Badger JH

References (18)

Title : Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum - McLean_2013_Proc.Natl.Acad.Sci.U.S.A_110_E2390
Author(s) : McLean JS , Lombardo MJ , Badger JH , Edlund A , Novotny M , Yee-Greenbaum J , Vyahhi N , Hall AP , Yang Y , Dupont CL , Ziegler MG , Chitsaz H , Allen AE , Yooseph S , Tesler G , Pevzner PA , Friedman RM , Nealson KH , Venter JC , Lasken RS
Ref : Proc Natl Acad Sci U S A , 110 :E2390 , 2013
Abstract : The "dark matter of life" describes microbes and even entire divisions of bacterial phyla that have evaded cultivation and have yet to be sequenced. We present a genome from the globally distributed but elusive candidate phylum TM6 and uncover its metabolic potential. TM6 was detected in a biofilm from a sink drain within a hospital restroom by analyzing cells using a highly automated single-cell genomics platform. We developed an approach for increasing throughput and effectively improving the likelihood of sampling rare events based on forming small random pools of single-flow-sorted cells, amplifying their DNA by multiple displacement amplification and sequencing all cells in the pool, creating a "mini-metagenome." A recently developed single-cell assembler, SPAdes, in combination with contig binning methods, allowed the reconstruction of genomes from these mini-metagenomes. A total of 1.07 Mb was recovered in seven contigs for this member of TM6 (JCVI TM6SC1), estimated to represent 90% of its genome. High nucleotide identity between a total of three TM6 genome drafts generated from pools that were independently captured, amplified, and assembled provided strong confirmation of a correct genomic sequence. TM6 is likely a Gram-negative organism and possibly a symbiont of an unknown host (nonfree living) in part based on its small genome, low-GC content, and lack of biosynthesis pathways for most amino acids and vitamins. Phylogenomic analysis of conserved single-copy genes confirms that TM6SC1 is a deeply branching phylum.
ESTHER : McLean_2013_Proc.Natl.Acad.Sci.U.S.A_110_E2390
PubMedSearch : McLean_2013_Proc.Natl.Acad.Sci.U.S.A_110_E2390
PubMedID: 23754396
Gene_locus related to this paper: 9bact-a0a0d2je38

Title : Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence - Chen_2011_BMC.Genomics_12_294
Author(s) : Chen Y , Stine OC , Badger JH , Gil AI , Nair GB , Nishibuchi M , Fouts DE
Ref : BMC Genomics , 12 :294 , 2011
Abstract : BACKGROUND: Vibrio parahaemolyticus is a common cause of foodborne disease. Beginning in 1996, a more virulent strain having serotype O3:K6 caused major outbreaks in India and other parts of the world, resulting in the emergence of a pandemic. Other serovariants of this strain emerged during its dissemination and together with the original O3:K6 were termed strains of the pandemic clone. Two genomes, one of this virulent strain and one pre-pandemic strain have been sequenced. We sequenced four additional genomes of V. parahaemolyticus in this study that were isolated from different geographical regions and time points. Comparative genomic analyses of six strains of V. parahaemolyticus isolated from Asia and Peru were performed in order to advance knowledge concerning the evolution of V. parahaemolyticus; specifically, the genetic changes contributing to serotype conversion and virulence. Two pre-pandemic strains and three pandemic strains, isolated from different geographical regions, were serotype O3:K6 and either toxin profiles (tdh+, trh-) or (tdh-, trh+). The sixth pandemic strain sequenced in this study was serotype O4:K68.
RESULTS: Genomic analyses revealed that the trh+ and tdh+ strains had different types of pathogenicity islands and mobile elements as well as major structural differences between the tdh pathogenicity islands of the pre-pandemic and pandemic strains. In addition, the results of single nucleotide polymorphism (SNP) analysis showed that 94% of the SNPs between O3:K6 and O4:K68 pandemic isolates were within a 141 kb region surrounding the O- and K-antigen-encoding gene clusters. The "core" genes of V. parahaemolyticus were also compared to those of V. cholerae and V. vulnificus, in order to delineate differences between these three pathogenic species. Approximately one-half (49-59%) of each species' core genes were conserved in all three species, and 14-24% of the core genes were species-specific and in different functional categories.
CONCLUSIONS: Our data support the idea that the pandemic strains are closely related and that recent South American outbreaks of foodborne disease caused by V. parahaemolyticus are closely linked to outbreaks in India. Serotype conversion from O3:K6 to O4:K68 was likely due to a recombination event involving a region much larger than the O-antigen- and K-antigen-encoding gene clusters. Major differences between pathogenicity islands and mobile elements are also likely driving the evolution of V. parahaemolyticus. In addition, our analyses categorized genes that may be useful in differentiating pathogenic Vibrios at the species level.
ESTHER : Chen_2011_BMC.Genomics_12_294
PubMedSearch : Chen_2011_BMC.Genomics_12_294
PubMedID: 21645368
Gene_locus related to this paper: vibpa-PHAC , vibpa-VP0148 , vibpa-VP0409 , vibpa-VP0429 , vibpa-VP0693 , vibpa-VP0837 , vibpa-VP0869 , vibpa-VP1025 , vibpa-VP1181 , vibpa-VP1678 , vibpa-VP2790 , vibpa-VP2974 , vibpa-VPA0054 , vibpa-VPA0070 , vibpa-VPA0468 , vibpa-VPA1061 , vibpa-VPA1249 , vibpa-VPA1467 , vibpa-VPA1496 , vibpa-VPA1595 , vibpa-y674 , vibpa-y969

Title : Streptomyces turgidiscabies Car8 contains a modular pathogenicity island that shares virulence genes with other actinobacterial plant pathogens - Huguet-Tapia_2011_Plasmid_65_118
Author(s) : Huguet-Tapia JC , Badger JH , Loria R , Pettis GS
Ref : Plasmid , 65 :118 , 2011
Abstract : Streptomyces turgidiscabies Car8 is an actinobacterium that causes the economically important disease potato scab. Pathogenesis in this species is associated with a mobile pathogenicity island (PAISt) that site specifically inserts into the bacA gene in Streptomyces spp. Here we provide the 674,223 bp sequence of PAISt, which consists of two non-overlapping modules of 105,364 and 568,859 bp. These modules are delimited by three copies of an 8 bp palindromic sequence (TTCATGAA), that also is the integration site (att) of the element. Putative tyrosine recombinase (IntSt) and excisionase (XisSt) proteins are encoded just upstream of att-R. PAISt has regions of synteny to pathogenic, symbiotic and saprophytic actinomycetes. The 105,364 bp PAISt module is identical to a genomic island in Streptomyces scabies 87-22, while the 568,859 bp module contains only a short region of synteny to that genome. However, both modules contain previously characterized and candidate virulence genes.
ESTHER : Huguet-Tapia_2011_Plasmid_65_118
PubMedSearch : Huguet-Tapia_2011_Plasmid_65_118
PubMedID: 21087627
Gene_locus related to this paper: 9acto-l7ffg2 , 9acto-l7fb12 , 9acto-l7f9l5 , 9acto-l7f9j6 , 9acto-l7exi7 , 9acto-l7fdw3 , 9acto-l7fde3 , 9acto-l7ez89 , 9acto-l7esm9 , 9acto-l7fet0 , 9acto-l7f9t1 , 9actn-l7fav1 , 9actn-l7f9n9 , 9actn-l7evr4 , 9actn-l7f5u9

Title : The complete genome sequence of Haloferax volcanii DS2, a model archaeon - Hartman_2010_PLoS.One_5_e9605
Author(s) : Hartman AL , Norais C , Badger JH , Delmas S , Haldenby S , Madupu R , Robinson J , Khouri H , Ren Q , Lowe TM , Maupin-Furlow J , Pohlschroder M , Daniels C , Pfeiffer F , Allers T , Eisen JA
Ref : PLoS ONE , 5 :e9605 , 2010
Abstract : BACKGROUND: Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general. METHODOLOGY/PRINCIPAL FINDINGS: We report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb). CONCLUSIONS/SIGNIFICANCE: The completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of Hfx. volcanii.
ESTHER : Hartman_2010_PLoS.One_5_e9605
PubMedSearch : Hartman_2010_PLoS.One_5_e9605
PubMedID: 20333302
Gene_locus related to this paper: halvd-d4gpd7 , halvd-d4gtr7 , halvd-d4gug3 , halvd-d4gug9 , halvd-d4gz20 , halvd-metxa

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 : Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas - Worden_2009_Science_324_268
Author(s) : Worden AZ , Lee JH , Mock T , Rouze P , Simmons MP , Aerts AL , Allen AE , Cuvelier ML , Derelle E , Everett MV , Foulon E , Grimwood J , Gundlach H , Henrissat B , Napoli C , McDonald SM , Parker MS , Rombauts S , Salamov A , von Dassow P , Badger JH , Coutinho PM , Demir E , Dubchak I , Gentemann C , Eikrem W , Gready JE , John U , Lanier W , Lindquist EA , Lucas S , Mayer KF , Moreau H , Not F , Otillar R , Panaud O , Pangilinan J , Paulsen I , Piegu B , Poliakov A , Robbens S , Schmutz J , Toulza E , Wyss T , Zelensky A , Zhou K , Armbrust EV , Bhattacharya D , Goodenough UW , Van de Peer Y , Grigoriev IV
Ref : Science , 324 :268 , 2009
Abstract : Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.
ESTHER : Worden_2009_Science_324_268
PubMedSearch : Worden_2009_Science_324_268
PubMedID: 19359590
Gene_locus related to this paper: 9chlo-c1e363 , 9chlo-c1ehp8 , 9chlo-c1fhv2 , 9chlo-c1mis3 , 9chlo-c1na62 , micpc-c1mh04 , micpc-c1mhj0 , micpc-c1mie7 , micpc-c1mj20 , micpc-c1mjh0 , micpc-c1mny7 , micpc-c1mpb2 , micpc-c1mrl2 , micpc-c1msr1 , micpc-c1mvk4 , micpc-c1mvx4 , micpc-c1n5d2 , micpc-c1n6i2 , micpc-c1n842 , micsr-c1dzu1 , micsr-c1e0v8 , micsr-c1e2u5 , micsr-c1e4q6 , micsr-c1e6z5 , micsr-c1e046 , micsr-c1e286 , micsr-c1eap0 , micsr-c1ec00 , micsr-c1edy4 , micsr-c1efl2 , micsr-c1eh15 , micsr-c1ei44 , micsr-c1eii9 , micsr-c1eiz1 , micsr-c1fft1 , micsr-c1fi89 , micsr-c1fj57 , micsr-c1e9f6 , micsr-c1e9u2 , micsr-c1fgg8 , micpc-c1mie3 , micpc-c1ms20 , micpc-c1n640 , miccc-c1e278 , micpc-c1mpa6

Title : The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms) - Yang_2009_PLoS.One_4_e6085
Author(s) : Yang JC , Madupu R , Durkin AS , Ekborg NA , Pedamallu CS , Hostetler JB , Radune D , Toms BS , Henrissat B , Coutinho PM , Schwarz S , Field L , Trindade-Silva AE , Soares CA , Elshahawi S , Hanora A , Schmidt EW , Haygood MG , Posfai J , Benner J , Madinger C , Nove J , Anton B , Chaudhary K , Foster J , Holman A , Kumar S , Lessard PA , Luyten YA , Slatko B , Wood N , Wu B , Teplitski M , Mougous JD , Ward N , Eisen JA , Badger JH , Distel DL
Ref : PLoS ONE , 4 :e6085 , 2009
Abstract : Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring marine bivalves of the family Teredinidae (shipworms). This species is the sole cultivated member of an endosymbiotic consortium thought to provide the host with enzymes, including cellulases and nitrogenase, critical for digestion of wood and supplementation of the host's nitrogen-deficient diet. T. turnerae is closely related to the free-living marine polysaccharide degrading bacterium Saccharophagus degradans str. 2-40 and to as yet uncultivated endosymbionts with which it coexists in shipworm cells. Like S. degradans, the T. turnerae genome encodes a large number of enzymes predicted to be involved in complex polysaccharide degradation (>100). However, unlike S. degradans, which degrades a broad spectrum (>10 classes) of complex plant, fungal and algal polysaccharides, T. turnerae primarily encodes enzymes associated with deconstruction of terrestrial woody plant material. Also unlike S. degradans and many other eubacteria, T. turnerae dedicates a large proportion of its genome to genes predicted to function in secondary metabolism. Despite its intracellular niche, the T. turnerae genome lacks many features associated with obligate intracellular existence (e.g. reduced genome size, reduced %G+C, loss of genes of core metabolism) and displays evidence of adaptations common to free-living bacteria (e.g. defense against bacteriophage infection). These results suggest that T. turnerae is likely a facultative intracellular ensosymbiont whose niche presently includes, or recently included, free-living existence. As such, the T. turnerae genome provides insights into the range of genomic adaptations associated with intracellular endosymbiosis as well as enzymatic mechanisms relevant to the recycling of plant materials in marine environments and the production of cellulose-derived biofuels.
ESTHER : Yang_2009_PLoS.One_4_e6085
PubMedSearch : Yang_2009_PLoS.One_4_e6085
PubMedID: 19568419
Gene_locus related to this paper: tertt-c5bif5 , tertt-c5bkb0 , tertt-c5bkv2 , tertt-c5bmq4 , tertt-c5bmw5 , tertt-c5bmx1 , tertt-c5bmz8 , tertt-c5bn23 , tertt-c5bn62 , tertt-c5bpb2 , tertt-c5bpu2 , tertt-c5bru8 , tertt-c5btp6 , tertt-c5buc2 , tertt-metx , tertt-c5br42 , tertt-c5bpt0 , tertt-c5btk3

Title : Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum - Wu_2009_PLoS.One_4_e4207
Author(s) : Wu D , Raymond J , Wu M , Chatterji S , Ren Q , Graham JE , Bryant DA , Robb F , Colman A , Tallon LJ , Badger JH , Madupu R , Ward NL , Eisen JA
Ref : PLoS ONE , 4 :e4207 , 2009
Abstract : In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an "Assembling the Tree of Life" project, we determined the genome sequence of Thermomicrobium roseum DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. Its genome is composed of two circular DNA elements, one of 2,006,217 bp (referred to as the chromosome) and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though few standard housekeeping genes are found on the megaplasmid, it does encode a complete system for chemotaxis including both chemosensory components and an entire flagellar apparatus. This is the first known example of a complete flagellar system being encoded on a plasmid and suggests a straightforward means for lateral transfer of flagellum-based motility. Phylogenomic analyses support the recent rRNA-based analyses that led to T. roseum being removed from the phylum Thermomicrobia and assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching member of this phylum, analysis of its genome provides insights into the evolution of the Chloroflexi. In addition, even though this species is not photosynthetic, analysis of the genome provides some insight into the origins of photosynthesis in the Chloroflexi. Metabolic pathway reconstructions and experimental studies revealed new aspects of the biology of this species. For example, we present evidence that T. roseum oxidizes CO aerobically, making it the first thermophile known to do so. In addition, we propose that glycosylation of its carotenoids plays a crucial role in the adaptation of the cell membrane to this bacterium's thermophilic lifestyle. Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain was isolated, show that close relatives of T. roseum DSM 5159 are present but have some key differences from the strain sequenced.
ESTHER : Wu_2009_PLoS.One_4_e4207
PubMedSearch : Wu_2009_PLoS.One_4_e4207
PubMedID: 19148287
Gene_locus related to this paper: therp-b9kxz7 , therp-b9l2i8 , therp-b9l396

Title : Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum - van den Berg_2008_Nat.Biotechnol_26_1161
Author(s) : van den Berg MA , Albang R , Albermann K , Badger JH , Daran JM , Driessen AJ , Garcia-Estrada C , Fedorova ND , Harris DM , Heijne WH , Joardar V , Kiel JA , Kovalchuk A , Martin JF , Nierman WC , Nijland JG , Pronk JT , Roubos JA , van der Klei IJ , van Peij NN , Veenhuis M , von Dohren H , Wagner C , Wortman J , Bovenberg RA
Ref : Nat Biotechnol , 26 :1161 , 2008
Abstract : Industrial penicillin production with the filamentous fungus Penicillium chrysogenum is based on an unprecedented effort in microbial strain improvement. To gain more insight into penicillin synthesis, we sequenced the 32.19 Mb genome of P. chrysogenum Wisconsin54-1255 and identified numerous genes responsible for key steps in penicillin production. DNA microarrays were used to compare the transcriptomes of the sequenced strain and a penicillinG high-producing strain, grown in the presence and absence of the side-chain precursor phenylacetic acid. Transcription of genes involved in biosynthesis of valine, cysteine and alpha-aminoadipic acid-precursors for penicillin biosynthesis-as well as of genes encoding microbody proteins, was increased in the high-producing strain. Some gene products were shown to be directly controlling beta-lactam output. Many key cellular transport processes involving penicillins and intermediates remain to be characterized at the molecular level. Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven metabolic engineering.
ESTHER : van den Berg_2008_Nat.Biotechnol_26_1161
PubMedSearch : van den Berg_2008_Nat.Biotechnol_26_1161
PubMedID: 18820685
Gene_locus related to this paper: pench-b6gw01 , pench-b6gwp9 , pench-b6gzt9 , pench-b6h2r5 , pench-b6h3c6 , pench-b6h3s3 , pench-b6h6w7 , pench-b6h7m0 , pench-b6h043 , pench-b6h270 , pench-b6h303 , pench-b6hcx0 , pench-b6hfx1 , pench-b6hjt6 , pench-b6hm64 , pench-b6hmg2 , pench-b6hnf2 , pench-b6hnf7 , pench-b6hph0 , pench-b6huc9 , penrw-b6hdc6 , pench-q3v6c9 , pencw-atg15 , pencw-b6gwt5 , pencw-b6gx34 , pencw-b6gzd8 , pencw-b6gzp7 , pencw-b6h2f4 , pencw-b6h2h0 , pencw-b6h2n4 , pencw-b6h3u7 , pencw-b6h4n3 , pencw-b6h4s6 , pencw-b6h5k2 , pencw-b6h6t6 , pencw-b6h7f0 , pencw-b6h7r1 , pencw-b6h8a0 , pencw-b6h8i1 , pencw-b6h828 , pencw-b6ha41 , pencw-b6hat0 , pencw-b6hb79 , pencw-b6hcq8 , pencw-b6hfx7 , pencw-b6hgb0 , pencw-b6hhg8 , pencw-b6hjj1 , pencw-b6hl02 , pencw-b6hmd9 , pencw-b6hmh5 , pencw-b6hmh7 , pencw-b6hpn2 , pencw-b6hpz6 , pencw-b6hqu4 , pencw-b6hs49 , pencw-b6hun6 , pencw-b6hv09 , pencw-cuti1 , pencw-cuti2 , pencw-dapb , pencw-b6had0 , pencw-b6h497 , pencw-b6gw76 , pencw-b6hs05 , pencw-b6h0h6 , penna-a0a1v6yep8 , penrw-b6huu8 , penrw-kex1 , penrw-cbpya , penrw-adrd

Title : The Phaeodactylum genome reveals the evolutionary history of diatom genomes - Bowler_2008_Nature_456_239
Author(s) : Bowler C , Allen AE , Badger JH , Grimwood J , Jabbari K , Kuo A , Maheswari U , Martens C , Maumus F , Otillar RP , Rayko E , Salamov A , Vandepoele K , Beszteri B , Gruber A , Heijde M , Katinka M , Mock T , Valentin K , Verret F , Berges JA , Brownlee C , Cadoret JP , Chiovitti A , Choi CJ , Coesel S , De Martino A , Detter JC , Durkin C , Falciatore A , Fournet J , Haruta M , Huysman MJ , Jenkins BD , Jiroutova K , Jorgensen RE , Joubert Y , Kaplan A , Kroger N , Kroth PG , La Roche J , Lindquist E , Lommer M , Martin-Jezequel V , Lopez PJ , Lucas S , Mangogna M , McGinnis K , Medlin LK , Montsant A , Oudot-Le Secq MP , Napoli C , Obornik M , Parker MS , Petit JL , Porcel BM , Poulsen N , Robison M , Rychlewski L , Rynearson TA , Schmutz J , Shapiro H , Siaut M , Stanley M , Sussman MR , Taylor AR , Vardi A , von Dassow P , Vyverman W , Willis A , Wyrwicz LS , Rokhsar DS , Weissenbach J , Armbrust EV , Green BR , Van de Peer Y , Grigoriev IV
Ref : Nature , 456 :239 , 2008
Abstract : Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes ( approximately 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.
ESTHER : Bowler_2008_Nature_456_239
PubMedSearch : Bowler_2008_Nature_456_239
PubMedID: 18923393
Gene_locus related to this paper: phatc-b7fp91 , phatc-b7fqd3 , phatc-b7frf9 , phatc-b7fry8 , phatc-b7ftw8 , phatc-b7fv70 , phatc-b7fw66 , phatc-b7g2b2 , phatc-b7g5z5 , phatc-b7g6f1 , phatc-b7g6r8 , phatc-b7g957 , phatc-b7ga73 , phatc-b7gb22 , phatc-b7gc60 , phatc-b7gdm3 , phatc-b7gdq6 , phatc-b7ge82 , phatc-b7gee0 , phatr-b7frs5 , phatr-b7g1k3 , phatr-b7s4a4 , thaps-b8bsy4 , thaps-b8cfn8 , phatc-b7g635 , phatc-b7gaj3 , thaps-b8c079

Title : Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice - Fouts_2008_PLoS.Genet_4_e1000141
Author(s) : Fouts DE , Tyler HL , DeBoy RT , Daugherty S , Ren Q , Badger JH , Durkin AS , Huot H , Shrivastava S , Kothari S , Dodson RJ , Mohamoud Y , Khouri H , Roesch LF , Krogfelt KA , Struve C , Triplett EW , Methe BA
Ref : PLoS Genet , 4 :e1000141 , 2008
Abstract : We report here the sequencing and analysis of the genome of the nitrogen-fixing endophyte, Klebsiella pneumoniae 342. Although K. pneumoniae 342 is a member of the enteric bacteria, it serves as a model for studies of endophytic, plant-bacterial associations due to its efficient colonization of plant tissues (including maize and wheat, two of the most important crops in the world), while maintaining a mutualistic relationship that encompasses supplying organic nitrogen to the host plant. Genomic analysis examined K. pneumoniae 342 for the presence of previously identified genes from other bacteria involved in colonization of, or growth in, plants. From this set, approximately one-third were identified in K. pneumoniae 342, suggesting additional factors most likely contribute to its endophytic lifestyle. Comparative genome analyses were used to provide new insights into this question. Results included the identification of metabolic pathways and other features devoted to processing plant-derived cellulosic and aromatic compounds, and a robust complement of transport genes (15.4%), one of the highest percentages in bacterial genomes sequenced. Although virulence and antibiotic resistance genes were predicted, experiments conducted using mouse models showed pathogenicity to be attenuated in this strain. Comparative genomic analyses with the presumed human pathogen K. pneumoniae MGH78578 revealed that MGH78578 apparently cannot fix nitrogen, and the distribution of genes essential to surface attachment, secretion, transport, and regulation and signaling varied between each genome, which may indicate critical divergences between the strains that influence their preferred host ranges and lifestyles (endophytic plant associations for K. pneumoniae 342 and presumably human pathogenesis for MGH78578). Little genome information is available concerning endophytic bacteria. The K. pneumoniae 342 genome will drive new research into this less-understood, but important category of bacterial-plant host relationships, which could ultimately enhance growth and nutrition of important agricultural crops and development of plant-derived products and biofuels.
ESTHER : Fouts_2008_PLoS.Genet_4_e1000141
PubMedSearch : Fouts_2008_PLoS.Genet_4_e1000141
PubMedID: 18654632
Gene_locus related to this paper: klep3-b5xp56 , klep3-b5xqp6 , klep3-b5xzn5 , klep3-b5xzy8 , klep3-bioh , klep3-menh , klep7-a6t8q2 , klep7-a6t9v6 , klep7-a6tb98 , klep7-mhpc , klep7-y243 , klep7-y1077 , klepn-c4x8q1 , klepn-w8uta0 , klep3-rutd

Title : Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus - Fedorova_2008_PLoS.Genet_4_e1000046
Author(s) : Fedorova ND , Khaldi N , Joardar VS , Maiti R , Amedeo P , Anderson MJ , Crabtree J , Silva JC , Badger JH , Albarraq A , Angiuoli S , Bussey H , Bowyer P , Cotty PJ , Dyer PS , Egan A , Galens K , Fraser-Liggett CM , Haas BJ , Inman JM , Kent R , Lemieux S , Malavazi I , Orvis J , Roemer T , Ronning CM , Sundaram JP , Sutton G , Turner G , Venter JC , White OR , Whitty BR , Youngman P , Wolfe KH , Goldman GH , Wortman JR , Jiang B , Denning DW , Nierman WC
Ref : PLoS Genet , 4 :e1000046 , 2008
Abstract : We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and up to 2% unique genes in each genome. While the core genes are 99.8% identical at the nucleotide level, identity for variable genes can be as low 40%. The most divergent loci appear to contain heterokaryon incompatibility (het) genes associated with fungal programmed cell death such as developmental regulator rosA. Cross-species comparison has revealed that 8.5%, 13.5% and 12.6%, respectively, of A. fumigatus, N. fischeri and A. clavatus genes are species-specific. These genes are significantly smaller in size than core genes, contain fewer exons and exhibit a subtelomeric bias. Most of them cluster together in 13 chromosomal islands, which are enriched for pseudogenes, transposons and other repetitive elements. At least 20% of A. fumigatus-specific genes appear to be functional and involved in carbohydrate and chitin catabolism, transport, detoxification, secondary metabolism and other functions that may facilitate the adaptation to heterogeneous environments such as soil or a mammalian host. Contrary to what was suggested previously, their origin cannot be attributed to horizontal gene transfer (HGT), but instead is likely to involve duplication, diversification and differential gene loss (DDL). The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated "gene dumps" and, perhaps, simultaneously, as "gene factories".
ESTHER : Fedorova_2008_PLoS.Genet_4_e1000046
PubMedSearch : Fedorova_2008_PLoS.Genet_4_e1000046
PubMedID: 18404212
Gene_locus related to this paper: aspcl-a1c4m6 , aspcl-a1c5a7 , aspcl-a1c6w3 , aspcl-a1c8p7 , aspcl-a1c8q9 , aspcl-a1c9k4 , aspcl-a1c759 , aspcl-a1c786 , aspcl-a1c823 , aspcl-a1c859 , aspcl-a1c881 , aspcl-a1c994 , aspcl-a1cag4 , aspcl-a1caj8 , aspcl-a1cas0 , aspcl-a1cc86 , aspcl-a1ccq2 , aspcl-a1cfv7 , aspcl-a1chj6 , aspcl-a1cif4 , aspcl-a1ck14 , aspcl-a1cke4 , aspcl-a1ckq1 , aspcl-a1cli1 , aspcl-a1cln8 , aspcl-a1cm72 , aspcl-a1cns2 , aspcl-a1cpk9 , aspcl-a1cra8 , aspcl-a1crr5 , aspcl-a1crs9 , aspcl-a1cs04 , aspcl-a1cs39 , aspcl-a1cu39 , aspcl-atg15 , aspcl-axe1 , aspcl-cuti1 , aspcl-cuti3 , aspcl-dapb , aspcl-dpp4 , aspcl-dpp5 , aspcl-faeb , aspcl-faec1 , aspcl-faec2 , aspfc-b0xp50 , aspfc-b0xu40 , aspfc-b0xzj6 , aspfc-b0y2h6 , aspfc-b0y962 , aspfc-b0yaj6 , aspfc-dpp5 , aspfu-DPP4 , aspfu-faeb1 , aspfu-faec , aspfu-ppme1 , aspfu-q4w9r3 , aspfu-q4w9t5 , aspfu-q4w9z4 , aspfu-q4wa57 , aspfu-q4wa78 , aspfu-q4wag0 , aspfu-q4wal3 , aspfu-q4wbc5 , aspfu-q4wbj7 , aspfu-q4wdg2 , aspfu-q4wf06 , aspfu-q4wf29 , aspfu-q4wf56 , aspfu-q4wfq9 , aspfu-q4wg73 , aspfu-q4wgm4 , aspfu-q4win2 , aspfu-q4wk31 , aspfu-q4wk44 , aspfu-q4wk90 , aspfu-q4wm12 , aspfu-q4wm84 , aspfu-q4wm86 , aspfu-q4wmr0 , aspfu-q4wny7 , aspfu-q4wp19 , aspfu-q4wpb9 , aspfu-q4wqj8 , aspfu-q4wqv2 , aspfu-q4wrr7 , aspfu-q4wu51 , aspfu-q4wub2 , aspfu-q4wui7 , aspfu-q4wuk8 , aspfu-q4wum3 , aspfu-q4wuw0 , aspfu-q4wvy1 , aspfu-q4ww22 , aspfu-q4wx13 , aspfu-q4wxd0 , aspfu-q4wxe4 , aspfu-q4wxr1 , aspfu-q4wyq5 , aspfu-q4wz16 , aspfu-q4wzd5 , aspfu-q4wzh6 , aspfu-q4x0n6 , aspfu-q4x1n0 , aspfu-q4x1w9 , aspfu-q4x078 , neofi-a1cwa6 , neofi-a1d4m8 , neofi-a1d4p0 , neofi-a1d5p2 , neofi-a1d104 , neofi-a1d380 , neofi-a1d512 , neofi-a1d654 , neofi-a1da18 , neofi-a1dal8 , neofi-a1df46 , neofi-a1dhj0 , neofi-a1di44 , neofi-a1dk35 , neofi-a1dki7 , neofi-a1dkt6 , neofi-a1dn55 , neofi-atg15 , neofi-axe1 , neofi-faeb1 , neofi-faeb2 , neofi-faec , aspcl-a1cd34 , aspcl-a1cd88 , neofi-a1dc66 , aspcl-a1ceh5 , neofi-a1dfr9 , aspfm-a0a084bf80 , aspcl-a1cqb5 , aspcl-a1cs44 , neofi-a1d517 , neofi-a1dbz0 , neofi-a1cuz0 , aspcl-a1c5e8 , neofi-a1d0b8 , aspcl-a1cdf0 , aspcl-a1ccd3 , neofi-a1da82 , neofi-a1d5e6 , aspcl-kex1 , aspcl-cbpya

Title : Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus - Myers_2007_Nat.Biotechnol_25_569
Author(s) : Myers GS , Parker D , Al-Hasani K , Kennan RM , Seemann T , Ren Q , Badger JH , Selengut JD , DeBoy RT , Tettelin H , Boyce JD , McCarl VP , Han X , Nelson WC , Madupu R , Mohamoud Y , Holley T , Fedorova N , Khouri H , Bottomley SP , Whittington RJ , Adler B , Songer JG , Rood JI , Paulsen IT
Ref : Nat Biotechnol , 25 :569 , 2007
Abstract : Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe. It differs markedly from small genomes of intracellular bacteria, retaining greater biosynthetic capabilities and lacking any evidence of extensive ongoing genome reduction. Comparative genomic microarray studies and bioinformatic analysis suggested that, despite its small size, almost 20% of the genome is derived from lateral gene transfer. Most of these regions seem to be associated with virulence. Metabolic reconstruction indicated unsuspected capabilities, including carbohydrate utilization, electron transfer and several aerobic pathways. Global transcriptional profiling and bioinformatic analysis enabled the prediction of virulence factors and cell surface proteins. Screening of these proteins against ovine antisera identified eight immunogenic proteins that are candidate antigens for a cross-protective vaccine.
ESTHER : Myers_2007_Nat.Biotechnol_25_569
PubMedSearch : Myers_2007_Nat.Biotechnol_25_569
PubMedID: 17468768
Gene_locus related to this paper: dicnv-a5evg0 , dicnv-a5ewn0 , dicnv-a5ewp3

Title : Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote - Eisen_2006_PLoS.Biol_4_e286
Author(s) : Eisen JA , Coyne RS , Wu M , Wu D , Thiagarajan M , Wortman JR , Badger JH , Ren Q , Amedeo P , Jones KM , Tallon LJ , Delcher AL , Salzberg SL , Silva JC , Haas BJ , Majoros WH , Farzad M , Carlton JM , Smith RK, Jr. , Garg J , Pearlman RE , Karrer KM , Sun L , Manning G , Elde NC , Turkewitz AP , Asai DJ , Wilkes DE , Wang Y , Cai H , Collins K , Stewart BA , Lee SR , Wilamowska K , Weinberg Z , Ruzzo WL , Wloga D , Gaertig J , Frankel J , Tsao CC , Gorovsky MA , Keeling PJ , Waller RF , Patron NJ , Cherry JM , Stover NA , Krieger CJ , del Toro C , Ryder HF , Williamson SC , Barbeau RA , Hamilton EP , Orias E
Ref : PLoS Biol , 4 :e286 , 2006
Abstract : The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.
ESTHER : Eisen_2006_PLoS.Biol_4_e286
PubMedSearch : Eisen_2006_PLoS.Biol_4_e286
PubMedID: 16933976
Gene_locus related to this paper: tetts-i7mam3 , tetts-i7ml33

Title : Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus - Badger_2006_J.Bacteriol_188_6841
Author(s) : Badger JH , Hoover TR , Brun YV , Weiner RM , Laub MT , Alexandre G , Mrazek J , Ren Q , Paulsen IT , Nelson KE , Khouri HM , Radune D , Sosa J , Dodson RJ , Sullivan SA , Rosovitz MJ , Madupu R , Brinkac LM , Durkin AS , Daugherty SC , Kothari SP , Giglio MG , Zhou L , Haft DH , Selengut JD , Davidsen TM , Yang Q , Zafar N , Ward NL
Ref : Journal of Bacteriology , 188 :6841 , 2006
Abstract : The dimorphic prosthecate bacteria (DPB) are alpha-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this work, the only member of this group for which genome sequence was available was the model freshwater organism Caulobacter crescentus. Here we describe the genome sequence of Hyphomonas neptunium, a marine member of the DPB that differs from C. crescentus in that H. neptunium uses its stalk as a reproductive structure. Genome analysis indicates that this organism shares more genes with C. crescentus than it does with Silicibacter pomeroyi (a closer relative according to 16S rRNA phylogeny), that it relies upon a heterotrophic strategy utilizing a wide range of substrates, that its cell cycle is likely to be regulated in a similar manner to that of C. crescentus, and that the outer membrane complements of H. neptunium and C. crescentus are remarkably similar. H. neptunium swarmer cells are highly motile via a single polar flagellum. With the exception of cheY and cheR, genes required for chemotaxis were absent in the H. neptunium genome. Consistent with this observation, H. neptunium swarmer cells did not respond to any chemotactic stimuli that were tested, which suggests that H. neptunium motility is a random dispersal mechanism for swarmer cells rather than a stimulus-controlled navigation system for locating specific environments. In addition to providing insights into bacterial development, the H. neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging.
ESTHER : Badger_2006_J.Bacteriol_188_6841
PubMedSearch : Badger_2006_J.Bacteriol_188_6841
PubMedID: 16980487
Gene_locus related to this paper: hypna-q0bwt8 , hypna-q0bwv5 , hypna-q0bww7 , hypna-q0bxb2 , hypna-q0bxr5 , hypna-q0by84 , hypna-q0byl3 , hypna-q0bz23 , hypna-q0bzi5 , hypna-q0c0f7 , hypna-q0c0f8 , hypna-q0c2v8 , hypna-q0c2w1 , hypna-q0c2w4 , hypna-q0c3g0 , hypna-q0c4j0 , hypna-q0c4n1 , hypna-q0c4q9 , hypna-q0c4v5 , hypna-q0c386 , hypna-q0c539 , hypna-q0c611

Title : Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment - Palenik_2006_Proc.Natl.Acad.Sci.U.S.A_103_13555
Author(s) : Palenik B , Ren Q , Dupont CL , Myers GS , Heidelberg JF , Badger JH , Madupu R , Nelson WC , Brinkac LM , Dodson RJ , Durkin AS , Daugherty SC , Sullivan SA , Khouri H , Mohamoud Y , Halpin R , Paulsen IT
Ref : Proc Natl Acad Sci U S A , 103 :13555 , 2006
Abstract : Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.
ESTHER : Palenik_2006_Proc.Natl.Acad.Sci.U.S.A_103_13555
PubMedSearch : Palenik_2006_Proc.Natl.Acad.Sci.U.S.A_103_13555
PubMedID: 16938853
Gene_locus related to this paper: syns3-q0i8r7 , syns3-q0i9w2 , syns3-q0i996 , syns3-q0ia13 , syns3-q0ia55 , syns3-q0ib73 , syns3-q0ibm2 , syns3-q0ibp1 , syns3-q0iby1 , syns9-q3ax89 , syns3-q0ibv4

Title : Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species - Fouts_2005_PLoS.Biol_3_e15
Author(s) : Fouts DE , Mongodin EF , Mandrell RE , Miller WG , Rasko DA , Ravel J , Brinkac LM , DeBoy RT , Parker CT , Daugherty SC , Dodson RJ , Durkin AS , Madupu R , Sullivan SA , Shetty JU , Ayodeji MA , Shvartsbeyn A , Schatz MC , Badger JH , Fraser CM , Nelson KE
Ref : PLoS Biol , 3 :e15 , 2005
Abstract : Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are associated with the insertion of phage- and plasmid-like genomic islands, as well as major variations in the lipooligosaccharide complex. Poly G tracts are longer, are greater in number, and show greater variability in C. upsaliensis than in the other species. Many genes involved in host colonization, including racR/S, cadF, cdt, ciaB, and flagellin genes, are conserved across the species, but variations that appear to be species specific are evident for a lipooligosaccharide locus, a capsular (extracellular) polysaccharide locus, and a novel Campylobacter putative licABCD virulence locus. The strains also vary in their metabolic profiles, as well as their resistance profiles to a range of antibiotics. It is evident that the newly identified hypothetical and conserved hypothetical proteins, as well as uncharacterized two-component regulatory systems and membrane proteins, may hold additional significant information on the major differences in virulence among the species, as well as the specificity of the strains for particular hosts.
ESTHER : Fouts_2005_PLoS.Biol_3_e15
PubMedSearch : Fouts_2005_PLoS.Biol_3_e15
PubMedID: 15660156
Gene_locus related to this paper: camje-CJ0796C , camjr-q5ht69 , camjr-q5ht95 , camjr-q5huc7 , camjr-q5hwg6 , camju-a3yll6

Title : The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus - Klenk_1997_Nature_390_364
Author(s) : Klenk HP , Clayton RA , Tomb JF , White O , Nelson KE , Ketchum KA , Dodson RJ , Gwinn M , Hickey EK , Peterson JD , Richardson DL , Kerlavage AR , Graham DE , Kyrpides NC , Fleischmann RD , Quackenbush J , Lee NH , Sutton GG , Gill S , Kirkness EF , Dougherty BA , McKenney K , Adams MD , Loftus B , Peterson S , Reich CI , McNeil LK , Badger JH , Glodek A , Zhou L , Overbeek R , Gocayne JD , Weidman JF , McDonald L , Utterback T , Cotton MD , Spriggs T , Artiach P , Kaine BP , Sykes SM , Sadow PW , D'Andrea KP , Bowman C , Fujii C , Garland SA , Mason TM , Olsen GJ , Fraser CM , Smith HO , Woese CR , Venter JC
Ref : Nature , 390 :364 , 1997
Abstract : Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon Methanococcus jannaschii. The genomes of these two Archaea indicate dramatic differences in the way these organisms sense their environment, perform regulatory and transport functions, and gain energy. In contrast to M. jannaschii, A. fulgidus has fewer restriction-modification systems, and none of its genes appears to contain inteins. A quarter (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved proteins, two-thirds of which are shared with M. jannaschii (428 ORFs). Another quarter of the genome encodes new proteins indicating substantial archaeal gene diversity.
ESTHER : Klenk_1997_Nature_390_364
PubMedSearch : Klenk_1997_Nature_390_364
PubMedID: 9389475
Gene_locus related to this paper: arcfu-AF0514 , arcfu-AF0675 , arcfu-AF1134 , arcfu-AF1563 , arcfu-AF1753 , arcfu-AF1763 , arcfu-est1 , arcfu-est2 , arcfu-est3 , arcfu-estea , arcfu-o28594 , arcfu-o29442 , arcfu-pcbd