Angiuoli SV

References (12)

Title : Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp - Bogdanove_2011_J.Bacteriol_193_5450
Author(s) : Bogdanove AJ , Koebnik R , Lu H , Furutani A , Angiuoli SV , Patil PB , Van Sluys MA , Ryan RP , Meyer DF , Han SW , Aparna G , Rajaram M , Delcher AL , Phillippy AM , Puiu D , Schatz MC , Shumway M , Sommer DD , Trapnell C , Benahmed F , Dimitrov G , Madupu R , Radune D , Sullivan S , Jha G , Ishihara H , Lee SW , Pandey A , Sharma V , Sriariyanun M , Szurek B , Vera-Cruz CM , Dorman KS , Ronald PC , Verdier V , Dow JM , Sonti RV , Tsuge S , Brendel VP , Rabinowicz PD , Leach JE , White FF , Salzberg SL
Ref : Journal of Bacteriology , 193 :5450 , 2011
Abstract : Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of Xanthomonas campestris pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology, Arabidopsis thaliana and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete Xanthomonas genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity.
ESTHER : Bogdanove_2011_J.Bacteriol_193_5450
PubMedSearch : Bogdanove_2011_J.Bacteriol_193_5450
PubMedID: 21784931
Gene_locus related to this paper: xanax-XAC4055 , xanca-CATD , xanca-estA1 , xanca-XCC0080 , xanca-XCC3164 , xanor-q5h5n1

Title : Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination - Budroni_2011_Proc.Natl.Acad.Sci.U.S.A_108_4494
Author(s) : Budroni S , Siena E , Dunning Hotopp JC , Seib KL , Serruto D , Nofroni C , Comanducci M , Riley DR , Daugherty SC , Angiuoli SV , Covacci A , Pizza M , Rappuoli R , Moxon ER , Tettelin H , Medini D
Ref : Proc Natl Acad Sci U S A , 108 :4494 , 2011
Abstract : Molecular data on a limited number of chromosomal loci have shown that the population of Neisseria meningitidis (Nm), a deadly human pathogen, is structured in distinct lineages. Given that the Nm population undergoes substantial recombination, the mechanisms resulting in the evolution of these lineages, their persistence in time, and the implications for the pathogenicity of the bacterium are not yet completely understood. Based on whole-genome sequencing, we show that Nm is structured in phylogenetic clades. Through acquisition of specific genes and through insertions and rearrangements, each clade has acquired and remodeled specific genomic tracts, with the potential to impact on the commensal and virulence behavior of Nm. Despite this clear evidence of a structured population, we confirm high rates of detectable recombination throughout the whole Nm chromosome. However, gene conversion events were found to be longer within clades than between clades, suggesting a DNA cleavage mechanism associated with the phylogeny of the species. We identify 22 restriction modification systems, probably acquired by horizontal gene transfer from outside of the species/genus, whose distribution in the different strains coincides with the phylogenetic clade structure. We provide evidence that these clade-associated restriction modification systems generate a differential barrier to DNA exchange consistent with the observed population structure. These findings have general implications for the emergence of lineage structure and virulence in recombining bacterial populations, and they could provide an evolutionary framework for the population biology of a number of other bacterial species that show contradictory population structure and dynamics.
ESTHER : Budroni_2011_Proc.Natl.Acad.Sci.U.S.A_108_4494
PubMedSearch : Budroni_2011_Proc.Natl.Acad.Sci.U.S.A_108_4494
PubMedID: 21368196
Gene_locus related to this paper: neigo-pip , neima-metx , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB1877

Title : Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species - Donati_2010_Genome.Biol_11_R107
Author(s) : Donati C , Hiller NL , Tettelin H , Muzzi A , Croucher NJ , Angiuoli SV , Oggioni M , Dunning Hotopp JC , Hu FZ , Riley DR , Covacci A , Mitchell TJ , Bentley SD , Kilian M , Ehrlich GD , Rappuoli R , Moxon ER , Masignani V
Ref : Genome Biol , 11 :R107 , 2010
Abstract : BACKGROUND: Streptococcus pneumoniae is one of the most important causes of microbial diseases in humans. The genomes of 44 diverse strains of S. pneumoniae were analyzed and compared with strains of non-pathogenic streptococci of the Mitis group.
RESULTS: Despite evidence of extensive recombination, the S. pneumoniae phylogenetic tree revealed six major lineages. With the exception of serotype 1, the tree correlated poorly with capsular serotype, geographical site of isolation and disease outcome. The distribution of dispensable genes--genes present in more than one strain but not in all strains--was consistent with phylogeny, although horizontal gene transfer events attenuated this correlation in the case of ancient lineages. Homologous recombination, involving short stretches of DNA, was the dominant evolutionary process of the core genome of S. pneumoniae. Genetic exchange occurred both within and across the borders of the species, and S. mitis was the main reservoir of genetic diversity of S. pneumoniae. The pan-genome size of S. pneumoniae increased logarithmically with the number of strains and linearly with the number of polymorphic sites of the sampled genomes, suggesting that acquired genes accumulate proportionately to the age of clones. Most genes associated with pathogenicity were shared by all S. pneumoniae strains, but were also present in S. mitis, S. oralis and S. infantis, indicating that these genes are not sufficient to determine virulence.
CONCLUSIONS: Genetic exchange with related species sharing the same ecological niche is the main mechanism of evolution of S. pneumoniae. The open pan-genome guarantees the species a quick and economical response to diverse environments.
ESTHER : Donati_2010_Genome.Biol_11_R107
PubMedSearch : Donati_2010_Genome.Biol_11_R107
PubMedID: 21034474

Title : Comparative genomics of the neglected human malaria parasite Plasmodium vivax - Carlton_2008_Nature_455_757
Author(s) : Carlton JM , Adams JH , Silva JC , Bidwell SL , Lorenzi H , Caler E , Crabtree J , Angiuoli SV , Merino EF , Amedeo P , Cheng Q , Coulson RM , Crabb BS , Del Portillo HA , Essien K , Feldblyum TV , Fernandez-Becerra C , Gilson PR , Gueye AH , Guo X , Kang'a S , Kooij TW , Korsinczky M , Meyer EV , Nene V , Paulsen I , White O , Ralph SA , Ren Q , Sargeant TJ , Salzberg SL , Stoeckert CJ , Sullivan SA , Yamamoto MM , Hoffman SL , Wortman JR , Gardner MJ , Galinski MR , Barnwell JW , Fraser-Liggett CM
Ref : Nature , 455 :757 , 2008
Abstract : The human malaria parasite Plasmodium vivax is responsible for 25-40% of the approximately 515 million annual cases of malaria worldwide. Although seldom fatal, the parasite elicits severe and incapacitating clinical symptoms and often causes relapses months after a primary infection has cleared. Despite its importance as a major human pathogen, P. vivax is little studied because it cannot be propagated continuously in the laboratory except in non-human primates. We sequenced the genome of P. vivax to shed light on its distinctive biological features, and as a means to drive development of new drugs and vaccines. Here we describe the synteny and isochore structure of P. vivax chromosomes, and show that the parasite resembles other malaria parasites in gene content and metabolic potential, but possesses novel gene families and potential alternative invasion pathways not recognized previously. Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species.
ESTHER : Carlton_2008_Nature_455_757
PubMedSearch : Carlton_2008_Nature_455_757
PubMedID: 18843361
Gene_locus related to this paper: plakh-b3lb44 , plavi-a5kcq0 , plavs-a5k2k6 , plavs-a5k3z4 , plavs-a5k4s6 , plavs-a5k5e4 , plavs-a5k7t5 , plavs-a5k686 , plavs-a5kaa1 , plavs-a5kaa3 , plavs-a5kas6 , plavs-a5kcm2

Title : Draft genome of the filarial nematode parasite Brugia malayi - Ghedin_2007_Science_317_1756
Author(s) : Ghedin E , Wang S , Spiro D , Caler E , Zhao Q , Crabtree J , Allen JE , Delcher AL , Guiliano DB , Miranda-Saavedra D , Angiuoli SV , Creasy T , Amedeo P , Haas B , El-Sayed NM , Wortman JR , Feldblyum T , Tallon L , Schatz M , Shumway M , Koo H , Salzberg SL , Schobel S , Pertea M , Pop M , White O , Barton GJ , Carlow CK , Crawford MJ , Daub J , Dimmic MW , Estes CF , Foster JM , Ganatra M , Gregory WF , Johnson NM , Jin J , Komuniecki R , Korf I , Kumar S , Laney S , Li BW , Li W , Lindblom TH , Lustigman S , Ma D , Maina CV , Martin DM , McCarter JP , McReynolds L , Mitreva M , Nutman TB , Parkinson J , Peregrin-Alvarez JM , Poole C , Ren Q , Saunders L , Sluder AE , Smith K , Stanke M , Unnasch TR , Ware J , Wei AD , Weil G , Williams DJ , Zhang Y , Williams SA , Fraser-Liggett C , Slatko B , Blaxter ML , Scott AL
Ref : Science , 317 :1756 , 2007
Abstract : Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the approximately 90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict approximately 11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during approximately 350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design.
ESTHER : Ghedin_2007_Science_317_1756
PubMedSearch : Ghedin_2007_Science_317_1756
PubMedID: 17885136
Gene_locus related to this paper: bruma-a8ndk6 , bruma-a8njt8 , bruma-a8nl88 , bruma-a8npi4 , bruma-a8npi6 , bruma-a8p6g9 , bruma-a8pah3 , bruma-a8pc38 , bruma-a8pek5 , bruma-a8piq4 , bruma-a8pnw8 , bruma-a8psu4 , bruma-a8pte1 , bruma-a8q606 , bruma-a8q632 , bruma-a8q937 , bruma-a8qav5 , bruma-a8qbd9 , bruma-a8qgj6 , bruma-a8qh78 , bruma-a8q143 , bruma-a0a024mej5 , bruma-a0a0k0jju9 , bruma-a0a0i9n517

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 : 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 : Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain - Gill_2005_J.Bacteriol_187_2426
Author(s) : Gill SR , Fouts DE , Archer GL , Mongodin EF , DeBoy RT , Ravel J , Paulsen IT , Kolonay JF , Brinkac L , Beanan M , Dodson RJ , Daugherty SC , Madupu R , Angiuoli SV , Durkin AS , Haft DH , Vamathevan J , Khouri H , Utterback T , Lee C , Dimitrov G , Jiang L , Qin H , Weidman J , Tran K , Kang K , Hance IR , Nelson KE , Fraser CM
Ref : Journal of Bacteriology , 187 :2426 , 2005
Abstract : Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous hospital- and community-acquired infections. Staphylococcus epidermidis has emerged as a causative agent of infections often associated with implanted medical devices. We have sequenced the approximately 2.8-Mb genome of S. aureus COL, an early methicillin-resistant isolate, and the approximately 2.6-Mb genome of S. epidermidis RP62a, a methicillin-resistant biofilm isolate. Comparative analysis of these and other staphylococcal genomes was used to explore the evolution of virulence and resistance between these two species. The S. aureus and S. epidermidis genomes are syntenic throughout their lengths and share a core set of 1,681 open reading frames. Genome islands in nonsyntenic regions are the primary source of variations in pathogenicity and resistance. Gene transfer between staphylococci and low-GC-content gram-positive bacteria appears to have shaped their virulence and resistance profiles. Integrated plasmids in S. epidermidis carry genes encoding resistance to cadmium and species-specific LPXTG surface proteins. A novel genome island encodes multiple phenol-soluble modulins, a potential S. epidermidis virulence factor. S. epidermidis contains the cap operon, encoding the polyglutamate capsule, a major virulence factor in Bacillus anthracis. Additional phenotypic differences are likely the result of single nucleotide polymorphisms, which are most numerous in cell envelope proteins. Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis.
ESTHER : Gill_2005_J.Bacteriol_187_2426
PubMedSearch : Gill_2005_J.Bacteriol_187_2426
PubMedID: 15774886
Gene_locus related to this paper: staau-LIP , staau-lipas , staau-MW0741 , staau-MW2456 , staau-q6gfm6 , staau-SA0011 , staau-SA0569 , staau-SA0572 , staau-SA0897 , staau-SA1143 , staau-SA2240 , staau-SA2306 , staau-SA2367 , staau-SA2422 , staau-SAV0321 , staau-SAV0446 , staau-SAV0457 , staau-SAV0655 , staau-SAV1014 , staau-SAV1765 , staau-SAV1793 , staau-SAV2188 , staau-SAV2350 , staau-SAV2484 , staau-SAV2594 , staep-lipas , staep-SE0011 , staep-SE0226 , staep-SE0386 , staep-SE0389 , staep-SE0424 , staep-SE0564 , staep-SE0714 , staep-SE0745 , staep-SE0980 , staep-SE1436 , staep-SE1460 , staep-SE1510 , staep-SE1780 , staep-SE1929 , staep-SERP2035 , staep-SE2050 , staep-SE2095 , staep-SE2213 , staep-SE2328

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 genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1 - Rasko_2004_Nucleic.Acids.Res_32_977
Author(s) : Rasko DA , Ravel J , Okstad OA , Helgason E , Cer RZ , Jiang L , Shores KA , Fouts DE , Tourasse NJ , Angiuoli SV , Kolonay J , Nelson WC , Kolsto AB , Fraser CM , Read TD
Ref : Nucleic Acids Research , 32 :977 , 2004
Abstract : We sequenced the complete genome of Bacillus cereus ATCC 10987, a non-lethal dairy isolate in the same genetic subgroup as Bacillus anthracis. Comparison of the chromosomes demonstrated that B.cereus ATCC 10987 was more similar to B.anthracis Ames than B.cereus ATCC 14579, while containing a number of unique metabolic capabilities such as urease and xylose utilization and lacking the ability to utilize nitrate and nitrite. Additionally, genetic mechanisms for variation of capsule carbohydrate and flagella surface structures were identified. Bacillus cereus ATCC 10987 contains a single large plasmid (pBc10987), of approximately 208 kb, that is similar in gene content and organization to B.anthracis pXO1 but is lacking the pathogenicity-associated island containing the anthrax lethal and edema toxin complex genes. The chromosomal similarity of B.cereus ATCC 10987 to B.anthracis Ames, as well as the fact that it contains a large pXO1-like plasmid, may make it a possible model for studying B.anthracis plasmid biology and regulatory cross-talk.
ESTHER : Rasko_2004_Nucleic.Acids.Res_32_977
PubMedSearch : Rasko_2004_Nucleic.Acids.Res_32_977
PubMedID: 14960714
Gene_locus related to this paper: bacan-BA1727 , bacan-BA2392 , bacan-BA2687 , bacan-BA3165 , bacan-BA3178 , bacan-BA3343 , bacan-BA4324 , bacan-BA5009 , bacan-BA5110 , bacc1-q72z64 , bacc1-q73a27 , bacc1-q73ab2 , bacc1-q73br9 , bacc1-q73bx8 , bacc1-q73c56 , bacc1-q73c93 , bacc1-q73cm7 , bacc1-q730c7 , bacc1-q731i0 , bacc1-q732y1 , bacc1-q732z3 , bacc1-q734r1 , bacc1-q735c5 , bacc1-q737t7 , bacc1-q738j2 , bacc1-q739p5 , bacce-BC0192 , bacce-BC0968 , bacce-BC1027 , bacce-BC1788 , bacce-BC1954 , bacce-BC2141 , bacce-BC2171 , bacce-BC3642 , bacce-BC4345 , bacce-BC4730 , bacce-BC4862 , bacce-BC4904 , bacce-BC5130 , bacce-BCE3188 , bacce-lipP , bacce-PHAC , bacce-q72yu1 , bacce-q73af5 , bacce-q735f1 , bacce-q736x9 , bacce-q738e6 , baccr-pepx

Title : Whole genome comparisons of serotype 4b and 1\/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species - Nelson_2004_Nucleic.Acids.Res_32_2386
Author(s) : Nelson KE , Fouts DE , Mongodin EF , Ravel J , DeBoy RT , Kolonay JF , Rasko DA , Angiuoli SV , Gill SR , Paulsen IT , Peterson J , White O , Nelson WC , Nierman W , Beanan MJ , Brinkac LM , Daugherty SC , Dodson RJ , Durkin AS , Madupu R , Haft DH , Selengut J , Van Aken S , Khouri H , Fedorova N , Forberger H , Tran B , Kathariou S , Wonderling LD , Uhlich GA , Bayles DO , Luchansky JB , Fraser CM
Ref : Nucleic Acids Research , 32 :2386 , 2004
Abstract : The genomes of three strains of Listeria monocytogenes that have been associated with food-borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69 strain-specific genes were identified in L.monocytogenes strains F2365 (serotype 4b, cheese isolate), F6854 (serotype 1/2a, frankfurter isolate) and H7858 (serotype 4b, meat isolate), respectively. Eighty-three genes were restricted to serotype 1/2a and 51 to serotype 4b strains. These strain- and serotype-specific genes probably contribute to observed differences in pathogenicity, and the ability of the organisms to survive and grow in their respective environmental niches. The serotype 1/2a-specific genes include an operon that encodes the rhamnose biosynthetic pathway that is associated with teichoic acid biosynthesis, as well as operons for five glycosyl transferases and an adenine-specific DNA methyltransferase. A total of 8603 and 105 050 high quality single nucleotide polymorphisms (SNPs) were found on the draft genome sequences of strain H7858 and strain F6854, respectively, when compared with strain F2365. Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs.
ESTHER : Nelson_2004_Nucleic.Acids.Res_32_2386
PubMedSearch : Nelson_2004_Nucleic.Acids.Res_32_2386
PubMedID: 15115801
Gene_locus related to this paper: lismc-c1l0d9 , lismf-q71xq4 , lismo-LMO0110 , lismo-LMO0493 , lismo-LMO0580 , lismo-LMO0752 , lismo-LMO0760 , lismo-LMO0857 , lismo-LMO0950 , lismo-LMO0951 , lismo-LMO0977 , lismo-LMO1128 , lismo-LMO1258 , lismo-LMO1674 , lismo-LMO2089 , lismo-LMO2109 , lismo-LMO2433 , lismo-LMO2450 , lismo-LMO2452 , lismo-LMO2453 , lismo-LMO2578 , lismo-LMO2677 , lismo-LMO2755 , lismo-metx

Title : Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii - Carlton_2002_Nature_419_512
Author(s) : Carlton JM , Angiuoli SV , Suh BB , Kooij TW , Pertea M , Silva JC , Ermolaeva MD , Allen JE , Selengut JD , Koo HL , Peterson JD , Pop M , Kosack DS , Shumway MF , Bidwell SL , Shallom SJ , Van Aken SE , Riedmuller SB , Feldblyum TV , Cho JK , Quackenbush J , Sedegah M , Shoaibi A , Cummings LM , Florens L , Yates JR , Raine JD , Sinden RE , Harris MA , Cunningham DA , Preiser PR , Bergman LW , Vaidya AB , van Lin LH , Janse CJ , Waters AP , Smith HO , White OR , Salzberg SL , Venter JC , Fraser CM , Hoffman SL , Gardner MJ , Carucci DJ
Ref : Nature , 419 :512 , 2002
Abstract : Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.
ESTHER : Carlton_2002_Nature_419_512
PubMedSearch : Carlton_2002_Nature_419_512
PubMedID: 12368865
Gene_locus related to this paper: playo-PY04076 , playo-PY04938 , playo-PY05572 , playo-q7pdu6 , playo-q7r7y2 , playo-q7rbj8 , playo-q7rdk4 , playo-q7rgi9 , playo-q7rh25 , playo-q7rki0 , playo-q7rl68 , playo-q7rl69 , playo-q7rmm1 , playo-q7rn16 , playo-q7rpk0 , playo-q7rq09 , playo-q7rq49 , playo-q7rq68