attaway T , Bell S , Bernard KE , Buhay CJ , Chandrabose MN , Dao M , Davis C , Delehaunty KD , Ding Y , Dinh HH , Dugan-Rocha S , Fulton LA , Gabisi RA , Garner TT , Godfrey J , Hawes AC , Hernandez J , Hines S , Holder M , Hume J , Jhangiani SN , Joshi V , Khan ZM , Kirkness EF , Cree A , Fowler RG , Lee S , Lewis LR , Li Z , Liu YS , Moore SM , Muzny D , Nazareth LV , Ngo DN , Okwuonu GO , Pai G , Parker D , Paul HA , Pfannkoch C , Pohl CS , Rogers YH , Ruiz SJ , Sabo A , Santibanez J , Schneider BW , Smith SM , Sodergren E , Svatek AF , Utterback TR , Vattathil S , Warren W , White CS , Chinwalla AT , Feng Y , Halpern AL , Hillier LW , Huang X , Minx P , Nelson JO , Pepin KH , Qin X , Sutton GG , Venter E , Walenz BP , Wallis JW , Worley KC , Yang SP , Jones SM , Marra MA , Rocchi M , Schein JE , Baertsch R , Clarke L , Csuros M , Glasscock J , Harris RA , Havlak P , Jackson AR , Jiang H , Liu Y , Messina DN , Shen Y , Song HX , Wylie T , Zhang L , Birney E , Han K , Konkel MK , Lee J , Smit AF , Ullmer B , Wang H , Xing J , Burhans R , Cheng Z , Karro JE , Ma J , Raney B , She X , Cox MJ , Demuth JP , Dumas LJ , Han SG , Hopkins J , Karimpour-Fard A , Kim YH , Pollack JR , Vinar T , Addo-Quaye C , Degenhardt J , Denby A , Hubisz MJ , Indap A , Kosiol C , Lahn BT , Lawson HA , Marklein A , Nielsen R , Vallender EJ , Clark AG , Ferguson B , Hernandez RD , Hirani K , Kehrer-Sawatzki H , Kolb J , Patil S , Pu LL , Ren Y , Smith DG , Wheeler DA , Schenck I , Ball EV , Chen R , Cooper DN , Giardine B , Hsu F , Kent WJ , Lesk A , Nelson DL , O'Brien W E , Prufer K , Stenson PD , Wallace JC , Ke H , Liu XM , Wang P , Xiang AP , Yang F , Barber GP , Haussler D , Karolchik D , Kern AD , Kuhn RM , Smith KE , Zwieg AS
Ref : Science , 316 :222 , 2007
Abstract : 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.
ESTHER : Gibbs_2007_Science_316_222
PubMedSearch : Gibbs_2007_Science_316_222
PubMedID: 17431167
Gene_locus related to this paper: macmu-3neur , macmu-ACHE , macmu-BCHE , macmu-f6rul6 , macmu-f6sz31 , macmu-f6the6 , macmu-f6unj2 , macmu-f6wtx1 , macmu-f6zkq5 , macmu-f7aa58 , macmu-f7ai42 , macmu-f7aim4 , macmu-f7buk8 , macmu-f7cfi8 , macmu-f7cnr2 , macmu-f7cu68 , macmu-f7flv1 , macmu-f7ggk1 , macmu-f7hir7 , macmu-g7n054 , macmu-KANSL3 , macmu-TEX30 , macmu-Y4neur , macmu-g7n4x3 , macmu-i2cy02 , macmu-f7ba84 , macmu-CES2 , macmu-h9er02 , macmu-a0a1d5rbr3 , macmu-a0a1d5q4k5 , macmu-g7mxj6 , macmu-f7dn71 , macmu-f7hkw9 , macmu-f7hm08 , macmu-g7mke4 , macmu-a0a1d5rh04 , macmu-h9fud6 , macmu-f6qwx1 , macmu-f7h4t2 , macmu-h9zaw9 , macmu-f7h550 , macmu-a0a1d5q9w1 , macmu-f7gkb9 , macmu-f7hp78 , macmu-a0a1d5qvu5

Title : Comparative genomics of emerging human ehrlichiosis agents - Dunning Hotopp_2006_PLoS.Genet_2_e21
Author(s) : Dunning Hotopp JC , Lin M , Madupu R , Crabtree J , Angiuoli SV , Eisen JA , Seshadri R , Ren Q , Wu M , Utterback TR , Smith S , Lewis M , Khouri H , Zhang C , Niu H , Lin Q , Ohashi N , Zhi N , Nelson W , Brinkac LM , Dodson RJ , Rosovitz MJ , Sundaram J , Daugherty SC , Davidsen T , Durkin AS , Gwinn M , Haft DH , Selengut JD , Sullivan SA , Zafar N , Zhou L , Benahmed F , Forberger H , Halpin R , Mulligan S , Robinson J , White O , Rikihisa Y , Tettelin H
Ref : PLoS Genet , 2 :e21 , 2006
Abstract : Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens.
ESTHER : Dunning Hotopp_2006_PLoS.Genet_2_e21
PubMedSearch : Dunning Hotopp_2006_PLoS.Genet_2_e21
PubMedID: 16482227
Gene_locus related to this paper: anapz-q2gj80 , anapz-q2gle9 , anapz-q2glf0 , anapz-q2gln7 , ehrch-q40iu0 , ehrch-q40jj7 , ehrcr-q2gfq9 , neosm-q2gcq8 , neosm-q2gdf2 , neosm-q2gcn8 , anapz-q2gk48 , ehrcr-q2ggj6

Title : The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans - Loftus_2005_Science_307_1321
Author(s) : Loftus BJ , Fung E , Roncaglia P , Rowley D , Amedeo P , Bruno D , Vamathevan J , Miranda M , Anderson IJ , Fraser JA , Allen JE , Bosdet IE , Brent MR , Chiu R , Doering TL , Donlin MJ , D'Souza CA , Fox DS , Grinberg V , Fu J , Fukushima M , Haas BJ , Huang JC , Janbon G , Jones SJ , Koo HL , Krzywinski MI , Kwon-Chung JK , Lengeler KB , Maiti R , Marra MA , Marra RE , Mathewson CA , Mitchell TG , Pertea M , Riggs FR , Salzberg SL , Schein JE , Shvartsbeyn A , Shin H , Shumway M , Specht CA , Suh BB , Tenney A , Utterback TR , Wickes BL , Wortman JR , Wye NH , Kronstad JW , Lodge JK , Heitman J , Davis RW , Fraser CM , Hyman RW
Ref : Science , 307 :1321 , 2005
Abstract : Cryptococcus neoformans is a basidiomycetous yeast ubiquitous in the environment, a model for fungal pathogenesis, and an opportunistic human pathogen of global importance. We have sequenced its approximately 20-megabase genome, which contains approximately 6500 intron-rich gene structures and encodes a transcriptome abundant in alternatively spliced and antisense messages. The genome is rich in transposons, many of which cluster at candidate centromeric regions. The presence of these transposons may drive karyotype instability and phenotypic variation. C. neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes.
ESTHER : Loftus_2005_Science_307_1321
PubMedSearch : Loftus_2005_Science_307_1321
PubMedID: 15653466
Gene_locus related to this paper: cryne-apth1 , cryne-ppme1 , cryne-q5k7g1 , cryne-q5k7h2 , cryne-q5k7p6 , cryne-q5k8p2 , cryne-q5k8s0 , cryne-q5k9e7 , cryne-q5k9p3 , cryne-q5k9y9 , cryne-q5k721 , cryne-q5k987 , cryne-q5ka03 , cryne-q5ka24 , cryne-q5ka58 , cryne-q5kat4 , cryne-q5kav3 , cryne-q5kbu4 , cryne-q5kbw4 , cryne-q5kc00 , cryne-q5kec5 , cryne-q5kei3 , cryne-q5kei7 , cryne-q5ker2 , cryne-q5key5 , cryne-q5kf48 , cryne-q5kfk6 , cryne-q5kfz0 , cryne-q5kgq3 , cryne-q5kh37 , cryne-q5khb0 , cryne-q5khb9 , cryne-q5kip7 , cryne-q5kiu5 , cryne-q5kj56 , cryne-q5kjf8 , cryne-q5kjh3 , cryne-q5kjp9 , cryne-q5kjw7 , cryne-q5kky1 , cryne-q5kkz7 , cryne-q5kl13 , cryne-q5klu9 , cryne-q5km63 , cryne-q5kme9 , cryne-q5kni1 , cryne-q5knq0 , cryne-q5knr2 , cryne-q5knw0 , cryne-q5kq08 , cryne-Q5KCH9 , cryne-q55ta1 , cryne-q5kjh4 , crynj-q5knp8 , crynj-q5kpe0

Title : Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes - Gardner_2005_Science_309_134
Author(s) : Gardner MJ , Bishop R , Shah T , de Villiers EP , Carlton JM , Hall N , Ren Q , Paulsen IT , Pain A , Berriman M , Wilson RJ , Sato S , Ralph SA , Mann DJ , Xiong Z , Shallom SJ , Weidman J , Jiang L , Lynn J , Weaver B , Shoaibi A , Domingo AR , Wasawo D , Crabtree J , Wortman JR , Haas B , Angiuoli SV , Creasy TH , Lu C , Suh B , Silva JC , Utterback TR , Feldblyum TV , Pertea M , Allen J , Nierman WC , Taracha EL , Salzberg SL , White OR , Fitzhugh HA , Morzaria S , Venter JC , Fraser CM , Nene V
Ref : Science , 309 :134 , 2005
Abstract : We report the genome sequence of Theileria parva, an apicomplexan pathogen causing economic losses to smallholder farmers in Africa. The parasite chromosomes exhibit limited conservation of gene synteny with Plasmodium falciparum, and its plastid-like genome represents the first example where all apicoplast genes are encoded on one DNA strand. We tentatively identify proteins that facilitate parasite segregation during host cell cytokinesis and contribute to persistent infection of transformed host cells. Several biosynthetic pathways are incomplete or absent, suggesting substantial metabolic dependence on the host cell. One protein family that may generate parasite antigenic diversity is not telomere-associated.
ESTHER : Gardner_2005_Science_309_134
PubMedSearch : Gardner_2005_Science_309_134
PubMedID: 15994558
Gene_locus related to this paper: thepa-q4mzr2 , thepa-q4n0b4 , thepa-q4n2i4 , thepa-q4n4i8 , thepa-q4n5d6 , thepa-q4n5m4 , thepa-q4n006 , thepa-q4n9g7 , thepa-q4n315 , thepa-q4n349 , thepa-q4n803

Title : The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses - Methe_2005_Proc.Natl.Acad.Sci.U.S.A_102_10913
Author(s) : Methe BA , Nelson KE , Deming JW , Momen B , Melamud E , Zhang X , Moult J , Madupu R , Nelson WC , Dodson RJ , Brinkac LM , Daugherty SC , Durkin AS , DeBoy RT , Kolonay JF , Sullivan SA , Zhou L , Davidsen TM , Wu M , Huston AL , Lewis M , Weaver B , Weidman JF , Khouri H , Utterback TR , Feldblyum TV , Fraser CM
Ref : Proc Natl Acad Sci U S A , 102 :10913 , 2005
Abstract : The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium Colwellia psychrerythraea 34H, a model for the study of life in permanently cold environments, reveals capabilities important to carbon and nutrient cycling, bioremediation, production of secondary metabolites, and cold-adapted enzymes. From a genomic perspective, cold adaptation is suggested in several broad categories involving changes to the cell membrane fluidity, uptake and synthesis of compounds conferring cryotolerance, and strategies to overcome temperature-dependent barriers to carbon uptake. Modeling of three-dimensional protein homology from bacteria representing a range of optimal growth temperatures suggests changes to proteome composition that may enhance enzyme effectiveness at low temperatures. Comparative genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a unique set of genes but by a collection of synergistic changes in overall genome content and amino acid composition.
ESTHER : Methe_2005_Proc.Natl.Acad.Sci.U.S.A_102_10913
PubMedSearch : Methe_2005_Proc.Natl.Acad.Sci.U.S.A_102_10913
PubMedID: 16043709
Gene_locus related to this paper: colp3-q47uc4 , colp3-q47uc7 , colp3-q47ut6 , colp3-q47ut7 , colp3-q47v81 , colp3-q47vk3 , colp3-q47vy9 , colp3-q47w94 , colp3-q47wj4 , colp3-q47wr2 , colp3-q47ws7 , colp3-q47ws9 , colp3-q47x08 , colp3-q47x48 , colp3-q47yd5 , colp3-q47ye2 , colp3-q47yq1 , colp3-q47yv1 , colp3-q47za7 , colp3-q47zp5 , colp3-q48ac9 , colp3-q48aj8 , colp3-q48aq9 , colp3-q480e1 , colp3-q481z4 , colp3-q482y8 , colp3-q484d8 , colp3-q484k3 , colp3-q485e4 , colp3-q485t4 , colp3-q486t5 , colp3-q487b7 , colp3-q487s5 , colp3-q488a3 , colp3-q488d2 , colp3-q488d8 , colp3-q488e7 , colp3-q488f8 , colp3-q488p2 , colp3-q489b1 , colp3-q489i6 , colp3-q47ya3

Title : Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial pan-genome - Tettelin_2005_Proc.Natl.Acad.Sci.U.S.A_102_13950
Author(s) : Tettelin H , Masignani V , Cieslewicz MJ , Donati C , Medini D , Ward NL , Angiuoli SV , Crabtree J , Jones AL , Durkin AS , DeBoy RT , Davidsen TM , Mora M , Scarselli M , Margarit y Ros I , Peterson JD , Hauser CR , Sundaram JP , Nelson WC , Madupu R , Brinkac LM , Dodson RJ , Rosovitz MJ , Sullivan SA , Daugherty SC , Haft DH , Selengut J , Gwinn ML , Zhou L , Zafar N , Khouri H , Radune D , Dimitrov G , Watkins K , O'Connor KJ , Smith S , Utterback TR , White O , Rubens CE , Grandi G , Madoff LC , Kasper DL , Telford JL , Wessels MR , Rappuoli R , Fraser CM
Ref : Proc Natl Acad Sci U S A , 102 :13950 , 2005
Abstract : The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and also limits genome-wide screens for vaccine candidates or for antimicrobial targets. We have generated the genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans. Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for approximately 80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.
ESTHER : Tettelin_2005_Proc.Natl.Acad.Sci.U.S.A_102_13950
PubMedSearch : Tettelin_2005_Proc.Natl.Acad.Sci.U.S.A_102_13950
PubMedID: 16172379
Gene_locus related to this paper: strag-ESTA , strag-GBS0040 , strag-GBS0107 , strag-GBS1828 , strag-pepx , strag-q3dah6 , strag-SAG0246 , strag-SAG0383 , strag-SAG0679 , strag-SAG0680 , strag-SAG0785 , strag-SAG0912 , strag-SAG1562 , strag-SAG2132

Title : The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough - Heidelberg_2004_Nat.Biotechnol_22_554
Author(s) : Heidelberg JF , Seshadri R , Haveman SA , Hemme CL , Paulsen IT , Kolonay JF , Eisen JA , Ward N , Methe B , Brinkac LM , Daugherty SC , DeBoy RT , Dodson RJ , Durkin AS , Madupu R , Nelson WC , Sullivan SA , Fouts D , Haft DH , Selengut J , Peterson JD , Davidsen TM , Zafar N , Zhou L , Radune D , Dimitrov G , Hance M , Tran K , Khouri H , Gill J , Utterback TR , Feldblyum TV , Wall JD , Voordouw G , Fraser CM
Ref : Nat Biotechnol , 22 :554 , 2004
Abstract : Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encoding enzymes for energy transduction, together with inferred cellular location of the enzymes, provides a basis for proposing an expansion to the 'hydrogen-cycling' model for increasing energy efficiency in this bacterium. Plasmid-encoded functions include modification of cell surface components, nitrogen fixation and a type-III protein secretion system. This genome sequence represents a substantial step toward the elucidation of pathways for reduction (and bioremediation) of pollutants such as uranium and chromium and offers a new starting point for defining this organism's complex anaerobic respiration.
ESTHER : Heidelberg_2004_Nat.Biotechnol_22_554
PubMedSearch : Heidelberg_2004_Nat.Biotechnol_22_554
PubMedID: 15077118
Gene_locus related to this paper: desvh-q72b36 , desvh-q72ed6 , desvh-q728i3 , desvh-q729w4 , desvh-q72b15

Title : Genome of Geobacter sulfurreducens: metal reduction in subsurface environments - Methe_2003_Science_302_1967
Author(s) : Methe BA , Nelson KE , Eisen JA , Paulsen IT , Nelson W , Heidelberg JF , Wu D , Wu M , Ward N , Beanan MJ , Dodson RJ , Madupu R , Brinkac LM , Daugherty SC , DeBoy RT , Durkin AS , Gwinn M , Kolonay JF , Sullivan SA , Haft DH , Selengut J , Davidsen TM , Zafar N , White O , Tran B , Romero C , Forberger HA , Weidman J , Khouri H , Feldblyum TV , Utterback TR , Van Aken SE , Lovley DR , Fraser CM
Ref : Science , 302 :1967 , 2003
Abstract : The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.
ESTHER : Methe_2003_Science_302_1967
PubMedSearch : Methe_2003_Science_302_1967
PubMedID: 14671304
Gene_locus related to this paper: geosl-q74a54 , geosl-q74ac8 , geosl-q74eb1 , geosl-q747u4 , geosl-q747v8 , geosl-q749w4

Title : Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis - Heidelberg_2002_Nat.Biotechnol_20_1118
Author(s) : Heidelberg JF , Paulsen IT , Nelson KE , Gaidos EJ , Nelson WC , Read TD , Eisen JA , Seshadri R , Ward N , Methe B , Clayton RA , Meyer T , Tsapin A , Scott J , Beanan M , Brinkac L , Daugherty S , DeBoy RT , Dodson RJ , Durkin AS , Haft DH , Kolonay JF , Madupu R , Peterson JD , Umayam LA , White O , Wolf AM , Vamathevan J , Weidman J , Impraim M , Lee K , Berry K , Lee C , Mueller J , Khouri H , Gill J , Utterback TR , McDonald LA , Feldblyum TV , Smith HO , Venter JC , Nealson KH , Fraser CM
Ref : Nat Biotechnol , 20 :1118 , 2002
Abstract : Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities, conferred in part by multicomponent, branched electron transport systems. Here we report the sequencing of the S. oneidensis genome, which consists of a 4,969,803-base pair circular chromosome with 4,758 predicted protein-encoding open reading frames (CDS) and a 161,613-base pair plasmid with 173 CDSs. We identified the first Shewanella lambda-like phage, providing a potential tool for further genome engineering. Genome analysis revealed 39 c-type cytochromes, including 32 previously unidentified in S. oneidensis, and a novel periplasmic [Fe] hydrogenase, which are integral members of the electron transport system. This genome sequence represents a critical step in the elucidation of the pathways for reduction (and bioremediation) of pollutants such as uranium (U) and chromium (Cr), and offers a starting point for defining this organism's complex electron transport systems and metal ion-reducing capabilities.
ESTHER : Heidelberg_2002_Nat.Biotechnol_20_1118
PubMedSearch : Heidelberg_2002_Nat.Biotechnol_20_1118
PubMedID: 12368813
Gene_locus related to this paper: sheon-BIOH , sheon-LYPA , sheon-PIP , sheon-PTRB , sheon-q8ej95 , sheon-SO0071 , sheon-SO0614 , sheon-SO0616 , sheon-SO0801 , sheon-SO0880 , sheoe-SO0967 , sheon-SO1006 , sheon-SO1224 , sheon-SO1310 , sheon-SO1534 , sheon-SO1539 , sheon-SO1686 , sheon-SO1743 , sheon-SO1976 , sheon-SO1999 , sheon-SO2024 , sheon-SO2047 , sheon-SO2055 , sheon-SO2223 , sheon-SO2333 , sheon-SO2473 , sheon-SO2582 , sheon-SO2753 , sheon-SO2934 , sheon-SO3025 , sheon-SO3900 , sheon-SO3990 , sheon-SO4252 , sheon-SO4400 , sheon-SO4537 , sheon-SO4543 , sheon-SO4574 , sheon-SO4618 , sheon-SO4650 , sheon-SOA0048 , shefn-SfSFGH , sheon-ym51

Title : Complete genome sequence of a virulent isolate of Streptococcus pneumoniae - Tettelin_2001_Science_293_498
Author(s) : Tettelin H , Nelson KE , Paulsen IT , Eisen JA , Read TD , Peterson S , Heidelberg J , DeBoy RT , Haft DH , Dodson RJ , Durkin AS , Gwinn M , Kolonay JF , Nelson WC , Peterson JD , Umayam LA , White O , Salzberg SL , Lewis MR , Radune D , Holtzapple E , Khouri H , Wolf AM , Utterback TR , Hansen CL , McDonald LA , Feldblyum TV , Angiuoli S , Dickinson T , Hickey EK , Holt IE , Loftus BJ , Yang F , Smith HO , Venter JC , Dougherty BA , Morrison DA , Hollingshead SK , Fraser CM
Ref : Science , 293 :498 , 2001
Abstract : The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines provide a substantial source of carbon and nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several surface-exposed proteins that may serve as potential vaccine candidates were identified. Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity.
ESTHER : Tettelin_2001_Science_293_498
PubMedSearch : Tettelin_2001_Science_293_498
PubMedID: 11463916
Gene_locus related to this paper: strp2-q04l35 , strpj-b8zns7 , strpn-AXE1 , strpn-b2dz20 , strpn-pepx , strpn-SP0614 , strpn-SP0666 , strpn-SP0777 , strpn-SP0902 , strpn-SP1343

Title : Complete genome sequence of Neisseria meningitidis serogroup B strain MC58 - Tettelin_2000_Science_287_1809
Author(s) : Tettelin H , Saunders NJ , Heidelberg J , Jeffries AC , Nelson KE , Eisen JA , Ketchum KA , Hood DW , Peden JF , Dodson RJ , Nelson WC , Gwinn ML , Deboy R , Peterson JD , Hickey EK , Haft DH , Salzberg SL , White O , Fleischmann RD , Dougherty BA , Mason T , Ciecko A , Parksey DS , Blair E , Cittone H , Clark EB , Cotton MD , Utterback TR , Khouri H , Qin H , Vamathevan J , Gill J , Scarlato V , Masignani V , Pizza M , Grandi G , Sun L , Smith HO , Fraser CM , Moxon ER , Rappuoli R , Venter JC
Ref : Science , 287 :1809 , 2000
Abstract : The 2,272,351-base pair genome of Neisseria meningitidis strain MC58 (serogroup B), a causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158 (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA transfer were identified; two of these contain genes encoding proteins involved in pathogenicity, and the third island contains coding sequences only for hypothetical proteins. Insights into the commensal and virulence behavior of N. meningitidis can be gleaned from the genome, in which sequences for structural proteins of the pilus are clustered and several coding regions unique to serogroup B capsular polysaccharide synthesis can be identified. Finally, N. meningitidis contains more genes that undergo phase variation than any pathogen studied to date, a mechanism that controls their expression and contributes to the evasion of the host immune system.
ESTHER : Tettelin_2000_Science_287_1809
PubMedSearch : Tettelin_2000_Science_287_1809
PubMedID: 10710307
Gene_locus related to this paper: neigo-pip , neima-metx , neimb-q9k0t9 , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB0868 , neime-NMB1828 , neime-NMB1877

Title : Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima - Nelson_1999_Nature_399_323
Author(s) : Nelson KE , Clayton RA , Gill SR , Gwinn ML , Dodson RJ , Haft DH , Hickey EK , Peterson JD , Nelson WC , Ketchum KA , McDonald L , Utterback TR , Malek JA , Linher KD , Garrett MM , Stewart AM , Cotton MD , Pratt MS , Phillips CA , Richardson D , Heidelberg J , Sutton GG , Fleischmann RD , Eisen JA , White O , Salzberg SL , Smith HO , Venter JC , Fraser CM
Ref : Nature , 399 :323 , 1999
Abstract : The 1,860,725-base-pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Of the Eubacteria sequenced to date, T. maritima has the highest percentage (24%) of genes that are most similar to archaeal genes. Eighty-one archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size from 4 to 20 kilobases. Conservation of gene order between T. maritima and Archaea in many of the clustered regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea.
ESTHER : Nelson_1999_Nature_399_323
PubMedSearch : Nelson_1999_Nature_399_323
PubMedID: 10360571
Gene_locus related to this paper: thema-ESTA , thema-q9x0d6 , thema-q9x042 , thema-TM0033 , thema-TM0053 , thema-TM0077 , thema-TM0336 , thema-TM1160 , thema-TM1350

Title : The complete genome sequence of the gastric pathogen Helicobacter pylori. - Tomb_1997_Nature_388_539
Author(s) : Tomb J-F , White O , Kerlavage AR , Clayton RA , Sutton GG , Fleischmann RD , Ketchum KA , Klenk H-P , Gill S , Dougherty BA , Nelson K , Quackenbush J , Zhou L , Kirkness EF , Peterson S , Loftus B , Richardson D , Dodson R , Khalak HG , Glodek A , McKenney K , FitzGerald LM , Lee N , Adams MD , Hickey EK , Berg DE , Gocayne JD , Utterback TR , Peterson JD , Kelley JM , Cotton MD , Weidman JM , Fujii C , Bowman C , Watthey L , Wallin E , Hayes WS , Borodovsky M , Karp PD , Smith HO , Fraser CM , Venter JC
Ref : Nature , 388 :539 , 1997
Abstract : Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.
ESTHER : Tomb_1997_Nature_388_539
PubMedSearch : Tomb_1997_Nature_388_539
PubMedID: 9252185
Gene_locus related to this paper: helpy-HP0739 , helpy-o25061

Title : The minimal gene complement of Mycoplasma genitalium - Fraser_1995_Science_270_397
Author(s) : Fraser CM , Gocayne JD , White O , Adams MD , Clayton RA , Fleischmann RD , Bult CJ , Kerlavage AR , Sutton G , Kelley JM , Fritchman RD , Weidman JF , Small KV , Sandusky M , Fuhrmann J , Nguyen D , Utterback TR , Saudek DM , Phillips CA , Merrick JM , Tomb JF , Dougherty BA , Bott KF , Hu PC , Lucier TS , Peterson SN , Smith HO , Hutchison CA, 3rd , Venter JC
Ref : Science , 270 :397 , 1995
Abstract : The complete nucleotide sequence (580,070 base pairs) of the Mycoplasma genitalium genome, the smallest known genome of any free-living organism, has been determined by whole-genome random sequencing and assembly. A total of only 470 predicted coding regions were identified that include genes required for DNA replication, transcription and translation, DNA repair, cellular transport, and energy metabolism. Comparison of this genome to that of Haemophilus influenzae suggests that differences in genome content are reflected as profound differences in physiology and metabolic capacity between these two organisms.
ESTHER : Fraser_1995_Science_270_397
PubMedSearch : Fraser_1995_Science_270_397
PubMedID: 7569993
Gene_locus related to this paper: mycge-esl1 , mycge-esl2 , mycge-esl3 , mycge-pip

Title : Whole-genome random sequencing and assembly of Haemophilus influenzae Rd - Fleischmann_1995_Science_269_496
Author(s) : Fleischmann RD , Adams MD , White O , Clayton RA , Kirkness EF , Kerlavage AR , Bult CJ , Tomb JF , Dougherty BA , Merrick JM , McKenney K , Sutton G , FitzHugh W , Fields C , Gocayne JD , Scott J , Shirley R , Liu LI , Glodek A , Kelley JM , Weidman JF , Phillips CA , Spriggs T , Hedblom E , Cotton MD , Utterback TR , Hanna MC , Nguyen DT , Saudek DM , Brandon RC , FineLD , Fritchman JL , Fuhrmann JL , Geoghagen NS , Gnehm CL , McDonald LA , Keith V , Small KV , Fraser CM , Smith HO , Venter JC
Ref : Science , 269 :496 , 1995
Abstract : An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The H. influenzae Rd genome sequence (Genome Sequence DataBase accession number L42023) represents the only complete genome sequence from a free-living organism.
ESTHER : Fleischmann_1995_Science_269_496
PubMedSearch : Fleischmann_1995_Science_269_496
PubMedID: 7542800
Gene_locus related to this paper: haein-HI0193 , haein-metx , haein-pldb , haein-sfgh , haein-y1552 , haein-yfbb