Segurens B

References (21)

Title : Complete genome sequence of the highly hemolytic strain Bacillus cereus F837\/76 - Auger_2012_J.Bacteriol_194_1630
Author(s) : Auger S , Galleron N , Segurens B , Dossat C , Bolotin A , Wincker P , Sorokin A
Ref : Journal of Bacteriology , 194 :1630 , 2012
Abstract : Highly hemolytic strain Bacillus cereus F837/76 was isolated in 1976 from a contaminated prostate wound. The complete nucleotide sequence of this strain reported here counts nearly 36,500 single-nucleotide differences from the closest sequenced strain, Bacillus thuringiensis Al Hakam. F827/76 also contains a 10-kb plasmid that was not detected in the Al Hakam strain.
ESTHER : Auger_2012_J.Bacteriol_194_1630
PubMedSearch : Auger_2012_J.Bacteriol_194_1630
PubMedID: 22374959
Gene_locus related to this paper: bacan-BA2392 , bacan-BA4324 , bacan-BA5110 , bacce-BC2171

Title : Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite - Denoeud_2011_Genome.Biol_12_R29
Author(s) : Denoeud F , Roussel M , Noel B , Wawrzyniak I , Da Silva C , Diogon M , Viscogliosi E , Brochier-Armanet C , Couloux A , Poulain J , Segurens B , Anthouard V , Texier C , Blot N , Poirier P , Ng GC , Tan KS , Artiguenave F , Jaillon O , Aury JM , Delbac F , Wincker P , Vivares CP , El Alaoui H
Ref : Genome Biol , 12 :R29 , 2011
Abstract : BACKGROUND: Blastocystis is a highly prevalent anaerobic eukaryotic parasite of humans and animals that is associated with various gastrointestinal and extraintestinal disorders. Epidemiological studies have identified different subtypes but no one subtype has been definitively correlated with disease.
RESULTS: Here we report the 18.8 Mb genome sequence of a Blastocystis subtype 7 isolate, which is the smallest stramenopile genome sequenced to date. The genome is highly compact and contains intriguing rearrangements. Comparisons with other available stramenopile genomes (plant pathogenic oomycete and diatom genomes) revealed effector proteins potentially involved in the adaptation to the intestinal environment, which were likely acquired via horizontal gene transfer. Moreover, Blastocystis living in anaerobic conditions harbors mitochondria-like organelles. An incomplete oxidative phosphorylation chain, a partial Krebs cycle, amino acid and fatty acid metabolisms and an iron-sulfur cluster assembly are all predicted to occur in these organelles. Predicted secretory proteins possess putative activities that may alter host physiology, such as proteases, protease-inhibitors, immunophilins and glycosyltransferases. This parasite also possesses the enzymatic machinery to tolerate oxidative bursts resulting from its own metabolism or induced by the host immune system.
CONCLUSIONS: This study provides insights into the genome architecture of this unusual stramenopile. It also proposes candidate genes with which to study the physiopathology of this parasite and thus may lead to further investigations into Blastocystis-host interactions.
ESTHER : Denoeud_2011_Genome.Biol_12_R29
PubMedSearch : Denoeud_2011_Genome.Biol_12_R29
PubMedID: 21439036
Gene_locus related to this paper: blaho-d8m103 , blaho-d8lw93

Title : Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea - Amselem_2011_PLoS.Genet_7_e1002230
Author(s) : Amselem J , Cuomo CA , van Kan JA , Viaud M , Benito EP , Couloux A , Coutinho PM , de Vries RP , Dyer PS , Fillinger S , Fournier E , Gout L , Hahn M , Kohn L , Lapalu N , Plummer KM , Pradier JM , Quevillon E , Sharon A , Simon A , ten Have A , Tudzynski B , Tudzynski P , Wincker P , Andrew M , Anthouard V , Beever RE , Beffa R , Benoit I , Bouzid O , Brault B , Chen Z , Choquer M , Collemare J , Cotton P , Danchin EG , Da Silva C , Gautier A , Giraud C , Giraud T , Gonzalez C , Grossetete S , Guldener U , Henrissat B , Howlett BJ , Kodira C , Kretschmer M , Lappartient A , Leroch M , Levis C , Mauceli E , Neuveglise C , Oeser B , Pearson M , Poulain J , Poussereau N , Quesneville H , Rascle C , Schumacher J , Segurens B , Sexton A , Silva E , Sirven C , Soanes DM , Talbot NJ , Templeton M , Yandava C , Yarden O , Zeng Q , Rollins JA , Lebrun MH , Dickman M
Ref : PLoS Genet , 7 :e1002230 , 2011
Abstract : Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
ESTHER : Amselem_2011_PLoS.Genet_7_e1002230
PubMedSearch : Amselem_2011_PLoS.Genet_7_e1002230
PubMedID: 21876677
Gene_locus related to this paper: botci-cutas , botci-q6rki2 , botf4-g2y7k8 , botfb-dapb , botfu-g2xyd8 , botfu-g2ynh8 , scls1-a7e814 , scls1-a7edc9 , scls1-a7edh1 , scls1-a7emm0 , scls1-a7eti8 , scls1-a7eu48 , scls1-a7f208 , scls1-dapb , botf4-g2xqp7 , scls1-a7eqq8 , botf4-g2xqc6 , scls1-a7ebs4 , botf4-g2xn51 , scls1-a7f5m9 , botf4-g2xti4 , botf4-g2xtu7 , botf4-g2yfp1 , scls1-a7f534 , botf4-g2yys3 , scls1-a7erz9 , botf4-g2y037 , botf4-g2y0e1 , scls1-a7f706 , scls1-a7ewt6 , botf4-g2yuj6 , botf1-m7u3d1 , botf1-m7u430 , botf1-m7tei8 , botf1-m7u0w9 , botf1-m7tij6 , botf1-m7u819 , botf1-m7u6d8 , botf1-m7tzd4 , botf1-m7tqd7 , botf1-m7tyz9 , botf1-m7unl9 , botf1-m7u429 , botf1-m7u4s5 , botf1-m7ul92 , botf1-m7tx42 , botf1-m7u9h4 , botf1-m7u187 , botf1-m7uz64 , botf1-m7u4q4 , botf1-m7u2f6 , botf1-m7tt59 , botf1-m7v3h2 , botf1-m7u6c9 , botf1-m7tud9 , botf1-m7u309 , scls1-a7et87 , botf4-g2ylt4 , scls1-a7f5a0 , scls1-a7f900 , botf4-g2yib9 , scls1-a7f3m9 , scls1-a7er46 , botf4-g2y3y4 , botf4-g2xyy5 , botf1-m7uct5 , scls1-a7ea78 , scls1-kex1 , scls1-cbpya , botfb-cbpya , scls1-a7ecx1

Title : The Medicago genome provides insight into the evolution of rhizobial symbioses - Young_2011_Nature_480_520
Author(s) : Young ND , Debelle F , Oldroyd GE , Geurts R , Cannon SB , Udvardi MK , Benedito VA , Mayer KF , Gouzy J , Schoof H , Van de Peer Y , Proost S , Cook DR , Meyers BC , Spannagl M , Cheung F , De Mita S , Krishnakumar V , Gundlach H , Zhou S , Mudge J , Bharti AK , Murray JD , Naoumkina MA , Rosen B , Silverstein KA , Tang H , Rombauts S , Zhao PX , Zhou P , Barbe V , Bardou P , Bechner M , Bellec A , Berger A , Berges H , Bidwell S , Bisseling T , Choisne N , Couloux A , Denny R , Deshpande S , Dai X , Doyle JJ , Dudez AM , Farmer AD , Fouteau S , Franken C , Gibelin C , Gish J , Goldstein S , Gonzalez AJ , Green PJ , Hallab A , Hartog M , Hua A , Humphray SJ , Jeong DH , Jing Y , Jocker A , Kenton SM , Kim DJ , Klee K , Lai H , Lang C , Lin S , Macmil SL , Magdelenat G , Matthews L , McCorrison J , Monaghan EL , Mun JH , Najar FZ , Nicholson C , Noirot C , O'Bleness M , Paule CR , Poulain J , Prion F , Qin B , Qu C , Retzel EF , Riddle C , Sallet E , Samain S , Samson N , Sanders I , Saurat O , Scarpelli C , Schiex T , Segurens B , Severin AJ , Sherrier DJ , Shi R , Sims S , Singer SR , Sinharoy S , Sterck L , Viollet A , Wang BB , Wang K , Wang M , Wang X , Warfsmann J , Weissenbach J , White DD , White JD , Wiley GB , Wincker P , Xing Y , Yang L , Yao Z , Ying F , Zhai J , Zhou L , Zuber A , Denarie J , Dixon RA , May GD , Schwartz DC , Rogers J , Quetier F , Town CD , Roe BA
Ref : Nature , 480 :520 , 2011
Abstract : Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing approximately 94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.
ESTHER : Young_2011_Nature_480_520
PubMedSearch : Young_2011_Nature_480_520
PubMedID: 22089132
Gene_locus related to this paper: medtr-b7fki4 , medtr-b7fmi1 , medtr-g7itl1 , medtr-g7iu67 , medtr-g7izm0 , medtr-g7j641 , medtr-g7jtf8 , medtr-g7jtg2 , medtr-g7jtg4 , medtr-g7kem3 , medtr-g7kml3 , medtr-g7ksx5 , medtr-g7leb3 , medtr-q1s5d8 , medtr-q1s9m3 , medtr-q1t171 , medtr-g7k9e1 , medtr-g7k9e3 , medtr-g7k9e5 , medtr-g7k9e8 , medtr-g7k9e9 , medtr-g7lbp2 , medtr-g7lch3 , medtr-g7ib94 , medtr-g7ljk8 , medtr-g7i6w5 , medtr-g7kvg4 , medtr-g7iam1 , medtr-g7iam3 , medtr-g7l754 , medtr-g7jr41 , medtr-g7l4f5 , medtr-g7l755 , medtr-a0a072vyl4 , medtr-g7jwk8 , medtr-a0a072vhg0 , medtr-a0a072vrv9 , medtr-g7kmk5 , medtr-a0a072uuf6 , medtr-a0a072urp3 , medtr-g7zzc3 , medtr-g7ie19 , medtr-g7kst7 , medtr-a0a072u5k5 , medtr-a0a072v056 , medtr-scp1 , medtr-g7kyn0 , medtr-g7inw6 , medtr-g7j3q3

Title : Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites - Barbe_2011_J.Bacteriol_193_5055
Author(s) : Barbe V , Bouzon M , Mangenot S , Badet B , Poulain J , Segurens B , Vallenet D , Marliere P , Weissenbach J
Ref : Journal of Bacteriology , 193 :5055 , 2011
Abstract : Streptomyces cattleya, a producer of the antibiotics thienamycin and cephamycin C, is one of the rare bacteria known to synthesize fluorinated metabolites. The genome consists of two linear replicons. The genes involved in fluorine metabolism and in the biosynthesis of the antibiotic thienamycin were mapped on both replicons.
ESTHER : Barbe_2011_J.Bacteriol_193_5055
PubMedSearch : Barbe_2011_J.Bacteriol_193_5055
PubMedID: 21868806
Gene_locus related to this paper: stren-f8jjf8 , stren-f8jk65 , stren-f8jly2 , stren-f8jm04 , stren-f8juv4 , stren-f8k466 , stren-f8jvj2 , stren-f8k4s8

Title : Complete genome sequence of Crohn's disease-associated adherent-invasive E. coli strain LF82 - Miquel_2010_PLoS.One_5_e12714
Author(s) : Miquel S , Peyretaillade E , Claret L , de Vallee A , Dossat C , Vacherie B , Zineb el H , Segurens B , Barbe V , Sauvanet P , Neut C , Colombel JF , Medigue C , Mojica FJ , Peyret P , Bonnet R , Darfeuille-Michaud A
Ref : PLoS ONE , 5 : , 2010
Abstract : BACKGROUND: Ileal lesions of Crohn's disease (CD) patients are abnormally colonized by pathogenic adherent-invasive Escherichia coli (AIEC) able to invade and to replicate within intestinal epithelial cells and macrophages. PRINCIPAL FINDINGS: We report here the complete genome sequence of E. coli LF82, the reference strain of adherent-invasive E. coli associated with ileal Crohn's disease. The LF82 genome of 4,881,487 bp total size contains a circular chromosome with a size of 4,773,108 bp and a plasmid of 108,379 bp. The analysis of predicted coding sequences (CDSs) within the LF82 flexible genome indicated that this genome is close to the avian pathogenic strain APEC_01, meningitis-associated strain S88 and urinary-isolated strain UTI89 with regards to flexible genome and single nucleotide polymorphisms in various virulence factors. Interestingly, we observed that strains LF82 and UTI89 adhered at a similar level to Intestine-407 cells and that like LF82, APEC_01 and UTI89 were highly invasive. However, A1EC strain LF82 had an intermediate killer phenotype compared to APEC-01 and UTI89 and the LF82 genome does not harbour most of specific virulence genes from ExPEC. LF82 genome has evolved from those of ExPEC B2 strains by the acquisition of Salmonella and Yersinia isolated or clustered genes or CDSs located on pLF82 plasmid and at various loci on the chromosome. CONCLUSION: LF82 genome analysis indicated that a number of genes, gene clusters and pathoadaptative mutations which have been acquired may play a role in virulence of AIEC strain LF82.
ESTHER : Miquel_2010_PLoS.One_5_e12714
PubMedSearch : Miquel_2010_PLoS.One_5_e12714
PubMedID: 20862302
Gene_locus related to this paper: ecoli-yeiG , ecoli-yqia

Title : The Ectocarpus genome and the independent evolution of multicellularity in brown algae - Cock_2010_Nature_465_617
Author(s) : Cock JM , Sterck L , Rouze P , Scornet D , Allen AE , Amoutzias G , Anthouard V , Artiguenave F , Aury JM , Badger JH , Beszteri B , Billiau K , Bonnet E , Bothwell JH , Bowler C , Boyen C , Brownlee C , Carrano CJ , Charrier B , Cho GY , Coelho SM , Collen J , Corre E , Da Silva C , Delage L , Delaroque N , Dittami SM , Doulbeau S , Elias M , Farnham G , Gachon CM , Gschloessl B , Heesch S , Jabbari K , Jubin C , Kawai H , Kimura K , Kloareg B , Kupper FC , Lang D , Le Bail A , LeBlanc C , Lerouge P , Lohr M , Lopez PJ , Martens C , Maumus F , Michel G , Miranda-Saavedra D , Morales J , Moreau H , Motomura T , Nagasato C , Napoli CA , Nelson DR , Nyvall-Collen P , Peters AF , Pommier C , Potin P , Poulain J , Quesneville H , Read B , Rensing SA , Ritter A , Rousvoal S , Samanta M , Samson G , Schroeder DC , Segurens B , Strittmatter M , Tonon T , Tregear JW , Valentin K , von Dassow P , Yamagishi T , Van de Peer Y , Wincker P
Ref : Nature , 465 :617 , 2010
Abstract : Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further.
ESTHER : Cock_2010_Nature_465_617
PubMedSearch : Cock_2010_Nature_465_617
PubMedID: 20520714
Gene_locus related to this paper: ectsi-d7fm61 , ectsi-d7fs16 , ectsi-d7fsv3 , ectsi-d7fte8 , ectsi-d7fux6 , ectsi-d7fvr0 , ectsi-d7fvu4 , ectsi-d7fwk0 , ectsi-d7fyh7 , ectsi-d7g0w7 , ectsi-d7g6g5 , ectsi-d7g484 , ectsi-d7g686 , ectsi-d8lca9 , ectsi-d8lfv2 , ectsi-d8lqg6 , ectsi-d8ltj9 , ectsi-d7fjz2 , ectsi-d7g376

Title : Genome sequences of Escherichia coli B strains REL606 and BL21(DE3) - Jeong_2009_J.Mol.Biol_394_644
Author(s) : Jeong H , Barbe V , Lee CH , Vallenet D , Yu DS , Choi SH , Couloux A , Lee SW , Yoon SH , Cattolico L , Hur CG , Park HS , Segurens B , Kim SC , Oh TK , Lenski RE , Studier FW , Daegelen P , Kim JF
Ref : Journal of Molecular Biology , 394 :644 , 2009
Abstract : Escherichia coli K-12 and B have been the subjects of classical experiments from which much of our understanding of molecular genetics has emerged. We present here complete genome sequences of two E. coli B strains, REL606, used in a long-term evolution experiment, and BL21(DE3), widely used to express recombinant proteins. The two genomes differ in length by 72,304 bp and have 426 single base pair differences, a seemingly large difference for laboratory strains having a common ancestor within the last 67 years. Transpositions by IS1 and IS150 have occurred in both lineages. Integration of the DE3 prophage in BL21(DE3) apparently displaced a defective prophage in the lambda attachment site of B. As might have been anticipated from the many genetic and biochemical experiments comparing B and K-12 over the years, the B genomes are similar in size and organization to the genome of E. coli K-12 MG1655 and have >99% sequence identity over approximately 92% of their genomes. E. coli B and K-12 differ considerably in distribution of IS elements and in location and composition of larger mobile elements. An unexpected difference is the absence of a large cluster of flagella genes in B, due to a 41 kbp IS1-mediated deletion. Gene clusters that specify the LPS core, O antigen, and restriction enzymes differ substantially, presumably because of horizontal transfer. Comparative analysis of 32 independently isolated E. coli and Shigella genomes, both commensals and pathogenic strains, identifies a minimal set of genes in common plus many strain-specific genes that constitute a large E. coli pan-genome.
ESTHER : Jeong_2009_J.Mol.Biol_394_644
PubMedSearch : Jeong_2009_J.Mol.Biol_394_644
PubMedID: 19786035
Gene_locus related to this paper: eco57-b3a913 , ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-yqia , ecoli-YfhR

Title : The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae - Pieretti_2009_BMC.Genomics_10_616
Author(s) : Pieretti I , Royer M , Barbe V , Carrere S , Koebnik R , Cociancich S , Couloux A , Darrasse A , Gouzy J , Jacques MA , Lauber E , Manceau C , Mangenot S , Poussier S , Segurens B , Szurek B , Verdier V , Arlat M , Rott P
Ref : BMC Genomics , 10 :616 , 2009
Abstract : BACKGROUND: The Xanthomonadaceae family contains two xylem-limited plant pathogenic bacterial species, Xanthomonas albilineans and Xylella fastidiosa. X. fastidiosa was the first completely sequenced plant pathogen. It is insect-vectored, has a reduced genome and does not possess hrp genes which encode a Type III secretion system found in most plant pathogenic bacteria. X. fastidiosa was excluded from the Xanthomonas group based on phylogenetic analyses with rRNA sequences.
RESULTS: The complete genome of X. albilineans was sequenced and annotated. X. albilineans, which is not known to be insect-vectored, also has a reduced genome and does not possess hrp genes. Phylogenetic analysis using X. albilineans genomic sequences showed that X. fastidiosa belongs to the Xanthomonas group. Order of divergence of the Xanthomonadaceae revealed that X. albilineans and X. fastidiosa experienced a convergent reductive genome evolution during their descent from the progenitor of the Xanthomonas genus. Reductive genome evolutions of the two xylem-limited Xanthomonadaceae were compared in light of their genome characteristics and those of obligate animal symbionts and pathogens. CONCLUSION: The two xylem-limited Xanthomonadaceae, during their descent from a common ancestral parent, experienced a convergent reductive genome evolution. Adaptation to the nutrient-poor xylem elements and to the cloistered environmental niche of xylem vessels probably favoured this convergent evolution. However, genome characteristics of X. albilineans differ from those of X. fastidiosa and obligate animal symbionts and pathogens, indicating that a distinctive process was responsible for the reductive genome evolution in this pathogen. The possible role in genome reduction of the unique toxin albicidin, produced by X. albilineans, is discussed.
ESTHER : Pieretti_2009_BMC.Genomics_10_616
PubMedSearch : Pieretti_2009_BMC.Genomics_10_616
PubMedID: 20017926
Gene_locus related to this paper: xanal-q53b17 , xanap-d2u924 , xanap-d2uar7 , xanap-d2ub15 , xanap-d2ucz4 , xanap-d2ue41 , xanap-d2ue72 , xanap-d2ueb5 , xanap-d2uf40 , xanap-d2ugg6 , xanap-d2ugj3 , xanap-d2ugr3 , xanap-d2ugv1 , xanap-d2ubh2 , xanap-d2ud71 , xanap-d2u9n1 , xanap-d2uci9

Title : Comparative genomics of protoploid Saccharomycetaceae - Souciet_2009_Genome.Res_19_1696
Author(s) : Souciet JL , Dujon B , Gaillardin C , Johnston M , Baret PV , Cliften P , Sherman DJ , Weissenbach J , Westhof E , Wincker P , Jubin C , Poulain J , Barbe V , Segurens B , Artiguenave F , Anthouard V , Vacherie B , Val ME , Fulton RS , Minx P , Wilson R , Durrens P , Jean G , Marck C , Martin T , Nikolski M , Rolland T , Seret ML , Casaregola S , Despons L , Fairhead C , Fischer G , Lafontaine I , Leh V , Lemaire M , De Montigny J , Neuveglise C , Thierry A , Blanc-Lenfle I , Bleykasten C , Diffels J , Fritsch E , Frangeul L , Goeffon A , Jauniaux N , Kachouri-Lafond R , Payen C , Potier S , Pribylova L , Ozanne C , Richard GF , Sacerdot C , Straub ML , Talla E
Ref : Genome Res , 19 :1696 , 2009
Abstract : Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.
ESTHER : Souciet_2009_Genome.Res_19_1696
PubMedSearch : Souciet_2009_Genome.Res_19_1696
PubMedID: 19525356
Gene_locus related to this paper: lactc-c5dci9 , lactc-c5ddi5 , lactc-c5dew5 , lactc-c5dez1 , lactc-c5df11 , lactc-c5dfh7 , lactc-c5dgd1 , lactc-c5dif7 , lactc-c5din7 , lactc-c5dja0 , lactc-c5dm95 , lactc-c5dn06 , lactc-c5dnn9 , lactc-c5e2g8 , lactc-c5e3n5 , lactc-c5e375 , zygrc-c5drr0 , zygrc-c5dvh0 , zygrc-c5dvl2 , zygrc-c5dvx0 , zygrc-c5dvz8 , zygrc-c5dx83 , zygrc-c5dxn5 , zygrc-c5dxq9 , zygrc-c5e0w1 , zygrc-c5e1e4 , zygrc-c5e1h2 , zygro-a0a1q2zt01 , 9sach-a0a0p1kuu1 , lactc-kex1 , zygrc-kex1

Title : Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity - Lapidus_2008_Chem.Biol.Interact_171_236
Author(s) : Lapidus A , Goltsman E , Auger S , Galleron N , Segurens B , Dossat C , Land ML , Broussolle V , Brillard J , Guinebretiere MH , Sanchis V , Nguen-The C , Lereclus D , Richardson P , Wincker P , Weissenbach J , Ehrlich SD , Sorokin A
Ref : Chemico-Biological Interactions , 171 :236 , 2008
Abstract : The Bacillus cereus group represents sporulating soil bacteria containing pathogenic strains which may cause diarrheic or emetic food poisoning outbreaks. Multiple locus sequence typing revealed a presence in natural samples of these bacteria of about 30 clonal complexes. Application of genomic methods to this group was however biased due to the major interest for representatives closely related to Bacillus anthracis. Albeit the most important food-borne pathogens were not yet defined, existing data indicate that they are scattered all over the phylogenetic tree. The preliminary analysis of the sequences of three genomes discussed in this paper narrows down the gaps in our knowledge of the B. cereus group. The strain NVH391-98 is a rare but particularly severe food-borne pathogen. Sequencing revealed that the strain should be a representative of a novel bacterial species, for which the name Bacillus cytotoxis or Bacillus cytotoxicus is proposed. This strain has a reduced genome size compared to other B. cereus group strains. Genome analysis revealed absence of sigma B factor and the presence of genes encoding diarrheic Nhe toxin, not detected earlier. The strain B. cereus F837/76 represents a clonal complex close to that of B. anthracis. Including F837/76, three such B. cereus strains had been sequenced. Alignment of genomes suggests that B. anthracis is their common ancestor. Since such strains often emerge from clinical cases, they merit a special attention. The third strain, KBAB4, is a typical facultative psychrophile generally found in soil. Phylogenic studies show that in nature it is the most active group in terms of gene exchange. Genomic sequence revealed high presence of extra-chromosomal genetic material (about 530kb) that may account for this phenomenon. Genes coding Nhe-like toxin were found on a big plasmid in this strain. This may indicate a potential mechanism of toxicity spread from the psychrophile strain community. The results of this genomic work and ecological compartments of different strains incite to consider a necessity of creating prophylactic vaccines against bacteria closely related to NVH391-98 and F837/76. Presumably developing of such vaccines can be based on the properties of non-pathogenic strains such as KBAB4 or ATCC14579 reported here or earlier. By comparing the protein coding genes of strains being sequenced in this project to others we estimate the shared proteome, or core genome, in the B. cereus group to be 3000+/-200 genes and the total proteome, or pan-genome, to be 20-25,000 genes.
ESTHER : Lapidus_2008_Chem.Biol.Interact_171_236
PubMedSearch : Lapidus_2008_Chem.Biol.Interact_171_236
PubMedID: 17434157
Gene_locus related to this paper: bacwk-A9VF42 , bacan-BA0954 , bacan-BA5009 , bacan-DHBF , bacce-BC0192 , bacce-BC2141 , bacce-BC2171 , bacce-BC2458 , bacce-BC3133 , bacce-BC4862 , bacce-BC5130 , bacce-c2zq05 , bacce-c2zsv2 , bacce-lipP , bacce-PHAC , bacce-q2edm4 , bacce-q72yu1 , baccn-a7gmc0 , baccn-a7gmj8 , baccn-a7gnr6 , baccn-a7gpf9 , baccn-a7gpl4 , baccn-a7gpr3 , baccn-a7gqf9 , baccn-a7gr85 , baccn-a7gsc6 , baccn-a7gse0 , baccn-a7gt87 , baccn-a7gu34 , baccn-a7gu90 , baccn-a7guq6 , baccr-pepx , bacmy-c3aae7 , bactu-c3ice0 , bacwk-a9vg55 , bacwk-a9vgr5 , bacwk-a9vju9 , bacwk-a9vkh7 , bacwk-a9vm76 , bacwk-a9vql0 , bacwk-a9vqm8 , bacwk-a9vtw7 , bacwk-a9vv54 , baccn-a7gp74

Title : The genome sequence of the model ascomycete fungus Podospora anserina - Espagne_2008_Genome.Biol_9_R77
Author(s) : Espagne E , Lespinet O , Malagnac F , Da Silva C , Jaillon O , Porcel BM , Couloux A , Aury JM , Segurens B , Poulain J , Anthouard V , Grossetete S , Khalili H , Coppin E , Dequard-Chablat M , Picard M , Contamine V , Arnaise S , Bourdais A , Berteaux-Lecellier V , Gautheret D , de Vries RP , Battaglia E , Coutinho PM , Danchin EG , Henrissat B , Khoury RE , Sainsard-Chanet A , Boivin A , Pinan-Lucarre B , Sellem CH , Debuchy R , Wincker P , Weissenbach J , Silar P
Ref : Genome Biol , 9 :R77 , 2008
Abstract : BACKGROUND: The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development. RESULTS: We present a 10X draft sequence of P. anserina genome, linked to the sequences of a large expressed sequence tag collection. Similar to higher eukaryotes, the P. anserina transcription/splicing machinery generates numerous non-conventional transcripts. Comparison of the P. anserina genome and orthologous gene set with the one of its close relatives, Neurospora crassa, shows that synteny is poorly conserved, the main result of evolution being gene shuffling in the same chromosome. The P. anserina genome contains fewer repeated sequences and has evolved new genes by duplication since its separation from N. crassa, despite the presence of the repeat induced point mutation mechanism that mutates duplicated sequences. We also provide evidence that frequent gene loss took place in the lineages leading to P. anserina and N. crassa. P. anserina contains a large and highly specialized set of genes involved in utilization of natural carbon sources commonly found in its natural biotope. It includes genes potentially involved in lignin degradation and efficient cellulose breakdown. CONCLUSION: The features of the P. anserina genome indicate a highly dynamic evolution since the divergence of P. anserina and N. crassa, leading to the ability of the former to use specific complex carbon sources that match its needs in its natural biotope.
ESTHER : Espagne_2008_Genome.Biol_9_R77
PubMedSearch : Espagne_2008_Genome.Biol_9_R77
PubMedID: 18460219
Gene_locus related to this paper: podan-b2a8u1 , podan-b2a9c4 , podan-b2a9k6 , podan-b2aa90 , podan-b2ab33 , podan-b2abs0 , podan-b2ac17 , podan-b2ack2 , podan-b2ad07 , podan-b2adj6 , podan-b2adk0 , podan-b2ae59 , podan-b2aee7 , podan-b2af51 , podan-b2afn5 , podan-b2afu6 , podan-b2akq7 , podan-b2aly0 , podan-b2am11 , podan-b2an24 , podan-b2ank1 , podan-b2apa8 , podan-b2api8 , podan-b2apj6 , podan-b2arl9 , podan-b2arz7 , podan-b2ase4 , podan-b2atn0 , podan-b2au46 , podan-b2aun9 , podan-b2av47 , podan-b2ava6 , podan-b2avm3 , podan-b2avu5 , podan-b2avx3 , podan-b2awk8 , podan-b2axk2 , podan-b2axz2 , podan-b2b1p7 , podan-b2b5e4 , podan-b2b6n7 , podan-b2b069 , podan-b2b073 , podan-b2b395 , podan-dapb , podan-b2afr0 , podan-b2a9k8 , podan-b2atb3 , podan-b2aca3 , podan-b2arv3 , podan-b2ank5 , podan-b2ax54 , podan-b2ad56 , podan-b2anm1 , podan-b2aya1 , podan-b2b164 , podan-a0a090d4h4 , podan-a0a090ccl8 , podan-b2b5p4 , podan-b2azp1 , podan-b2af75 , podan-b2alm5 , podan-b2ass5 , podan-b2aez8 , podan-kex1 , podan-cbpya

Title : Comparative analysis of Acinetobacters: three genomes for three lifestyles - Vallenet_2008_PLoS.One_3_e1805
Author(s) : Vallenet D , Nordmann P , Barbe V , Poirel L , Mangenot S , Bataille E , Dossat C , Gas S , Kreimeyer A , Lenoble P , Oztas S , Poulain J , Segurens B , Robert C , Abergel C , Claverie JM , Raoult D , Medigue C , Weissenbach J , Cruveiller S
Ref : PLoS ONE , 3 :e1805 , 2008
Abstract : Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil.
ESTHER : Vallenet_2008_PLoS.One_3_e1805
PubMedSearch : Vallenet_2008_PLoS.One_3_e1805
PubMedID: 18350144
Gene_locus related to this paper: acib1-e8pgf8 , acib3-b7guy6 , acib3-b7h156 , acib3-metx , aciba-d0c992 , aciba-k1epl1 , aciba-k6lkl9 , acibc-b2huf4 , acibc-b2i0a2 , acibc-b2i0w9 , acibc-b2i2b0 , acibs-b0vt32 , acibt-a3m1g6 , acibt-a3m5r6 , acibt-a3m5t3 , acibt-a3m5x2 , acibt-a3m627 , acibt-a3m707 , aciby-b0v723 , acica-d0s0a7 , aciju-d0sj67 , aciba-f5iht4 , aciba-a0a009wzt4

Title : Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia - Giraud_2007_Science_316_1307
Author(s) : Giraud E , Moulin L , Vallenet D , Barbe V , Cytryn E , Avarre JC , Jaubert M , Simon D , Cartieaux F , Prin Y , Bena G , Hannibal L , Fardoux J , Kojadinovic M , Vuillet L , Lajus A , Cruveiller S , Rouy Z , Mangenot S , Segurens B , Dossat C , Franck WL , Chang WS , Saunders E , Bruce D , Richardson P , Normand P , Dreyfus B , Pignol D , Stacey G , Emerich D , Vermeglio A , Medigue C , Sadowsky M
Ref : Science , 316 :1307 , 2007
Abstract : Leguminous plants (such as peas and soybeans) and rhizobial soil bacteria are symbiotic partners that communicate through molecular signaling pathways, resulting in the formation of nodules on legume roots and occasionally stems that house nitrogen-fixing bacteria. Nodule formation has been assumed to be exclusively initiated by the binding of bacterial, host-specific lipochito-oligosaccharidic Nod factors, encoded by the nodABC genes, to kinase-like receptors of the plant. Here we show by complete genome sequencing of two symbiotic, photosynthetic, Bradyrhizobium strains, BTAi1 and ORS278, that canonical nodABC genes and typical lipochito-oligosaccharidic Nod factors are not required for symbiosis in some legumes. Mutational analyses indicated that these unique rhizobia use an alternative pathway to initiate symbioses, where a purine derivative may play a key role in triggering nodule formation.
ESTHER : Giraud_2007_Science_316_1307
PubMedSearch : Giraud_2007_Science_316_1307
PubMedID: 17540897
Gene_locus related to this paper: brasb-a5e8s7 , brasb-a5e9h9 , brasb-a5e9x2 , brasb-a5eac3 , brasb-a5eb24 , brasb-a5ech6 , brasb-a5eck9 , brasb-a5ed44 , brasb-a5edz7 , brasb-a5ee62 , brasb-a5ees1 , brasb-a5ef53 , brasb-a5efp3 , brasb-a5efp4 , brasb-a5eg29 , brasb-a5eh09 , brasb-a5ei81 , brasb-a5eiy7 , brasb-a5ej26 , brasb-a5ek41 , brasb-a5elh0 , brasb-a5ema7 , brasb-a5emc8 , brasb-a5eml7 , brasb-a5ene5 , brasb-a5ent6 , brasb-a5eny8 , brasb-a5ep81 , brasb-a5eph8 , brasb-a5epv4 , brasb-a5epx9 , brasb-a5eqb3 , brasb-a5erc8 , brasb-a5esb1 , brasb-a5ese9 , brasb-a5esl7 , brasb-a5esv5 , brasb-a5esw6 , brasb-a5etk7 , brasb-a5eul1 , braso-a4yk16 , braso-a4yl66 , braso-a4ylm4 , braso-a4ylr9 , braso-a4ylx7 , braso-a4ymj8 , braso-a4ynl1 , braso-a4ypd9 , braso-a4yqh3 , braso-a4yr10 , braso-a4yri0 , braso-a4yt56 , braso-a4yul4 , braso-a4yw76 , braso-a4ywb6 , braso-a4yxg2 , braso-a4yy49 , braso-a4yyj6 , braso-a4yzd7 , braso-a4yzh0 , braso-a4z0q9 , braso-a4z0v7 , braso-a4z1h1 , braso-a4z1p1 , braso-a4z1p8 , braso-a4z1v6 , braso-a4z2a5 , braso-a4z152 , braso-a4yl32 , brasb-a5et63 , brasb-a5emr8 , braso-a4ynl2 , brasb-a5eqb2 , braso-a4yr63

Title : Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome - Sirand-Pugnet_2007_PLoS.Genet_3_e75
Author(s) : Sirand-Pugnet P , Lartigue C , Marenda M , Jacob D , Barre A , Barbe V , Schenowitz C , Mangenot S , Couloux A , Segurens B , de Daruvar A , Blanchard A , Citti C
Ref : PLoS Genet , 3 :e75 , 2007
Abstract : Mycoplasmas are commonly described as the simplest self-replicating organisms, whose evolution was mainly characterized by genome downsizing with a proposed evolutionary scenario similar to that of obligate intracellular bacteria such as insect endosymbionts. Thus far, analysis of mycoplasma genomes indicates a low level of horizontal gene transfer (HGT) implying that DNA acquisition is strongly limited in these minimal bacteria. In this study, the genome of the ruminant pathogen Mycoplasma agalactiae was sequenced. Comparative genomic data and phylogenetic tree reconstruction revealed that approximately 18% of its small genome (877,438 bp) has undergone HGT with the phylogenetically distinct mycoides cluster, which is composed of significant ruminant pathogens. HGT involves genes often found as clusters, several of which encode lipoproteins that usually play an important role in mycoplasma-host interaction. A decayed form of a conjugative element also described in a member of the mycoides cluster was found in the M. agalactiae genome, suggesting that HGT may have occurred by mobilizing a related genetic element. The possibility of HGT events among other mycoplasmas was evaluated with the available sequenced genomes. Our data indicate marginal levels of HGT among Mycoplasma species except for those described above and, to a lesser extent, for those observed in between the two bird pathogens, M. gallisepticum and M. synoviae. This first description of large-scale HGT among mycoplasmas sharing the same ecological niche challenges the generally accepted evolutionary scenario in which gene loss is the main driving force of mycoplasma evolution. The latter clearly differs from that of other bacteria with small genomes, particularly obligate intracellular bacteria that are isolated within host cells. Consequently, mycoplasmas are not only able to subvert complex hosts but presumably have retained sexual competence, a trait that may prevent them from genome stasis and contribute to adaptation to new hosts.
ESTHER : Sirand-Pugnet_2007_PLoS.Genet_3_e75
PubMedSearch : Sirand-Pugnet_2007_PLoS.Genet_3_e75
PubMedID: 17511520
Gene_locus related to this paper: mycap-a5ixe1 , mycap-a5ixe2 , mycap-a5ixk0 , mycap-a5ixt9 , mycap-a5iy19 , mycap-a5iza3 , mycap-a5ixl0

Title : The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla - Jaillon_2007_Nature_449_463
Author(s) : Jaillon O , Aury JM , Noel B , Policriti A , Clepet C , Casagrande A , Choisne N , Aubourg S , Vitulo N , Jubin C , Vezzi A , Legeai F , Hugueney P , Dasilva C , Horner D , Mica E , Jublot D , Poulain J , Bruyere C , Billault A , Segurens B , Gouyvenoux M , Ugarte E , Cattonaro F , Anthouard V , Vico V , Del Fabbro C , Alaux M , Di Gaspero G , Dumas V , Felice N , Paillard S , Juman I , Moroldo M , Scalabrin S , Canaguier A , Le Clainche I , Malacrida G , Durand E , Pesole G , Laucou V , Chatelet P , Merdinoglu D , Delledonne M , Pezzotti M , Lecharny A , Scarpelli C , Artiguenave F , Pe ME , Valle G , Morgante M , Caboche M , Adam-Blondon AF , Weissenbach J , Quetier F , Wincker P
Ref : Nature , 449 :463 , 2007
Abstract : The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
ESTHER : Jaillon_2007_Nature_449_463
PubMedSearch : Jaillon_2007_Nature_449_463
PubMedID: 17721507
Gene_locus related to this paper: vitvi-a5b6n6 , vitvi-a5b7c0 , vitvi-a5b8l9 , vitvi-a5bji4 , vitvi-a5bxd7 , vitvi-a5c1g2 , vitvi-a5c8p7 , vitvi-a7ntu2 , vitvi-a7pnb4 , vitvi-a7pus9 , vitvi-a7q3d1 , vitvi-a7qpz3 , vitvi-BIG8.1 , vitvi-d7sqb8 , vitvi-d7ssp2 , vitvi-d7sx57 , vitvi-d7t734 , vitvi-d7t940 , vitvi-d7tef1 , vitvi-d7tg96 , vitvi-d7tle9 , vitvi-d7tmb8 , vitvi-d7tpk8 , vitvi-d7tve2 , vitvi-d7tvr0 , vitvi-d7ubd6 , vitvi-f6hhx5 , vitvi-f6hi76 , vitvi-f6hqe0 , vitvi-f6hzf1.1 , vitvi-f6hzf1.2 , vitvi-d7ssd7 , vitvi-d7ssd8 , vitvi-d7ssd9 , vitvi-d7u935 , vitvi-f6gyw1 , vitvi-f6gyw2 , vitvi-f6gyw4 , vitvi-f6hqf1 , vitvi-f6hqf4 , vitvi-d7tum4 , vitvi-d7tba3 , vitvi-d7stm8 , vitvi-d7t3j3 , vitvi-d7uce5 , vitvi-f6he55 , vitvi-d7thp4 , vitvi-d7tfe6 , vitvi-e0cv10 , vitvi-f6gtp7 , vitvi-f6hva3 , vitvi-d7tqu0 , vitvi-f6hqq0 , vitvi-d7tci5 , vitvi-d7sut7 , vitvi-d7sut6 , vitvi-f6h317 , vitvi-f6h318 , vitvi-f6hsf1 , vitvi-f6hqd1 , vitvi-f6hqd0 , vitvi-f6hfp6 , vitvi-d7u2i4 , vitvi-f6gsx7 , vitvi-d7si01 , vitvi-d7si06 , vitvi-f6hz08 , vitvi-d7tr61 , vitvi-e0crl0 , vitvi-f6hrz4 , vitvi-f6i7l0

Title : A tale of two oxidation states: bacterial colonization of arsenic-rich environments - Muller_2007_PLoS.Genet_3_e53
Author(s) : Muller D , Medigue C , Koechler S , Barbe V , Barakat M , Talla E , Bonnefoy V , Krin E , Arsene-Ploetze F , Carapito C , Chandler M , Cournoyer B , Cruveiller S , Dossat C , Duval S , Heymann M , Leize E , Lieutaud A , Lievremont D , Makita Y , Mangenot S , Nitschke W , Ortet P , Perdrial N , Schoepp B , Siguier P , Simeonova DD , Rouy Z , Segurens B , Turlin E , Vallenet D , Van Dorsselaer A , Weiss S , Weissenbach J , Lett MC , Danchin A , Bertin PN
Ref : PLoS Genet , 3 :e53 , 2007
Abstract : Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the beta-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth.
ESTHER : Muller_2007_PLoS.Genet_3_e53
PubMedSearch : Muller_2007_PLoS.Genet_3_e53
PubMedID: 17432936
Gene_locus related to this paper: herar-a4g4w8 , herar-a4g5p0 , herar-a4g6p3 , herar-a4g378 , herar-a4g411 , herar-a4g622 , herar-a4g818 , herar-a4g899 , herar-a4gac3 , herar-metx , herar-a4g8n7

Title : Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila - Vodovar_2006_Nat.Biotechnol_24_673
Author(s) : Vodovar N , Vallenet D , Cruveiller S , Rouy Z , Barbe V , Acosta C , Cattolico L , Jubin C , Lajus A , Segurens B , Vacherie B , Wincker P , Weissenbach J , Lemaitre B , Medigue C , Boccard F
Ref : Nat Biotechnol , 24 :673 , 2006
Abstract : Pseudomonas entomophila is an entomopathogenic bacterium that, upon ingestion, kills Drosophila melanogaster as well as insects from different orders. The complete sequence of the 5.9-Mb genome was determined and compared to the sequenced genomes of four Pseudomonas species. P. entomophila possesses most of the catabolic genes of the closely related strain P. putida KT2440, revealing its metabolically versatile properties and its soil lifestyle. Several features that probably contribute to its entomopathogenic properties were disclosed. Unexpectedly for an animal pathogen, P. entomophila is devoid of a type III secretion system and associated toxins but rather relies on a number of potential virulence factors such as insecticidal toxins, proteases, putative hemolysins, hydrogen cyanide and novel secondary metabolites to infect and kill insects. Genome-wide random mutagenesis revealed the major role of the two-component system GacS/GacA that regulates most of the potential virulence factors identified.
ESTHER : Vodovar_2006_Nat.Biotechnol_24_673
PubMedSearch : Vodovar_2006_Nat.Biotechnol_24_673
PubMedID: 16699499
Gene_locus related to this paper: pseae-PA1622 , psee4-q1i2k0 , psee4-q1i3a7 , psee4-q1i3n8 , psee4-q1i4y6 , psee4-q1i4z6 , psee4-q1i5s3 , psee4-q1i5s9 , psee4-q1i6r6 , psee4-q1i9a0 , psee4-q1i9c3 , psee4-q1i9h5 , psee4-q1i9t2 , psee4-q1iaa7 , psee4-q1ibu9 , psee4-q1icm5 , psee4-q1idp8 , psee4-q1idv7 , psee4-q1ie27 , psee4-q1ie44 , psee4-q1ifj6 , psee4-q1ifn8 , psee4-q1ig13 , psee4-q1ige4 , psep1-a5wax1 , psepg-b0kir7 , psepk-q88nk6 , psepu-METX , psepu-PHAZ , psepu-PIP , psepu-PP1617 , psepu-PP4178 , psepu-PP4551 , psee4-q1icg3

Title : Deciphering the evolution and metabolism of an anammox bacterium from a community genome - Strous_2006_Nature_440_790
Author(s) : Strous M , Pelletier E , Mangenot S , Rattei T , Lehner A , Taylor MW , Horn M , Daims H , Bartol-Mavel D , Wincker P , Barbe V , Fonknechten N , Vallenet D , Segurens B , Schenowitz-Truong C , Medigue C , Collingro A , Snel B , Dutilh BE , Op den Camp HJ , van der Drift C , Cirpus I , van de Pas-Schoonen KT , Harhangi HR , van Niftrik L , Schmid M , Keltjens J , van de Vossenberg J , Kartal B , Meier H , Frishman D , Huynen MA , Mewes HW , Weissenbach J , Jetten MS , Wagner M , Le Paslier D
Ref : Nature , 440 :790 , 2006
Abstract : Anaerobic ammonium oxidation (anammox) has become a main focus in oceanography and wastewater treatment. It is also the nitrogen cycle's major remaining biochemical enigma. Among its features, the occurrence of hydrazine as a free intermediate of catabolism, the biosynthesis of ladderane lipids and the role of cytoplasm differentiation are unique in biology. Here we use environmental genomics--the reconstruction of genomic data directly from the environment--to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis from a complex bioreactor community. The genome data illuminate the evolutionary history of the Planctomycetes and allow us to expose the genetic blueprint of the organism's special properties. Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility.
ESTHER : Strous_2006_Nature_440_790
PubMedSearch : Strous_2006_Nature_440_790
PubMedID: 16598256
Gene_locus related to this paper: 9bact-q1py93 , 9bact-q1q3k9 , 9bact-q1q414

Title : Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia - Aury_2006_Nature_444_171
Author(s) : Aury JM , Jaillon O , Duret L , Noel B , Jubin C , Porcel BM , Segurens B , Daubin V , Anthouard V , Aiach N , Arnaiz O , Billaut A , Beisson J , Blanc I , Bouhouche K , Camara F , Duharcourt S , Guigo R , Gogendeau D , Katinka M , Keller AM , Kissmehl R , Klotz C , Koll F , Le Mouel A , Lepere G , Malinsky S , Nowacki M , Nowak JK , Plattner H , Poulain J , Ruiz F , Serrano V , Zagulski M , Dessen P , Betermier M , Weissenbach J , Scarpelli C , Schachter V , Sperling L , Meyer E , Cohen J , Wincker P
Ref : Nature , 444 :171 , 2006
Abstract : The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.
ESTHER : Aury_2006_Nature_444_171
PubMedSearch : Aury_2006_Nature_444_171
PubMedID: 17086204
Gene_locus related to this paper: parte-a0bds8 , parte-a0bga5 , parte-a0bnp2 , parte-a0bnt1 , parte-a0bpr4 , parte-a0btv5 , parte-a0byt1 , parte-a0bz94 , parte-a0c0b8 , parte-a0c0q4 , parte-a0c1z8 , parte-a0c3e0 , parte-a0c9f4 , parte-a0c962 , parte-a0cb90 , parte-a0cck1 , parte-a0cj40 , parte-a0cq13 , parte-a0cqw8 , parte-a0crq3 , parte-a0cu52 , parte-a0cur9 , parte-a0cxu4 , parte-a0cyf3 , parte-a0czs5 , parte-a0d1l8 , parte-a0d9i7 , parte-a0d589 , parte-a0de29 , parte-a0dem3 , parte-a0dg79 , parte-a0diq2 , parte-a0dk36 , parte-a0dkh0 , parte-a0dld4 , parte-a0dnw2 , parte-a0drp9 , parte-a0drx0 , parte-a0duj9 , parte-a0dvl0 , parte-a0dwm9 , parte-a0dy72 , parte-a0dz74 , parte-a0e0g8 , parte-a0e0z4 , parte-a0e1p0 , parte-a0e4m9 , parte-a0e8v9 , parte-a0e9r1 , parte-a0e581 , parte-a0ecy9 , parte-a0ecz4 , parte-a0ef67 , parte-a0d7k3

Title : Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype - Jaillon_2004_Nature_431_946
Author(s) : Jaillon O , Aury JM , Brunet F , Petit JL , Stange-Thomann N , Mauceli E , Bouneau L , Fischer C , Ozouf-Costaz C , Bernot A , Nicaud S , Jaffe D , Fisher S , Lutfalla G , Dossat C , Segurens B , Dasilva C , Salanoubat M , Levy M , Boudet N , Castellano S , Anthouard V , Jubin C , Castelli V , Katinka M , Vacherie B , Biemont C , Skalli Z , Cattolico L , Poulain J , de Berardinis V , Cruaud C , Duprat S , Brottier P , Coutanceau JP , Gouzy J , Parra G , Lardier G , Chapple C , McKernan KJ , McEwan P , Bosak S , Kellis M , Volff JN , Guigo R , Zody MC , Mesirov J , Lindblad-Toh K , Birren B , Nusbaum C , Kahn D , Robinson-Rechavi M , Laudet V , Schachter V , Quetier F , Saurin W , Scarpelli C , Wincker P , Lander ES , Weissenbach J , Roest Crollius H
Ref : Nature , 431 :946 , 2004
Abstract : Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests approximately 900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.
ESTHER : Jaillon_2004_Nature_431_946
PubMedSearch : Jaillon_2004_Nature_431_946
PubMedID: 15496914
Gene_locus related to this paper: tetng-3neur , tetng-4neur , tetng-ACHE , tetng-BCHE , tetng-h3cfz4 , tetng-h3ci57 , tetng-h3cl30 , tetng-h3cnh2 , tetng-nlgn2b , tetng-h3czr1 , tetng-h3dbr5 , tetng-nlgn2a , tetng-nlgn3b , tetng-q4ref8 , tetng-q4rjp3 , tetng-q4rjy3 , tetng-q4rk53 , tetng-q4rk63 , tetng-q4rk66 , tetng-q4rkk3 , tetng-q4rli3 , tetng-q4rn09 , tetng-q4rqj4 , tetng-q4rqz6 , tetng-q4rr22 , tetng-q4rru9 , tetng-q4rtq6 , tetng-q4rvf8 , tetng-q4rwa0 , tetng-q4rx90 , tetng-q4ryv8 , tetng-q4ryz3 , tetng-q4s0h8 , tetng-q4s5x0 , tetng-q4s6r1 , tetng-q4s6t6 , tetng-q4s7e3 , tetng-q4s7x6 , tetng-q4s8t5 , tetng-q4s9w9 , tetng-q4s050 , tetng-q4s091 , tetng-q4s144 , tetng-q4s309 , tetng-q4s578 , tetng-q4sal4 , tetng-q4sbm6 , tetng-q4sbp0 , tetng-q4sbu0 , tetng-q4sd49 , tetng-q4ser6 , tetng-q4sfm7 , tetng-q4sgm5 , tetng-q4sgv2 , tetng-q4sh74 , tetng-q4shl7 , tetng-q4si60 , tetng-q4sie5 , tetng-q4sku6 , tetng-q4smu0 , tetng-q4smy3 , tetng-q4snp0 , tetng-q4snq3 , tetng-q4spa7 , tetng-q4spq0 , tetng-q4sqr3 , tetng-q4sty0 , tetng-q4suu2 , tetng-q4suz1 , tetng-q4sxh3 , tetng-q4syn6 , tetng-q4szk0 , tetng-q4szy0 , tetng-q4t3m9 , tetng-q4t4a1 , tetng-q4t6m1 , tetng-q4t7r6 , tetng-q4t173 , tetng-q4t826 , tetng-q4t920 , tetng-q4ta33 , tetng-q4tab8 , tetng-q4tb62 , tetng-q4tbe2 , tetng-h3dbw2 , tetng-h3cpc8 , tetng-h3cjy0 , tetng-h3d966 , tetng-h3d3e3 , tetng-h3d961 , tetng-h3ctg6 , tetng-h3dde8 , tetng-h3dde9 , tetng-h3det9 , tetng-h3cre8 , tetng-h3dfb4 , tetng-h3clj8