Barrell BG

References (28)

Title : Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis - Holden_2009_PLoS.One_4_e6072
Author(s) : Holden MT , Hauser H , Sanders M , Ngo TH , Cherevach I , Cronin A , Goodhead I , Mungall K , Quail MA , Price C , Rabbinowitsch E , Sharp S , Croucher NJ , Chieu TB , Mai NT , Diep TS , Chinh NT , Kehoe M , Leigh JA , Ward PN , Dowson CG , Whatmore AM , Chanter N , Iversen P , Gottschalk M , Slater JD , Smith HE , Spratt BG , Xu J , Ye C , Bentley S , Barrell BG , Schultsz C , Maskell DJ , Parkhill J
Ref : PLoS ONE , 4 :e6072 , 2009
Abstract : BACKGROUND: Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections in humans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has been described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: The sequencing of whole genomes of S. suis isolates provides opportunities to investigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the same lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis was used to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species for which genome sequences are currently available. Accordingly, approximately 40% of the approximately 2 Mb genome is unique in comparison to other Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation; virtually all of the genome is common to the S. suis strains. The only exceptions are three approximately 90 kb regions, present in the two isolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are coding sequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes in putative virulence and colonization factors. CONCLUSIONS/SIGNIFICANCE: The genomic inventories of genetically related S. suis strains, isolated from distinct hosts and diseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer has contributed to the evolution of drug resistance.
ESTHER : Holden_2009_PLoS.One_4_e6072
PubMedSearch : Holden_2009_PLoS.One_4_e6072
PubMedID: 19603075
Gene_locus related to this paper: strsu-q302y4 , strsy-a4vus4 , strsy-a4vwf6

Title : The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients - Holden_2009_J.Bacteriol_191_261
Author(s) : Holden MT , Seth-Smith HM , Crossman LC , Sebaihia M , Bentley SD , Cerdeno-Tarraga AM , Thomson NR , Bason N , Quail MA , Sharp S , Cherevach I , Churcher C , Goodhead I , Hauser H , Holroyd N , Mungall K , Scott P , Walker D , White B , Rose H , Iversen P , Mil-Homens D , Rocha EP , Fialho AM , Baldwin A , Dowson C , Barrell BG , Govan JR , Vandamme P , Hart CA , Mahenthiralingam E , Parkhill J
Ref : Journal of Bacteriology , 191 :261 , 2009
Abstract : Bacterial infections of the lungs of cystic fibrosis (CF) patients cause major complications in the treatment of this common genetic disease. Burkholderia cenocepacia infection is particularly problematic since this organism has high levels of antibiotic resistance, making it difficult to eradicate; the resulting chronic infections are associated with severe declines in lung function and increased mortality rates. B. cenocepacia strain J2315 was isolated from a CF patient and is a member of the epidemic ET12 lineage that originated in Canada or the United Kingdom and spread to Europe. The 8.06-Mb genome of this highly transmissible pathogen comprises three circular chromosomes and a plasmid and encodes a broad array of functions typical of this metabolically versatile genus, as well as numerous virulence and drug resistance functions. Although B. cenocepacia strains can be isolated from soil and can be pathogenic to both plants and man, J2315 is representative of a lineage of B. cenocepacia rarely isolated from the environment and which spreads between CF patients. Comparative analysis revealed that ca. 21% of the genome is unique in comparison to other strains of B. cenocepacia, highlighting the genomic plasticity of this species. Pseudogenes in virulence determinants suggest that the pathogenic response of J2315 may have been recently selected to promote persistence in the CF lung. The J2315 genome contains evidence that its unique and highly adapted genetic content has played a significant role in its success as an epidemic CF pathogen.
ESTHER : Holden_2009_J.Bacteriol_191_261
PubMedSearch : Holden_2009_J.Bacteriol_191_261
PubMedID: 18931103
Gene_locus related to this paper: burcj-b4e794 , 9burk-a0u8m3 , burcj-b4ek59 , burcj-b4ehl7 , burca-q1bk56 , burce-a0a088tsj6 , burcj-b4ecv6

Title : Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis - Ward_2009_BMC.Genomics_10_54
Author(s) : Ward PN , Holden MT , Leigh JA , Lennard N , Bignell A , Barron A , Clark L , Quail MA , Woodward J , Barrell BG , Egan SA , Field TR , Maskell D , Kehoe M , Dowson CG , Chanter N , Whatmore AM , Bentley SD , Parkhill J
Ref : BMC Genomics , 10 :54 , 2009
Abstract : BACKGROUND: Streptococcus uberis, a Gram positive bacterial pathogen responsible for a significant proportion of bovine mastitis in commercial dairy herds, colonises multiple body sites of the cow including the gut, genital tract and mammary gland. Comparative analysis of the complete genome sequence of S. uberis strain 0140J was undertaken to help elucidate the biology of this effective bovine pathogen. RESULTS: The genome revealed 1,825 predicted coding sequences (CDSs) of which 62 were identified as pseudogenes or gene fragments. Comparisons with related pyogenic streptococci identified a conserved core (40%) of orthologous CDSs. Intriguingly, S. uberis 0140J displayed a lower number of mobile genetic elements when compared with other pyogenic streptococci, however bacteriophage-derived islands and a putative genomic island were identified. Comparative genomics analysis revealed most similarity to the genomes of Streptococcus agalactiae and Streptococcus equi subsp. zooepidemicus. In contrast, streptococcal orthologs were not identified for 11% of the CDSs, indicating either unique retention of ancestral sequence, or acquisition of sequence from alternative sources. Functions including transport, catabolism, regulation and CDSs encoding cell envelope proteins were over-represented in this unique gene set; a limited array of putative virulence CDSs were identified. CONCLUSION: S. uberis utilises nutritional flexibility derived from a diversity of metabolic options to successfully occupy a discrete ecological niche. The features observed in S. uberis are strongly suggestive of an opportunistic pathogen adapted to challenging and changing environmental parameters.
ESTHER : Ward_2009_BMC.Genomics_10_54
PubMedSearch : Ward_2009_BMC.Genomics_10_54
PubMedID: 19175920
Gene_locus related to this paper: stru0-b9drp1 , stru0-b9dsd7 , stru0-b9dum0 , stru0-b9dvu1 , stru0-pepx

Title : The genome of the blood fluke Schistosoma mansoni - Berriman_2009_Nature_460_352
Author(s) : Berriman M , Haas BJ , LoVerde PT , Wilson RA , Dillon GP , Cerqueira GC , Mashiyama ST , Al-Lazikani B , Andrade LF , Ashton PD , Aslett MA , Bartholomeu DC , Blandin G , Caffrey CR , Coghlan A , Coulson R , Day TA , Delcher A , DeMarco R , Djikeng A , Eyre T , Gamble JA , Ghedin E , Gu Y , Hertz-Fowler C , Hirai H , Hirai Y , Houston R , Ivens A , Johnston DA , Lacerda D , Macedo CD , McVeigh P , Ning Z , Oliveira G , Overington JP , Parkhill J , Pertea M , Pierce RJ , Protasio AV , Quail MA , Rajandream MA , Rogers J , Sajid M , Salzberg SL , Stanke M , Tivey AR , White O , Williams DL , Wortman J , Wu W , Zamanian M , Zerlotini A , Fraser-Liggett CM , Barrell BG , El-Sayed NM
Ref : Nature , 460 :352 , 2009
Abstract : Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.
ESTHER : Berriman_2009_Nature_460_352
PubMedSearch : Berriman_2009_Nature_460_352
PubMedID: 19606141
Gene_locus related to this paper: schma-ACHE1 , schma-ACHE2 , schma-c4qb79 , schma-c4qmk4 , schma-g4v9h7 , schma-BCHE , schma-g4vmf3

Title : The genome of the simian and human malaria parasite Plasmodium knowlesi - Pain_2008_Nature_455_799
Author(s) : Pain A , Bohme U , Berry AE , Mungall K , Finn RD , Jackson AP , Mourier T , Mistry J , Pasini EM , Aslett MA , Balasubrammaniam S , Borgwardt K , Brooks K , Carret C , Carver TJ , Cherevach I , Chillingworth T , Clark TG , Galinski MR , Hall N , Harper D , Harris D , Hauser H , Ivens A , Janssen CS , Keane T , Larke N , Lapp S , Marti M , Moule S , Meyer IM , Ormond D , Peters N , Sanders M , Sanders S , Sargeant TJ , Simmonds M , Smith F , Squares R , Thurston S , Tivey AR , Walker D , White B , Zuiderwijk E , Churcher C , Quail MA , Cowman AF , Turner CM , Rajandream MA , Kocken CH , Thomas AW , Newbold CI , Barrell BG , Berriman M
Ref : Nature , 455 :799 , 2008
Abstract : Plasmodium knowlesi is an intracellular malaria parasite whose natural vertebrate host is Macaca fascicularis (the 'kra' monkey); however, it is now increasingly recognized as a significant cause of human malaria, particularly in southeast Asia. Plasmodium knowlesi was the first malaria parasite species in which antigenic variation was demonstrated, and it has a close phylogenetic relationship to Plasmodium vivax, the second most important species of human malaria parasite (reviewed in ref. 4). Despite their relatedness, there are important phenotypic differences between them, such as host blood cell preference, absence of a dormant liver stage or 'hypnozoite' in P. knowlesi, and length of the asexual cycle (reviewed in ref. 4). Here we present an analysis of the P. knowlesi (H strain, Pk1(A+) clone) nuclear genome sequence. This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome and other sequenced Plasmodium genomes. In contrast to other Plasmodium genomes, putative variant antigen families are dispersed throughout the genome and are associated with intrachromosomal telomere repeats. One of these families, the KIRs, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry.
ESTHER : Pain_2008_Nature_455_799
PubMedSearch : Pain_2008_Nature_455_799
PubMedID: 18843368
Gene_locus related to this paper: plakh-b3kz42 , plakh-b3kz45 , plakh-b3l0y4 , plakh-b3l1r3 , plakh-b3l8u5 , plakh-b3l336 , plakh-b3l571 , plakh-b3la01 , plakh-b3lb44

Title : Genome plasticity of BCG and impact on vaccine efficacy - Brosch_2007_Proc.Natl.Acad.Sci.U.S.A_104_5596
Author(s) : Brosch R , Gordon SV , Garnier T , Eiglmeier K , Frigui W , Valenti P , Dos Santos S , Duthoy S , Lacroix C , Garcia-Pelayo C , Inwald JK , Golby P , Garcia JN , Hewinson RG , Behr MA , Quail MA , Churcher C , Barrell BG , Parkhill J , Cole ST
Ref : Proc Natl Acad Sci U S A , 104 :5596 , 2007
Abstract : To understand the evolution, attenuation, and variable protective efficacy of bacillus Calmette-Guerin (BCG) vaccines, Mycobacterium bovis BCG Pasteur 1173P2 has been subjected to comparative genome and transcriptome analysis. The 4,374,522-bp genome contains 3,954 protein-coding genes, 58 of which are present in two copies as a result of two independent tandem duplications, DU1 and DU2. DU1 is restricted to BCG Pasteur, although four forms of DU2 exist; DU2-I is confined to early BCG vaccines, like BCG Japan, whereas DU2-III and DU2-IV occur in the late vaccines. The glycerol-3-phosphate dehydrogenase gene, glpD2, is one of only three genes common to all four DU2 variants, implying that BCG requires higher levels of this enzyme to grow on glycerol. Further amplification of the DU2 region is ongoing, even within vaccine preparations used to immunize humans. An evolutionary scheme for BCG vaccines was established by analyzing DU2 and other markers. Lesions in genes encoding sigma-factors and pleiotropic transcriptional regulators, like PhoR and Crp, were also uncovered in various BCG strains; together with gene amplification, these affect gene expression levels, immunogenicity, and, possibly, protection against tuberculosis. Furthermore, the combined findings suggest that early BCG vaccines may even be superior to the later ones that are more widely used.
ESTHER : Brosch_2007_Proc.Natl.Acad.Sci.U.S.A_104_5596
PubMedSearch : Brosch_2007_Proc.Natl.Acad.Sci.U.S.A_104_5596
PubMedID: 17372194
Gene_locus related to this paper: myctu-a85a , myctu-a85b , myctu-a85c , myctu-bpoC , myctu-cut3 , myctu-cutas2 , myctu-d5yk66 , myctu-ephB , myctu-ephc , myctu-ephd , myctu-ephE , myctu-hpx , myctu-linb , myctu-lipG , myctu-lipJ , myctu-LIPS , myctu-lipv , myctu-LPQC , myctu-LPQP , myctu-MBTB , myctu-metx , myctu-mpt51 , myctu-MT1628 , myctu-p71654 , myctu-p95011 , myctu-PKS6 , myctu-PKS13 , myctu-ppe42 , myctu-ppe63 , myctu-Rv1430 , myctu-RV0045C , myctu-Rv0077c , myctu-Rv0151c , myctu-Rv0152c , myctu-Rv0159c , myctu-Rv0160c , myctu-rv0183 , myctu-Rv0217c , myctu-Rv0220 , myctu-Rv0272c , myctu-RV0293C , myctu-RV0457C , myctu-RV0519C , myctu-RV0774C , myctu-RV0782 , myctu-RV0840C , myctu-Rv1069c , myctu-Rv1076 , myctu-RV1123C , myctu-Rv1184c , myctu-Rv1191 , myctu-RV1192 , myctu-RV1215C , myctu-Rv1399c , myctu-Rv1400c , myctu-Rv1426c , myctu-RV1639C , myctu-RV1683 , myctu-RV1758 , myctu-Rv1800 , myctu-Rv1833c , myctu-Rv2045c , myctu-RV2054 , myctu-Rv2284 , myctu-RV2296 , myctu-Rv2385 , myctu-Rv2485c , myctu-RV2627C , myctu-RV2672 , myctu-RV2695 , myctu-RV2765 , myctu-RV2800 , myctu-RV2854 , myctu-Rv2970c , myctu-Rv3084 , myctu-Rv3097c , myctu-rv3177 , myctu-Rv3312c , myctu-RV3452 , myctu-RV3473C , myctu-Rv3487c , myctu-Rv3569c , myctu-Rv3591c , myctu-RV3724 , myctu-Rv3802c , myctu-Rv3822 , myctu-y0571 , myctu-y963 , myctu-Y1834 , myctu-y1835 , myctu-y2079 , myctu-yc88 , myctu-ym23 , myctu-ym24 , myctu-YR15 , myctu-yt28

Title : Complete genome of acute rheumatic fever-associated serotype M5 Streptococcus pyogenes strain manfredo - Holden_2007_J.Bacteriol_189_1473
Author(s) : Holden MT , Scott A , Cherevach I , Chillingworth T , Churcher C , Cronin A , Dowd L , Feltwell T , Hamlin N , Holroyd S , Jagels K , Moule S , Mungall K , Quail MA , Price C , Rabbinowitsch E , Sharp S , Skelton J , Whitehead S , Barrell BG , Kehoe M , Parkhill J
Ref : Journal of Bacteriology , 189 :1473 , 2007
Abstract : Comparisons of the 1.84-Mb genome of serotype M5 Streptococcus pyogenes strain Manfredo with previously sequenced genomes emphasized the role of prophages in diversification of S. pyogenes and the close relationship between strain Manfredo and MGAS8232, another acute rheumatic fever-associated strain.
ESTHER : Holden_2007_J.Bacteriol_189_1473
PubMedSearch : Holden_2007_J.Bacteriol_189_1473
PubMedID: 17012393
Gene_locus related to this paper: strpy-ESTA , strpy-PEPXP , strpy-SPY1308 , strpy-SPYM18.1727

Title : The genome of the African trypanosome Trypanosoma brucei - Berriman_2005_Science_309_416
Author(s) : Berriman M , Ghedin E , Hertz-Fowler C , Blandin G , Renauld H , Bartholomeu DC , Lennard NJ , Caler E , Hamlin NE , Haas B , Bohme U , Hannick L , Aslett MA , Shallom J , Marcello L , Hou L , Wickstead B , Alsmark UC , Arrowsmith C , Atkin RJ , Barron AJ , Bringaud F , Brooks K , Carrington M , Cherevach I , Chillingworth TJ , Churcher C , Clark LN , Corton CH , Cronin A , Davies RM , Doggett J , Djikeng A , Feldblyum T , Field MC , Fraser A , Goodhead I , Hance Z , Harper D , Harris BR , Hauser H , Hostetler J , Ivens A , Jagels K , Johnson D , Johnson J , Jones K , Kerhornou AX , Koo H , Larke N , Landfear S , Larkin C , Leech V , Line A , Lord A , MacLeod A , Mooney PJ , Moule S , Martin DM , Morgan GW , Mungall K , Norbertczak H , Ormond D , Pai G , Peacock CS , Peterson J , Quail MA , Rabbinowitsch E , Rajandream MA , Reitter C , Salzberg SL , Sanders M , Schobel S , Sharp S , Simmonds M , Simpson AJ , Tallon L , Turner CM , Tait A , Tivey AR , Van Aken S , Walker D , Wanless D , Wang S , White B , White O , Whitehead S , Woodward J , Wortman J , Adams MD , Embley TM , Gull K , Ullu E , Barry JD , Fairlamb AH , Opperdoes F , Barrell BG , Donelson JE , Hall N , Fraser CM , Melville SE , El-Sayed NM
Ref : Science , 309 :416 , 2005
Abstract : African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence and analysis of the 11 megabase-sized chromosomes of Trypanosoma brucei. The 26-megabase genome contains 9068 predicted genes, including approximately 900 pseudogenes and approximately 1700 T. brucei-specific genes. Large subtelomeric arrays contain an archive of 806 variant surface glycoprotein (VSG) genes used by the parasite to evade the mammalian immune system. Most VSG genes are pseudogenes, which may be used to generate expressed mosaic genes by ectopic recombination. Comparisons of the cytoskeleton and endocytic trafficking systems with those of humans and other eukaryotic organisms reveal major differences. A comparison of metabolic pathways encoded by the genomes of T. brucei, T. cruzi, and Leishmania major reveals the least overall metabolic capability in T. brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified.
ESTHER : Berriman_2005_Science_309_416
PubMedSearch : Berriman_2005_Science_309_416
PubMedID: 16020726
Gene_locus related to this paper: tryb2-q6h9e3 , tryb2-q6ha27 , tryb2-q38cd5 , tryb2-q38cd6 , tryb2-q38cd7 , tryb2-q38dc1 , tryb2-q38de4 , tryb2-q38ds6 , tryb2-q38dx1 , tryb2-q380z6 , tryb2-q382c1 , tryb2-q382l4 , tryb2-q383a9 , tryb2-q386e3 , tryb2-q387r7 , tryb2-q388n1 , tryb2-q389w3 , trybr-PEPTB , trycr-q4cq28 , trycr-q4cq94 , trycr-q4cq95 , trycr-q4cq96 , trycr-q4csm0 , trycr-q4cwv3 , trycr-q4cx66 , trycr-q4cxr6 , trycr-q4cyc5 , trycr-q4cyf6 , trycr-q4d3a2 , trycr-q4d3x3 , trycr-q4d3y4 , trycr-q4d6h1 , trycr-q4d8h8 , trycr-q4d8h9 , trycr-q4d8i0 , trycr-q4d786 , trycr-q4d975 , trycr-q4da08 , trycr-q4dap6 , trycr-q4dbm2 , trycr-q4dbn1 , trycr-q4ddw7 , trycr-q4de42 , trycr-q4dhn8 , trycr-q4dkk8 , trycr-q4dkk9 , trycr-q4dm56 , trycr-q4dqa6 , trycr-q4dt91 , trycr-q4dvp2 , trycr-q4dw34 , trycr-q4dwm3 , trycr-q4dy49 , trycr-q4dy82 , trycr-q4dzp6 , trycr-q4e3m8 , trycr-q4e4t5 , trycr-q4e5d1 , trycr-q4e5z2

Title : Complete genome sequence and lytic phase transcription profile of a Coccolithovirus - Wilson_2005_Science_309_1090
Author(s) : Wilson WH , Schroeder DC , Allen MJ , Holden MT , Parkhill J , Barrell BG , Churcher C , Hamlin N , Mungall K , Norbertczak H , Quail MA , Price C , Rabbinowitsch E , Walker D , Craigon M , Roy D , Ghazal P
Ref : Science , 309 :1090 , 2005
Abstract : The genus Coccolithovirus is a recently discovered group of viruses that infect the globally important marine calcifying microalga Emiliania huxleyi. Among the 472 predicted genes of the 407,339-base pair genome are a variety of unexpected genes, most notably those involved in biosynthesis of ceramide, a sphingolipid known to induce apoptosis. Uniquely for algal viruses, it also contains six RNA polymerase subunits and a novel promoter, suggesting this virus encodes its own transcription machinery. Microarray transcriptomic analysis reveals that 65% of the predicted virus-encoded genes are expressed during lytic infection of E. huxleyi.
ESTHER : Wilson_2005_Science_309_1090
PubMedSearch : Wilson_2005_Science_309_1090
PubMedID: 16099989
Gene_locus related to this paper: 9phyc-q4a2b6 , 9phyc-q4a3c9 , ehv86-q4a332

Title : The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation - Thomson_2005_Genome.Res_15_629
Author(s) : Thomson NR , Yeats C , Bell K , Holden MT , Bentley SD , Livingstone M , Cerdeno-Tarraga AM , Harris B , Doggett J , Ormond D , Mungall K , Clarke K , Feltwell T , Hance Z , Sanders M , Quail MA , Price C , Barrell BG , Parkhill J , Longbottom D
Ref : Genome Res , 15 :629 , 2005
Abstract : The obligate intracellular bacterial pathogen Chlamydophila abortus strain S26/3 (formerly the abortion subtype of Chlamydia psittaci) is an important cause of late gestation abortions in ruminants and pigs. Furthermore, although relatively rare, zoonotic infection can result in acute illness and miscarriage in pregnant women. The complete genome sequence was determined and shows a high level of conservation in both sequence and overall gene content in comparison to other Chlamydiaceae. The 1,144,377-bp genome contains 961 predicted coding sequences, 842 of which are conserved with those of Chlamydophila caviae and Chlamydophila pneumoniae. Within this conserved Cp. abortus core genome we have identified the major regions of variation and have focused our analysis on these loci, several of which were found to encode highly variable protein families, such as TMH/Inc and Pmp families, which are strong candidates for the source of diversity in host tropism and disease causation in this group of organisms. Significantly, Cp. abortus lacks any toxin genes, and also lacks genes involved in tryptophan metabolism and nucleotide salvaging (guaB is present as a pseudogene), suggesting that the genetic basis of niche adaptation of this species is distinct from those previously proposed for other chlamydial species.
ESTHER : Thomson_2005_Genome.Res_15_629
PubMedSearch : Thomson_2005_Genome.Res_15_629
PubMedID: 15837807
Gene_locus related to this paper: chlab-q5l5y2 , chlab-q5l6t6

Title : Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance - Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_9786
Author(s) : Holden MT , Feil EJ , Lindsay JA , Peacock SJ , Day NP , Enright MC , Foster TJ , Moore CE , Hurst L , Atkin R , Barron A , Bason N , Bentley SD , Chillingworth C , Chillingworth T , Churcher C , Clark L , Corton C , Cronin A , Doggett J , Dowd L , Feltwell T , Hance Z , Harris B , Hauser H , Holroyd S , Jagels K , James KD , Lennard N , Line A , Mayes R , Moule S , Mungall K , Ormond D , Quail MA , Rabbinowitsch E , Rutherford K , Sanders M , Sharp S , Simmonds M , Stevens K , Whitehead S , Barrell BG , Spratt BG , Parkhill J
Ref : Proc Natl Acad Sci U S A , 101 :9786 , 2004
Abstract : Staphylococcus aureus is an important nosocomial and community-acquired pathogen. Its genetic plasticity has facilitated the evolution of many virulent and drug-resistant strains, presenting a major and constantly changing clinical challenge. We sequenced the approximately 2.8-Mbp genomes of two disease-causing S. aureus strains isolated from distinct clinical settings: a recent hospital-acquired representative of the epidemic methicillin-resistant S. aureus EMRSA-16 clone (MRSA252), a clinically important and globally prevalent lineage; and a representative of an invasive community-acquired methicillin-susceptible S. aureus clone (MSSA476). A comparative-genomics approach was used to explore the mechanisms of evolution of clinically important S. aureus genomes and to identify regions affecting virulence and drug resistance. The genome sequences of MRSA252 and MSSA476 have a well conserved core region but differ markedly in their accessory genetic elements. MRSA252 is the most genetically diverse S. aureus strain sequenced to date: approximately 6% of the genome is novel compared with other published genomes, and it contains several unique genetic elements. MSSA476 is methicillin-susceptible, but it contains a novel Staphylococcal chromosomal cassette (SCC) mec-like element (designated SCC(476)), which is integrated at the same site on the chromosome as SCCmec elements in MRSA strains but encodes a putative fusidic acid resistance protein. The crucial role that accessory elements play in the rapid evolution of S. aureus is clearly illustrated by comparing the MSSA476 genome with that of an extremely closely related MRSA community-acquired strain; the differential distribution of large mobile elements carrying virulence and drug-resistance determinants may be responsible for the clinically important phenotypic differences in these strains.
ESTHER : Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_9786
PubMedSearch : Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_9786
PubMedID: 15213324
Gene_locus related to this paper: staau-d2feb3 , staau-d2uin3 , staau-LIP , staau-lipas , staau-MW0741 , staau-MW2456 , staau-q6gfm6 , staau-SA0011 , staau-SA0569 , staau-SA0572 , staau-SA0897 , staau-SA1143 , staau-SA2240 , staau-SA2306 , staau-SA2367 , staau-SA2422 , staau-SAV0321 , staau-SAV0446 , staau-SAV0457 , staau-SAV0655 , staau-SAV1014 , staau-SAV1765 , staau-SAV1793 , staau-SAV2188 , staau-SAV2350 , staau-SAV2594

Title : Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei - Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_14240
Author(s) : Holden MT , Titball RW , Peacock SJ , Cerdeno-Tarraga AM , Atkins T , Crossman LC , Pitt T , Churcher C , Mungall K , Bentley SD , Sebaihia M , Thomson NR , Bason N , Beacham IR , Brooks K , Brown KA , Brown NF , Challis GL , Cherevach I , Chillingworth T , Cronin A , Crossett B , Davis P , DeShazer D , Feltwell T , Fraser A , Hance Z , Hauser H , Holroyd S , Jagels K , Keith KE , Maddison M , Moule S , Price C , Quail MA , Rabbinowitsch E , Rutherford K , Sanders M , Simmonds M , Songsivilai S , Stevens K , Tumapa S , Vesaratchavest M , Whitehead S , Yeats C , Barrell BG , Oyston PC , Parkhill J
Ref : Proc Natl Acad Sci U S A , 101 :14240 , 2004
Abstract : Burkholderia pseudomallei is a recognized biothreat agent and the causative agent of melioidosis. This Gram-negative bacterium exists as a soil saprophyte in melioidosis-endemic areas of the world and accounts for 20% of community-acquired septicaemias in northeastern Thailand where half of those affected die. Here we report the complete genome of B. pseudomallei, which is composed of two chromosomes of 4.07 megabase pairs and 3.17 megabase pairs, showing significant functional partitioning of genes between them. The large chromosome encodes many of the core functions associated with central metabolism and cell growth, whereas the small chromosome carries more accessory functions associated with adaptation and survival in different niches. Genomic comparisons with closely and more distantly related bacteria revealed a greater level of gene order conservation and a greater number of orthologous genes on the large chromosome, suggesting that the two replicons have distinct evolutionary origins. A striking feature of the genome was the presence of 16 genomic islands (GIs) that together made up 6.1% of the genome. Further analysis revealed these islands to be variably present in a collection of invasive and soil isolates but entirely absent from the clonally related organism B. mallei. We propose that variable horizontal gene acquisition by B. pseudomallei is an important feature of recent genetic evolution and that this has resulted in a genetically diverse pathogenic species.
ESTHER : Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_14240
PubMedSearch : Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_14240
PubMedID: 15377794
Gene_locus related to this paper: burma-a5j5w8 , burma-a5tj72 , burma-a5tq93 , burma-metx , burma-q62a61 , burma-q62ar2.1 , burma-q62ar2.2 , burma-q62ax8 , burma-q62b60 , burma-q62b79 , burma-q62bh9 , burma-q62bl4 , burma-q62bl7 , burma-q62c00 , burma-q62cg5 , burma-q62d41 , burma-q62d56 , burma-q62d83 , burma-q62dg2 , burma-q62du7 , burma-q62e67 , burma-q62eb8 , burma-q62ed8 , burma-q62f28 , burma-q62fx7 , burma-q62g26 , burma-q62gx9 , burma-q62gy2 , burma-q62hq2 , burma-q62i62 , burma-q62ib8 , burma-q62ie8 , burma-q62j07 , burma-q62j15 , burma-q62jn5 , burma-q62jy7 , burma-q62kb7 , burma-q62kg0 , burma-q62kh9 , burma-q62lp7 , burma-q62m40 , burma-q62mc3 , burma-q62mf4 , burma-q62mq7 , burma-q629m1 , burma-q629p4 , burma-q629u0 , burp1-q3jvq2 , burps-a4lm41 , burps-q3v7s4 , burps-q63hx2 , burps-q63i95 , burps-q63im5 , burps-q63is4 , burps-q63ja6 , burps-q63ja9 , burps-q63jh5 , burps-q63l17 , burps-q63l41 , burps-q63l44 , burps-q63lt9 , burps-q63me1 , burps-q63mj7 , burps-q63mj8 , burps-q63mn8 , burps-q63mr2 , burps-q63n52 , burps-q63p18 , burps-q63p99 , burps-q63ug2 , burps-q63ug5 , burps-q63xf9 , burps-q63y36 , burps-q63y45 , burps-q63y52 , burps-q63y59 , burta-q2t474 , burps-hboh

Title : The complete genome sequence of Mycobacterium bovis - Garnier_2003_Proc.Natl.Acad.Sci.U.S.A_100_7877
Author(s) : Garnier T , Eiglmeier K , Camus JC , Medina N , Mansoor H , Pryor M , Duthoy S , Grondin S , Lacroix C , Monsempe C , Simon S , Harris B , Atkin R , Doggett J , Mayes R , Keating L , Wheeler PR , Parkhill J , Barrell BG , Cole ST , Gordon SV , Hewinson RG
Ref : Proc Natl Acad Sci U S A , 100 :7877 , 2003
Abstract : Mycobacterium bovis is the causative agent of tuberculosis in a range of animal species and man, with worldwide annual losses to agriculture of $3 billion. The human burden of tuberculosis caused by the bovine tubercle bacillus is still largely unknown. M. bovis was also the progenitor for the M. bovis bacillus Calmette-Guerin vaccine strain, the most widely used human vaccine. Here we describe the 4,345,492-bp genome sequence of M. bovis AF2122/97 and its comparison with the genomes of Mycobacterium tuberculosis and Mycobacterium leprae. Strikingly, the genome sequence of M. bovis is >99.95% identical to that of M. tuberculosis, but deletion of genetic information has led to a reduced genome size. Comparison with M. leprae reveals a number of common gene losses, suggesting the removal of functional redundancy. Cell wall components and secreted proteins show the greatest variation, indicating their potential role in host-bacillus interactions or immune evasion. Furthermore, there are no genes unique to M. bovis, implying that differential gene expression may be the key to the host tropisms of human and bovine bacilli. The genome sequence therefore offers major insight on the evolution, host preference, and pathobiology of M. bovis.
ESTHER : Garnier_2003_Proc.Natl.Acad.Sci.U.S.A_100_7877
PubMedSearch : Garnier_2003_Proc.Natl.Acad.Sci.U.S.A_100_7877
PubMedID: 12788972
Gene_locus related to this paper: myctu-a85a , myctu-a85b , myctu-a85c , myctu-bpoC , myctu-cut3 , myctu-cutas1 , myctu-cutas2 , myctu-d5yk66 , myctu-ephB , myctu-ephc , myctu-ephd , myctu-ephE , myctu-hpx , myctu-linb , myctu-lipG , myctu-lipJ , myctu-LIPS , myctu-lipv , myctu-LPQC , myctu-LPQP , myctu-MBTB , myctu-metx , myctu-mpt51 , myctu-MT1628 , myctu-MT3441 , myctu-p71654 , myctu-p95011 , myctu-PKS6 , myctu-PKS13 , myctu-ppe42 , myctu-ppe63 , myctu-Rv1430 , myctu-RV0045C , myctu-Rv0077c , myctu-Rv0151c , myctu-Rv0152c , myctu-Rv0159c , myctu-Rv0160c , myctu-rv0183 , myctu-Rv0217c , myctu-Rv0220 , myctu-Rv0272c , myctu-RV0293C , myctu-RV0421C , myctu-RV0457C , myctu-RV0519C , myctu-RV0774C , myctu-RV0782 , myctu-RV0840C , myctu-Rv1069c , myctu-Rv1076 , myctu-RV1123C , myctu-Rv1184c , myctu-Rv1190 , myctu-Rv1191 , myctu-RV1192 , myctu-RV1215C , myctu-Rv1399c , myctu-Rv1400c , myctu-Rv1426c , myctu-RV1639C , myctu-RV1683 , myctu-RV1758 , myctu-Rv1800 , myctu-Rv1833c , myctu-Rv2045c , myctu-RV2054 , myctu-Rv2284 , myctu-RV2296 , myctu-Rv2385 , myctu-Rv2485c , myctu-RV2627C , myctu-RV2672 , myctu-RV2695 , myctu-RV2765 , myctu-RV2800 , myctu-RV2854 , myctu-Rv2970c , myctu-Rv3084 , myctu-Rv3097c , myctu-rv3177 , myctu-Rv3312c , myctu-RV3452 , myctu-RV3473C , myctu-Rv3487c , myctu-Rv3569c , myctu-RV3724 , myctu-Rv3802c , myctu-Rv3822 , myctu-y0571 , myctu-y963 , myctu-Y1834 , myctu-y1835 , myctu-y2079 , myctu-Y2307 , myctu-yc88 , myctu-ym23 , myctu-ym24 , myctu-YR15 , myctu-yt28

Title : The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129 - Cerdeno-Tarraga_2003_Nucleic.Acids.Res_31_6516
Author(s) : Cerdeno-Tarraga AM , Efstratiou A , Dover LG , Holden MT , Pallen M , Bentley SD , Besra GS , Churcher C , James KD , De Zoysa A , Chillingworth T , Cronin A , Dowd L , Feltwell T , Hamlin N , Holroyd S , Jagels K , Moule S , Quail MA , Rabbinowitsch E , Rutherford KM , Thomson NR , Unwin L , Whitehead S , Barrell BG , Parkhill J
Ref : Nucleic Acids Research , 31 :6516 , 2003
Abstract : Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod belonging to the genus Corynebacterium and the actinomycete group of organisms. The organism produces a potent bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which causes the symptoms of diphtheria. This potentially fatal infectious disease is controlled in many developed countries by an effective immunisation programme. However, the disease has made a dramatic return in recent years, in particular within the Eastern European region. The largest, and still on-going, outbreak since the advent of mass immunisation started within Russia and the newly independent states of the former Soviet Union in the 1990s. We have sequenced the genome of a UK clinical isolate (biotype gravis strain NCTC13129), representative of the clone responsible for this outbreak. The genome consists of a single circular chromosome of 2 488 635 bp, with no plasmids. It provides evidence that recent acquisition of pathogenicity factors goes beyond the toxin itself, and includes iron-uptake systems, adhesins and fimbrial proteins. This is in contrast to Corynebacterium's nearest sequenced pathogenic relative, Mycobacterium tuberculosis, where there is little evidence of recent horizontal DNA acquisition. The genome itself shows an unusually extreme large-scale compositional bias, being noticeably higher in G+C near the origin than at the terminus.
ESTHER : Cerdeno-Tarraga_2003_Nucleic.Acids.Res_31_6516
PubMedSearch : Cerdeno-Tarraga_2003_Nucleic.Acids.Res_31_6516
PubMedID: 14602910
Gene_locus related to this paper: cordi-DIP1007 , cordi-DIP1729 , cordi-q6ned6 , cordi-q6nes3 , cordi-q6nes4 , cordi-q6nes6 , cordi-q6nes8 , cordi-q6nev5 , cordi-q6nex0 , cordi-q6nez6 , cordi-q6nf79 , cordi-q6nfa8 , cordi-q6nfg5 , cordi-q6nfz1 , cordi-q6ng42 , cordi-q6ngl8 , cordi-q6nhd8 , cordi-q6niz3 , cordi-q6nj46 , cordi-q6njn3 , cordi-q6njn4 , cordi-q6njt5 , cordi-q6nkb6 , cordk-h2hkn5

Title : Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei - Bentley_2003_Lancet_361_637
Author(s) : Bentley SD , Maiwald M , Murphy LD , Pallen MJ , Yeats CA , Dover LG , Norbertczak HT , Besra GS , Quail MA , Harris DE , von Herbay A , Goble A , Rutter S , Squares R , Squares S , Barrell BG , Parkhill J , Relman DA
Ref : Lancet , 361 :637 , 2003
Abstract : BACKGROUND: Whipple's disease is a rare multisystem chronic infection, involving the intestinal tract as well as various other organs. The causative agent, Tropheryma whipplei, is a Gram-positive bacterium about which little is known. Our aim was to investigate the biology of this organism by generating and analysing the complete DNA sequence of its genome. METHODS: We isolated and propagated T whipplei strain TW08/27 from the cerebrospinal fluid of a patient diagnosed with Whipple's disease. We generated the complete sequence of the genome by the whole genome shotgun method, and analysed it with a combination of automatic and manual bioinformatic techniques. FINDINGS: Sequencing revealed a condensed 925938 bp genome with a lack of key biosynthetic pathways and a reduced capacity for energy metabolism. A family of large surface proteins was identified, some associated with large amounts of non-coding repetitive DNA, and an unexpected degree of sequence variation. INTERPRETATION: The genome reduction and lack of metabolic capabilities point to a host-restricted lifestyle for the organism. The sequence variation indicates both known and novel mechanisms for the elaboration and variation of surface structures, and suggests that immune evasion and host interaction play an important part in the lifestyle of this persistent bacterial pathogen.
ESTHER : Bentley_2003_Lancet_361_637
PubMedSearch : Bentley_2003_Lancet_361_637
PubMedID: 12606174
Gene_locus related to this paper: trowh-TW083.1 , trowh-TW083.2 , trowh-TWT693

Title : Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica - Parkhill_2003_Nat.Genet_35_32
Author(s) : Parkhill J , Sebaihia M , Preston A , Murphy LD , Thomson N , Harris DE , Holden MT , Churcher CM , Bentley SD , Mungall KL , Cerdeno-Tarraga AM , Temple L , James K , Harris B , Quail MA , Achtman M , Atkin R , Baker S , Basham D , Bason N , Cherevach I , Chillingworth T , Collins M , Cronin A , Davis P , Doggett J , Feltwell T , Goble A , Hamlin N , Hauser H , Holroyd S , Jagels K , Leather S , Moule S , Norberczak H , O'Neil S , Ormond D , Price C , Rabbinowitsch E , Rutter S , Sanders M , Saunders D , Seeger K , Sharp S , Simmonds M , Skelton J , Squares R , Squares S , Stevens K , Unwin L , Whitehead S , Barrell BG , Maskell DJ
Ref : Nat Genet , 35 :32 , 2003
Abstract : Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica are closely related Gram-negative beta-proteobacteria that colonize the respiratory tracts of mammals. B. pertussis is a strict human pathogen of recent evolutionary origin and is the primary etiologic agent of whooping cough. B. parapertussis can also cause whooping cough, and B. bronchiseptica causes chronic respiratory infections in a wide range of animals. We sequenced the genomes of B. bronchiseptica RB50 (5,338,400 bp; 5,007 predicted genes), B. parapertussis 12822 (4,773,551 bp; 4,404 genes) and B. pertussis Tohama I (4,086,186 bp; 3,816 genes). Our analysis indicates that B. parapertussis and B. pertussis are independent derivatives of B. bronchiseptica-like ancestors. During the evolution of these two host-restricted species there was large-scale gene loss and inactivation; host adaptation seems to be a consequence of loss, not gain, of function, and differences in virulence may be related to loss of regulatory or control functions.
ESTHER : Parkhill_2003_Nat.Genet_35_32
PubMedSearch : Parkhill_2003_Nat.Genet_35_32
PubMedID: 12910271
Gene_locus related to this paper: borbr-BB0273 , borbr-BB0570 , borbr-BB0670 , borbr-BB1064 , borbr-BB1079 , borbr-BB1247 , borbr-BB1498 , borbr-BB2718 , borbr-BB4129 , borbr-BB4247 , borbr-MHPC , borbr-q7wdw1 , borbr-q7wiz8 , borbr-q7wk25 , borbr-q7wmc2 , borbr-q7wpd9 , borpa-q7w3f3 , borpa-q7w9v8 , borpe-BIOH , borpe-BP0300 , borpe-BP2114 , borpe-BP2146 , borpe-BP2511 , borpe-BP3096 , borpe-BP3623 , borpe-BP3691 , borpe-CATD2 , borpe-METX , borpe-O30449 , borpe-PHBC , borpe-q7vsl4 , borpe-q7vt07 , borpe-q7vtg0 , borpe-q7vtv2 , borpe-q7vus4 , borpe-q7vuv4 , borpe-q7vv11 , borpe-q7vv48 , borpe-q7vvf6 , borpe-q7vwu4 , borpe-q7vyn0 , borpe-q7vyq4 , borpe-q7vz26 , borpe-q7vzb4 , borpe-q7vzj6 , borpe-q7w073

Title : Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13 - Hall_2002_Nature_419_527
Author(s) : Hall N , Pain A , Berriman M , Churcher C , Harris B , Harris D , Mungall K , Bowman S , Atkin R , Baker S , Barron A , Brooks K , Buckee CO , Burrows C , Cherevach I , Chillingworth C , Chillingworth T , Christodoulou Z , Clark L , Clark R , Corton C , Cronin A , Davies R , Davis P , Dear P , Dearden F , Doggett J , Feltwell T , Goble A , Goodhead I , Gwilliam R , Hamlin N , Hance Z , Harper D , Hauser H , Hornsby T , Holroyd S , Horrocks P , Humphray S , Jagels K , James KD , Johnson D , Kerhornou A , Knights A , Konfortov B , Kyes S , Larke N , Lawson D , Lennard N , Line A , Maddison M , McLean J , Mooney P , Moule S , Murphy L , Oliver K , Ormond D , Price C , Quail MA , Rabbinowitsch E , Rajandream MA , Rutter S , Rutherford KM , Sanders M , Simmonds M , Seeger K , Sharp S , Smith R , Squares R , Squares S , Stevens K , Taylor K , Tivey A , Unwin L , Whitehead S , Woodward J , Sulston JE , Craig A , Newbold C , Barrell BG
Ref : Nature , 419 :527 , 2002
Abstract : Since the sequencing of the first two chromosomes of the malaria parasite, Plasmodium falciparum, there has been a concerted effort to sequence and assemble the entire genome of this organism. Here we report the sequence of chromosomes 1, 3-9 and 13 of P. falciparum clone 3D7--these chromosomes account for approximately 55% of the total genome. We describe the methods used to map, sequence and annotate these chromosomes. By comparing our assemblies with the optical map, we indicate the completeness of the resulting sequence. During annotation, we assign Gene Ontology terms to the predicted gene products, and observe clustering of some malaria-specific terms to specific chromosomes. We identify a highly conserved sequence element found in the intergenic region of internal var genes that is not associated with their telomeric counterparts.
ESTHER : Hall_2002_Nature_419_527
PubMedSearch : Hall_2002_Nature_419_527
PubMedID: 12368867
Gene_locus related to this paper: plaf7-c0h4q4 , plafa-MAL6P1.135 , plafa-PFD0185C , plafa-PFI1775W , plafa-PFI1800W

Title : Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) - Bentley_2002_Nature_417_141
Author(s) : Bentley SD , Chater KF , Cerdeno-Tarraga AM , Challis GL , Thomson NR , James KD , Harris DE , Quail MA , Kieser H , Harper D , Bateman A , Brown S , Chandra G , Chen CW , Collins M , Cronin A , Fraser A , Goble A , Hidalgo J , Hornsby T , Howarth S , Huang CH , Kieser T , Larke L , Murphy L , Oliver K , O'Neil S , Rabbinowitsch E , Rajandream MA , Rutherford K , Rutter S , Seeger K , Saunders D , Sharp S , Squares R , Squares S , Taylor K , Warren T , Wietzorrek A , Woodward J , Barrell BG , Parkhill J , Hopwood DA
Ref : Nature , 417 :141 , 2002
Abstract : Streptomyces coelicolor is a representative of the group of soil-dwelling, filamentous bacteria responsible for producing most natural antibiotics used in human and veterinary medicine. Here we report the 8,667,507 base pair linear chromosome of this organism, containing the largest number of genes so far discovered in a bacterium. The 7,825 predicted genes include more than 20 clusters coding for known or predicted secondary metabolites. The genome contains an unprecedented proportion of regulatory genes, predominantly those likely to be involved in responses to external stimuli and stresses, and many duplicated gene sets that may represent 'tissue-specific' isoforms operating in different phases of colonial development, a unique situation for a bacterium. An ancient synteny was revealed between the central 'core' of the chromosome and the whole chromosome of pathogens Mycobacterium tuberculosis and Corynebacterium diphtheriae. The genome sequence will greatly increase our understanding of microbial life in the soil as well as aiding the generation of new drug candidates by genetic engineering.
ESTHER : Bentley_2002_Nature_417_141
PubMedSearch : Bentley_2002_Nature_417_141
PubMedID: 12000953
Gene_locus related to this paper: strco-cxest , strco-cxest2 , strco-ester , strco-estli , strco-MMYT , strco-ORF3 , strco-q9f2m1 , strco-q9rdq9 , strco-q9x8r0 , strco-SC1A6.21 , strco-SC3F7.14 , strco-SC4C2.18 , strco-SC10F4.23 , strco-SCBAC20F6.10 , strco-SCD95A , strco-SCE8.12C , strco-SCE63.01 , strco-SCF43.16C , strco-SCJ9A.33C , strco-SCO0047 , strco-SCO0135 , strco-SCO0490 , strco-SCO0503 , strco-SCO0556.1 , strco-SCO0556.2 , strco-SCO1265 , strco-SCO2123 , strco-SCO2516 , strco-SCO2723 , strco-SCO2761 , strco-SCO3396 , strco-SCO3772 , strco-SCO4160 , strco-SCO4900 , strco-SCO5215 , strco-SCO5986 , strco-SCO6351 , strco-SCO6488 , strco-SCO7057 , strco-SCO7121 , strco-SCO7396 , strco-SCO7609 , strco-SCOT , strco-SLPD , strco-TAP

Title : The genome sequence of Schizosaccharomyces pombe - Wood_2002_Nature_415_871
Author(s) : Wood V , Gwilliam R , Rajandream MA , Lyne M , Lyne R , Stewart A , Sgouros J , Peat N , Hayles J , Baker S , Basham D , Bowman S , Brooks K , Brown D , Brown S , Chillingworth T , Churcher C , Collins M , Connor R , Cronin A , Davis P , Feltwell T , Fraser A , Gentles S , Goble A , Hamlin N , Harris D , Hidalgo J , Hodgson G , Holroyd S , Hornsby T , Howarth S , Huckle EJ , Hunt S , Jagels K , James K , Jones L , Jones M , Leather S , McDonald S , McLean J , Mooney P , Moule S , Mungall K , Murphy L , Niblett D , Odell C , Oliver K , O'Neil S , Pearson D , Quail MA , Rabbinowitsch E , Rutherford K , Rutter S , Saunders D , Seeger K , Sharp S , Skelton J , Simmonds M , Squares R , Squares S , Stevens K , Taylor K , Taylor RG , Tivey A , Walsh S , Warren T , Whitehead S , Woodward J , Volckaert G , Aert R , Robben J , Grymonprez B , Weltjens I , Vanstreels E , Rieger M , Schafer M , Muller-Auer S , Gabel C , Fuchs M , Dusterhoft A , Fritzc C , Holzer E , Moestl D , Hilbert H , Borzym K , Langer I , Beck A , Lehrach H , Reinhardt R , Pohl TM , Eger P , Zimmermann W , Wedler H , Wambutt R , Purnelle B , Goffeau A , Cadieu E , Dreano S , Gloux S , Lelaure V , Mottier S , Galibert F , Aves SJ , Xiang Z , Hunt C , Moore K , Hurst SM , Lucas M , Rochet M , Gaillardin C , Tallada VA , Garzon A , Thode G , Daga RR , Cruzado L , Jimenez J , Sanchez M , del Rey F , Benito J , Dominguez A , Revuelta JL , Moreno S , Armstrong J , Forsburg SL , Cerutti L , Lowe T , McCombie WR , Paulsen I , Potashkin J , Shpakovski GV , Ussery D , Barrell BG , Nurse P
Ref : Nature , 415 :871 , 2002
Abstract : We have sequenced and annotated the genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.
ESTHER : Wood_2002_Nature_415_871
PubMedSearch : Wood_2002_Nature_415_871
PubMedID: 11859360
Gene_locus related to this paper: schpo-APTH1 , schpo-be46 , schpo-BST1 , schpo-C2E11.08 , schpo-C14C4.15C , schpo-C22H12.03 , schpo-C23C4.16C , schpo-C57A10.08C , schpo-dyr , schpo-este1 , schpo-KEX1 , schpo-PCY1 , schpo-pdat , schpo-PLG7 , schpo-ppme1 , schpo-q9c0y8 , schpo-SPAC4A8.06C , schpo-C22A12.06C , schpo-SPAC977.15 , schpo-SPAPB1A11.02 , schpo-SPBC14C8.15 , schpo-SPBC530.12C , schpo-SPBC1711.12 , schpo-SPBPB2B2.02 , schpo-SPCC5E4.05C , schpo-SPCC417.12 , schpo-SPCC1672.09 , schpo-yb4e , schpo-yblh , schpo-ydw6 , schpo-ye7a , schpo-ye63 , schpo-ye88 , schpo-yeld , schpo-yk68 , schpo-clr3 , schpo-ykv6

Title : Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18 - Parkhill_2001_Nature_413_848
Author(s) : Parkhill J , Dougan G , James KD , Thomson NR , Pickard D , Wain J , Churcher C , Mungall KL , Bentley SD , Holden MT , Sebaihia M , Baker S , Basham D , Brooks K , Chillingworth T , Connerton P , Cronin A , Davis P , Davies RM , Dowd L , White N , Farrar J , Feltwell T , Hamlin N , Haque A , Hien TT , Holroyd S , Jagels K , Krogh A , Larsen TS , Leather S , Moule S , O'Gaora P , Parry C , Quail M , Rutherford K , Simmonds M , Skelton J , Stevens K , Whitehead S , Barrell BG
Ref : Nature , 413 :848 , 2001
Abstract : Salmonella enterica serovar Typhi (S. typhi) is the aetiological agent of typhoid fever, a serious invasive bacterial disease of humans with an annual global burden of approximately 16 million cases, leading to 600,000 fatalities. Many S. enterica serovars actively invade the mucosal surface of the intestine but are normally contained in healthy individuals by the local immune defence mechanisms. However, S. typhi has evolved the ability to spread to the deeper tissues of humans, including liver, spleen and bone marrow. Here we have sequenced the 4,809,037-base pair (bp) genome of a S. typhi (CT18) that is resistant to multiple drugs, revealing the presence of hundreds of insertions and deletions compared with the Escherichia coli genome, ranging in size from single genes to large islands. Notably, the genome sequence identifies over two hundred pseudogenes, several corresponding to genes that are known to contribute to virulence in Salmonella typhimurium. This genetic degradation may contribute to the human-restricted host range for S. typhi. CT18 harbours a 218,150-bp multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2), which shows recent common ancestry with a virulence plasmid of Yersinia pestis.
ESTHER : Parkhill_2001_Nature_413_848
PubMedSearch : Parkhill_2001_Nature_413_848
PubMedID: 11677608
Gene_locus related to this paper: salen-OPDB , salti-q8z717 , salty-AES , salty-BIOH , salty-ENTF , salty-FES , salty-IROD , salty-IROE , salty-PLDB , salty-STM2547 , salty-STM4506 , salty-STY1441 , salty-STY2428 , salty-STY3846 , salty-yafa , salty-YBFF , salty-ycfp , salty-YFBB , salty-YJFP , salty-YQIA

Title : Massive gene decay in the leprosy bacillus - Cole_2001_Nature_409_1007
Author(s) : Cole ST , Eiglmeier K , Parkhill J , James KD , Thomson NR , Wheeler PR , Honore N , Garnier T , Churcher C , Harris D , Mungall K , Basham D , Brown D , Chillingworth T , Connor R , Davies RM , Devlin K , Duthoy S , Feltwell T , Fraser A , Hamlin N , Holroyd S , Hornsby T , Jagels K , Lacroix C , Maclean J , Moule S , Murphy L , Oliver K , Quail MA , Rajandream MA , Rutherford KM , Rutter S , Seeger K , Simon S , Simmonds M , Skelton J , Squares R , Squares S , Stevens K , Taylor K , Whitehead S , Woodward JR , Barrell BG
Ref : Nature , 409 :1007 , 2001
Abstract : Leprosy, a chronic human neurological disease, results from infection with the obligate intracellular pathogen Mycobacterium leprae, a close relative of the tubercle bacillus. Mycobacterium leprae has the longest doubling time of all known bacteria and has thwarted every effort at culture in the laboratory. Comparing the 3.27-megabase (Mb) genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus with that of Mycobacterium tuberculosis (4.41 Mb) provides clear explanations for these properties and reveals an extreme case of reductive evolution. Less than half of the genome contains functional genes but pseudogenes, with intact counterparts in M. tuberculosis, abound. Genome downsizing and the current mosaic arrangement appear to have resulted from extensive recombination events between dispersed repetitive sequences. Gene deletion and decay have eliminated many important metabolic activities including siderophore production, part of the oxidative and most of the microaerophilic and anaerobic respiratory chains, and numerous catabolic systems and their regulatory circuits.
ESTHER : Cole_2001_Nature_409_1007
PubMedSearch : Cole_2001_Nature_409_1007
PubMedID: 11234002
Gene_locus related to this paper: mycle-a85a , mycle-a85b , mycle-a85c , mycle-lipG , mycle-LPQC , mycle-metx , mycle-ML0314 , mycle-ML0370 , mycle-ML0376 , mycle-ML1339 , mycle-ML1444 , mycle-ML1632 , mycle-ML1633 , mycle-ML1921 , mycle-ML2269 , mycle-ML2297 , mycle-ML2359 , mycle-ML2603 , mycle-mpt5 , mycle-PKS13 , mycle-PTRB , mycle-q9cc62 , mycle-q9cdb3

Title : Genome sequence of Yersinia pestis, the causative agent of plague. - Parkhill_2001_Nature_413_523
Author(s) : Parkhill J , Wren BW , Thomson NR , Titball RW , Holden MTG , Prentice MB , Sebaihia M , James KD , Churcher C , Mungall KL , Baker S , Basham D , Bentley SD , Brooks K , Cerdeno-Tarraga AM , Chillingworth T , Cronin A , Davies RM , Davis P , Dougan G , Feltwell T , Hamlin N , Holroyd S , Jagels K , Karlyshev AV , Leather S , Moule S , Oyston PCF , Quail M , Rutherford K , Simmonds M , Skelton J , Stevens K , Whitehead S , Barrell BG
Ref : Nature , 413 :523 , 2001
Abstract : The Gram-negative bacterium Yersinia pestis is the causative agent of the systemic invasive infectious disease classically referred to as plague, and has been responsible for three human pandemics: the Justinian plague (sixth to eighth centuries), the Black Death (fourteenth to nineteenth centuries) and modern plague (nineteenth century to the present day). The recent identification of strains resistant to multiple drugs and the potential use of Y. pestis as an agent of biological warfare mean that plague still poses a threat to human health. Here we report the complete genome sequence of Y. pestis strain CO92, consisting of a 4.65-megabase (Mb) chromosome and three plasmids of 96.2 kilobases (kb), 70.3 kb and 9.6 kb. The genome is unusually rich in insertion sequences and displays anomalies in GC base-composition bias, indicating frequent intragenomic recombination. Many genes seem to have been acquired from other bacteria and viruses (including adhesins, secretion systems and insecticidal toxins). The genome contains around 150 pseudogenes, many of which are remnants of a redundant enteropathogenic lifestyle. The evidence of ongoing genome fluidity, expansion and decay suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a unique insight into the ways in which new and highly virulent pathogens evolve.
ESTHER : Parkhill_2001_Nature_413_523
PubMedSearch : Parkhill_2001_Nature_413_523
PubMedID: 11586360
Gene_locus related to this paper: yerpe-BIOH , yerpe-dlhh , yerpe-IRP1 , yerpe-PIP , yerpe-PLDB , yerpe-PTRB , yerpe-q8zey9 , yerpe-y1616 , yerpe-y3224 , yerpe-YBTT , yerpe-YPLA , yerpe-YPO0180 , yerpe-YPO0667 , yerpe-YPO0773 , yerpe-YPO0776 , yerpe-YPO0986 , yerpe-YPO1501 , yerpe-YPO1997 , yerpe-YPO2002 , yerpe-YPO2336 , yerpe-YPO2526 , yerpe-YPO2638 , yerpe-YPO2814 , yerpe-YPO4014

Title : Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491 - Parkhill_2000_Nature_404_502
Author(s) : Parkhill J , Achtman M , James KD , Bentley SD , Churcher C , Klee SR , Morelli G , Basham D , Brown D , Chillingworth T , Davies RM , Davis P , Devlin K , Feltwell T , Hamlin N , Holroyd S , Jagels K , Leather S , Moule S , Mungall K , Quail MA , Rajandream MA , Rutherford KM , Simmonds M , Skelton J , Whitehead S , Spratt BG , Barrell BG
Ref : Nature , 404 :502 , 2000
Abstract : Neisseria meningitidis causes bacterial meningitis and is therefore responsible for considerable morbidity and mortality in both the developed and the developing world. Meningococci are opportunistic pathogens that colonize the nasopharynges and oropharynges of asymptomatic carriers. For reasons that are still mostly unknown, they occasionally gain access to the blood, and subsequently to the cerebrospinal fluid, to cause septicaemia and meningitis. N. meningitidis strains are divided into a number of serogroups on the basis of the immunochemistry of their capsular polysaccharides; serogroup A strains are responsible for major epidemics and pandemics of meningococcal disease, and therefore most of the morbidity and mortality associated with this disease. Here we have determined the complete genome sequence of a serogroup A strain of Neisseria meningitidis, Z2491. The sequence is 2,184,406 base pairs in length, with an overall G+C content of 51.8%, and contains 2,121 predicted coding sequences. The most notable feature of the genome is the presence of many hundreds of repetitive elements, ranging from short repeats, positioned either singly or in large multiple arrays, to insertion sequences and gene duplications of one kilobase or more. Many of these repeats appear to be involved in genome fluidity and antigenic variation in this important human pathogen.
ESTHER : Parkhill_2000_Nature_404_502
PubMedSearch : Parkhill_2000_Nature_404_502
PubMedID: 10761919
Gene_locus related to this paper: neima-metx , neimb-q9k0t9 , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB1877 , neimf-a1kta9 , neime-r0tza2

Title : The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences - Parkhill_2000_Nature_403_665
Author(s) : Parkhill J , Wren BW , Mungall K , Ketley JM , Churcher C , Basham D , Chillingworth T , Davies RM , Feltwell T , Holroyd S , Jagels K , Karlyshev AV , Moule S , Pallen MJ , Penn CW , Quail MA , Rajandream MA , Rutherford KM , van Vliet AH , Whitehead S , Barrell BG
Ref : Nature , 403 :665 , 2000
Abstract : Campylobacter jejuni, from the delta-epsilon group of proteobacteria, is a microaerophilic, Gram-negative, flagellate, spiral bacterium-properties it shares with the related gastric pathogen Helicobacter pylori. It is the leading cause of bacterial food-borne diarrhoeal disease throughout the world. In addition, infection with C. jejuni is the most frequent antecedent to a form of neuromuscular paralysis known as Guillain-Barre syndrome. Here we report the genome sequence of C. jejuni NCTC11168. C. jejuni has a circular chromosome of 1,641,481 base pairs (30.6% G+C) which is predicted to encode 1,654 proteins and 54 stable RNA species. The genome is unusual in that there are virtually no insertion sequences or phage-associated sequences and very few repeat sequences. One of the most striking findings in the genome was the presence of hypervariable sequences. These short homopolymeric runs of nucleotides were commonly found in genes encoding the biosynthesis or modification of surface structures, or in closely linked genes of unknown function. The apparently high rate of variation of these homopolymeric tracts may be important in the survival strategy of C. jejuni.
ESTHER : Parkhill_2000_Nature_403_665
PubMedSearch : Parkhill_2000_Nature_403_665
PubMedID: 10688204
Gene_locus related to this paper: camco-e0qbj3 , camco-q4hhu5 , camje-a3zji1 , camje-CJ0796C , camjr-q5ht69 , camju-a3yll6 , camju-Q9ZF63

Title : The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum - Bowman_1999_Nature_400_532
Author(s) : Bowman S , Lawson D , Basham D , Brown D , Chillingworth T , Churcher CM , Craig A , Davies RM , Devlin K , Feltwell T , Gentles S , Gwilliam R , Hamlin N , Harris D , Holroyd S , Hornsby T , Horrocks P , Jagels K , Jassal B , Kyes S , McLean J , Moule S , Mungall K , Murphy L , Oliver K , Quail MA , Rajandream MA , Rutter S , Skelton J , Squares R , Squares S , Sulston JE , Whitehead S , Woodward JR , Newbold C , Barrell BG
Ref : Nature , 400 :532 , 1999
Abstract : Analysis of Plasmodium falciparum chromosome 3, and comparison with chromosome 2, highlights novel features of chromosome organization and gene structure. The sub-telomeric regions of chromosome 3 show a conserved order of features, including repetitive DNA sequences, members of multigene families involved in pathogenesis and antigenic variation, a number of conserved pseudogenes, and several genes of unknown function. A putative centromere has been identified that has a core region of about 2 kilobases with an extremely high (adenine + thymidine) composition and arrays of tandem repeats. We have predicted 215 protein-coding genes and two transfer RNA genes in the 1,060,106-base-pair chromosome sequence. The predicted protein-coding genes can be divided into three main classes: 52.6% are not spliced, 45.1% have a large exon with short additional 5' or 3' exons, and 2.3% have a multiple exon structure more typical of higher eukaryotes.
ESTHER : Bowman_1999_Nature_400_532
PubMedSearch : Bowman_1999_Nature_400_532
PubMedID: 10448855
Gene_locus related to this paper: plafa-PFC0950C

Title : Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence - Cole_1998_Nature_393_537
Author(s) : Cole ST , Brosch R , Parkhill J , Garnier T , Churcher C , Harris D , Gordon SV , Eiglmeier K , Gas S , Barry CE, 3rd , Tekaia F , Badcock K , Basham D , Brown D , Chillingworth T , Connor R , Davies R , Devlin K , Feltwell T , Gentles S , Hamlin N , Holroyd S , Hornsby T , Jagels K , Krogh A , McLean J , Moule S , Murphy L , Oliver K , Osborne J , Quail MA , Rajandream MA , Rogers J , Rutter S , Seeger K , Skelton J , Squares R , Squares S , Sulston JE , Taylor K , Whitehead S , Barrell BG
Ref : Nature , 393 :537 , 1998
Abstract : Countless millions of people have died from tuberculosis, a chronic infectious disease caused by the tubercle bacillus. The complete genome sequence of the best-characterized strain of Mycobacterium tuberculosis, H37Rv, has been determined and analysed in order to improve our understanding of the biology of this slow-growing pathogen and to help the conception of new prophylactic and therapeutic interventions. The genome comprises 4,411,529 base pairs, contains around 4,000 genes, and has a very high guanine + cytosine content that is reflected in the biased amino-acid content of the proteins. M. tuberculosis differs radically from other bacteria in that a very large portion of its coding capacity is devoted to the production of enzymes involved in lipogenesis and lipolysis, and to two new families of glycine-rich proteins with a repetitive structure that may represent a source of antigenic variation.
ESTHER : Cole_1998_Nature_393_537
PubMedSearch : Cole_1998_Nature_393_537
PubMedID: 9634230
Gene_locus related to this paper: myctu-a85a , myctu-a85b , myctu-a85c , myctu-bpoC , myctu-cut3 , myctu-cutas1 , myctu-cutas2 , myctu-d5yk66 , myctu-ephA , myctu-ephB , myctu-ephc , myctu-ephd , myctu-ephE , myctu-ephF , myctu-hpx , myctu-linb , myctu-lipG , myctu-lipJ , myctu-LIPS , myctu-lipv , myctu-LPQC , myctu-LPQP , myctu-MBTB , myctu-metx , myctu-mpt51 , myctu-MT1628 , myctu-MT3441 , myctu-p71654 , myctu-p95011 , myctu-PKS6 , myctu-PKS13 , myctu-ppe42 , myctu-ppe63 , myctu-Rv1430 , myctu-RV0045C , myctu-Rv0077c , myctu-Rv0151c , myctu-Rv0152c , myctu-Rv0159c , myctu-Rv0160c , myctu-rv0183 , myctu-Rv0217c , myctu-Rv0220 , myctu-Rv0272c , myctu-RV0293C , myctu-RV0421C , myctu-RV0457C , myctu-RV0519C , myctu-RV0774C , myctu-RV0782 , myctu-RV0840C , myctu-Rv1069c , myctu-Rv1076 , myctu-RV1123C , myctu-Rv1184c , myctu-Rv1190 , myctu-Rv1191 , myctu-RV1192 , myctu-RV1215C , myctu-Rv1399c , myctu-Rv1400c , myctu-Rv1426c , myctu-RV1639C , myctu-RV1683 , myctu-RV1758 , myctu-Rv1800 , myctu-Rv1833c , myctu-RV2054 , myctu-RV2296 , myctu-Rv2385 , myctu-Rv2485c , myctu-RV2627C , myctu-RV2672 , myctu-RV2695 , myctu-RV2765 , myctu-RV2800 , myctu-RV2854 , myctu-Rv2970c , myctu-Rv3084 , myctu-Rv3097c , myctu-rv3177 , myctu-Rv3312c , myctu-RV3452 , myctu-RV3473C , myctu-Rv3487c , myctu-Rv3569c , myctu-Rv3591c , myctu-RV3724 , myctu-Rv3802c , myctu-Rv3822 , myctu-y0571 , myctu-y963 , myctu-Y1834 , myctu-y1835 , myctu-y2079 , myctu-Y2307 , myctu-yc88 , myctu-ym23 , myctu-ym24 , myctu-YR15 , myctu-yt28

Title : The nucleotide sequence of Saccharomyces cerevisiae chromosome IV - Jacq_1997_Nature_387_75
Author(s) : Jacq C , Alt-Morbe J , Andre B , Arnold W , Bahr A , Ballesta JP , Bargues M , Baron L , Becker A , Biteau N , Blocker H , Blugeon C , Boskovic J , Brandt P , Bruckner M , Buitrago MJ , Coster F , Delaveau T , del Rey F , Dujon B , Eide LG , Garcia-Cantalejo JM , Goffeau A , Gomez-Peris AC , Granotier C , Hanemann V , Hankeln T , Hoheisel JD , Jager W , Jimenez A , Jonniaux JL , Kramer C , Kuster H , Laamanen P , Legros Y , Louis E , Muller-Rieker S , Monnet A , Moro M , Muller-Auer S , Nussbaumer B , Paricio N , Paulin L , Perea J , Perez-Alonso M , Perez-Ortin JE , Pohl TM , Prydz H , Purnelle B , Rasmussen SW , Remacha M , Revuelta JL , Rieger M , Salom D , Saluz HP , Saiz JE , Saren AM , Schafer M , Scharfe M , Schmidt ER , Schneider C , Scholler P , Schwarz S , Soler-Mira A , Urrestarazu LA , Verhasselt P , Vissers S , Voet M , Volckaert G , Wagner G , Wambutt R , Wedler E , Wedler H , Wolfl S , Harris DE , Bowman S , Brown D , Churcher CM , Connor R , Dedman K , Gentles S , Hamlin N , Hunt S , Jones L , McDonald S , Murphy L , Niblett D , Odell C , Oliver K , Rajandream MA , Richards C , Shore L , Walsh SV , Barrell BG , Dietrich FS , Mulligan J , Allen E , Araujo R , Aviles E , Berno A , Carpenter J , Chen E , Cherry JM , Chung E , Duncan M , Hunicke-Smith S , Hyman R , Komp C , Lashkari D , Lew H , Lin D , Mosedale D , Nakahara K , Namath A , Oefner P , Oh C , Petel FX , Roberts D , Schramm S , Schroeder M , Shogren T , Shroff N , Winant A , Yelton M , Botstein D , Davis RW , Johnston M , Hillier L , Riles L , Albermann K , Hani J , Heumann K , Kleine K , Mewes HW , Zollner A , Zaccaria P
Ref : Nature , 387 :75 , 1997
Abstract : The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome IV has been determined. Apart from chromosome XII, which contains the 1-2 Mb rDNA cluster, chromosome IV is the longest S. cerevisiae chromosome. It was split into three parts, which were sequenced by a consortium from the European Community, the Sanger Centre, and groups from St Louis and Stanford in the United States. The sequence of 1,531,974 base pairs contains 796 predicted or known genes, 318 (39.9%) of which have been previously identified. Of the 478 new genes, 225 (28.3%) are homologous to previously identified genes and 253 (32%) have unknown functions or correspond to spurious open reading frames (ORFs). On average there is one gene approximately every two kilobases. Superimposed on alternating regional variations in G+C composition, there is a large central domain with a lower G+C content that contains all the yeast transposon (Ty) elements and most of the tRNA genes. Chromosome IV shares with chromosomes II, V, XII, XIII and XV some long clustered duplications which partly explain its origin.
ESTHER : Jacq_1997_Nature_387_75
PubMedSearch : Jacq_1997_Nature_387_75
PubMedID: 9169867
Gene_locus related to this paper: yeast-dlhh , yeast-ECM18 , yeast-YDL109C , yeast-YDR428C , yeast-YDR444W

Title : Life with 6000 genes - Goffeau_1996_Science_274_563
Author(s) : Goffeau A , Barrell BG , Bussey H , Davis RW , Dujon B , Feldmann H , Galibert F , Hoheisel JD , Jacq C , Johnston M , Louis EJ , Mewes HW , Murakami Y , Philippsen P , Tettelin H , Oliver SG
Ref : Science , 274 :546 , 1996
Abstract : The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.
ESTHER : Goffeau_1996_Science_274_563
PubMedSearch : Goffeau_1996_Science_274_563
PubMedID: 8849441
Gene_locus related to this paper: yeast-ATG15 , yeast-SAY1