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1. The Genome of the African Trypanosome Trypanosoma brucei

Author

Berriman, Matthew, Ghedin, Elodie, Hertz-Fowler, Christiane, Blandin, Gaëlle, Renauld, Hubert, Bartholomeu, Daniella C., Lennard, Nicola J., Caler, Elisabet, Hamlin, Nancy E., Haas, Brian, Böhme, Ulrike, Hannick, Linda, Aslett, Martin A., Shallom, Joshua, Marcello, Lucio, Hou, Lihua, Wickstead, Bill, Arrowsmith, Claire, Atkin, Rebecca J., Barron, Andrew J., Bringaud, Frederic, Brooks, Karen, Carrington, Mark, Cherevach, Inna, Chillingworth, Tracey-Jane, Churcher, Carol, Clark, Louise N., Corton, Craig H., Cronin, Ann, Davies, Rob M., Doggett, Jonathon, Djikeng, Appolinaire, Feldblyum, Tamara, Field, Mark C., Fraser, Audrey, Goodhead, Ian, Hance, Zahra, Harper, David, Harris, Barbara R., Hauser, Heidi, Hostetler, Jessica, Ivens, Al, Jagels, Kay, Johnson, David, Johnson, Justin, Jones, Kristine, Kerhornou, Arnaud X., Koo, Hean, Larke, Natasha, Landfear, Scott, Larkin, Christopher, Leech, Vanessa, Line, Alexandra, Lord, Angela, MacLeod, Annette, Mooney, Paul J., Moule, Sharon, Morgan, Gareth W., Mungall, Karen, Norbertczak, Halina, Ormond, Doug, Pai, Grace, Peacock, Chris S., Peterson, Jeremy, Quail, Michael A., Rabbinowitsch, Ester, Rajandream, Marie-Adele, Reitter, Chris, Salzberg, Steven L., Sanders, Mandy, Schobel, Seth, Sharp, Sarah, Simmonds, Mark, Simpson, Anjana J., Tallon, Luke, Tait, Andrew, Tivey, Adrian R., Van Aken, Susan, Walker, Danielle, Wanless, David, Wang, Shiliang, White, Brian, White, Owen, Whitehead, Sally, Woodward, John, Wortman, Jennifer, Adams, Mark D., Embley, T. Martin, Gull, Keith, Ullu, Elisabetta, Barry, J. David, Fairlamb, Alan H., Opperdoes, Fred, Barrell, Barclay G., Donelson, John E., Hall, Neil, Fraser, Claire M., Melville, Sara E., and El-Sayed, Najib M.

Published
2005

2. Genomic Plasticity of the Causative Agent of Melioidosis, Burkholderia pseudomallei

Author

Titball, Richard W., Peacock, Sharon J., Cerdeño-Tárraga, Ana M., Atkins, Timothy, Crossman, Lisa C., Pitt, Tyrone, Churcher, Carol, Mungall, Karen, Bentley, Stephen D., Sebaihia, Mohammed, Thomson, Nicholas R., Bason, Nathalie, Beacham, Ifor R., Brooks, Karen, Brown, Katherine A., Brown, Nat F., Challis, Greg L., Cherevach, Inna, Chillingworth, Tracy, Cronin, Ann, Crossett, Ben, Davis, Paul, DeShazer, David, Feltwell, Theresa, Fraser, Audrey, Hance, Zahra, Hauser, Heidi, Holroyd, Simon, Jagels, Kay, Keith, Karen E., Maddison, Mark, Moule, Sharon, Price, Claire, Quail, Michael A., Rabbinowitsch, Ester, Rutherford, Kim, Sanders, Mandy, Simmonds, Mark, Songsivilai, Sirirurg, Stevens, Kim, Tumapa, Sarinna, Vesaratchavest, Monkgol, Whitehead, Sally, Yeats, Corin, Barrell, Bart G., Parkhill, Julian, and Greenberg, E. Peter

Published
2004

3. Complete Genomes of Two Clinical Staphylococcus aureus Strains: Evidence for the Rapid Evolution of Virulence and Drug Resistance

Author

Feil, Edward J., Lindsay, Jodi A., Peacock, Sharon J., Enright, Mark C., Foster, Tim J., Moore, Catrin E., Hurst, Laurence, Atkin, Rebecca, Barron, Andrew, Bason, Nathalie, Bentley, Stephen D., Chillingworth, Carol, Chillingworth, Tracey, Churcher, Carol, Clark, Louise, Corton, Craig, Cronin, Ann, Doggett, Jon, Dowd, Linda, Feltwell, Theresa, Hance, Zahra, Harris, Barbara, Hauser, Heidi, Holroyd, Simon, Jagels, Kay, James, Keith D., Lennard, Nicola, Line, Alexandra, Mayes, Rebecca, Moule, Sharon, Mungall, Karen, Ormond, Douglas, Quail, Michael A., Rabbinowitsch, Ester, Rutherford, Kim, Sanders, Mandy, Sharp, Sarah, Simmonds, Mark, Stevens, Kim, Whitehead, Sally, Barrell, Bart G., Spratt, Brian G., Parkhill, Julian, and Mekalanos, John J.

Published
2004

4. Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility

Author

Pearson, Melanie M., Sebaihia, Mohammed, Churcher, Carol, Quail, Michael A., Seshasayee, Aswin S., Luscombe, Nicholas M., Abdellah, Zahra, Arrosmith, Claire, Atkin, Becky, Chillingworth, Tracey, Hauser, Heidi, Jagels, Kay, Moule, Sharon, Mungall, Karen, Norbertczak, Halina, Rabbinowitsch, Ester, Walker, Danielle, Whithead, Sally, Thomson, Nicholas R., Rather, Philip N., Parkhill, Julian, and Mobley., Harry L.T.

Subjects
Nucleotide sequence -- Physiological aspects, Nucleotide sequence -- Research, Gram-negative bacteria -- Genetic aspects, Gram-negative bacteria -- Research, Urinary tract infections -- Risk factors, Urinary tract infections -- Genetic aspects, Urinary tract infections -- Research, Biological sciences
Abstract

The gram-negative enteric bacterium Proteus mirabilis is a frequent cause of urinary tract infections in individuals with long-term indwelling catheters or with complicated urinary tracts (e.g., due to spinal cord injury or anatomic abnormality). P. mirabilis bacteriuria may lead to acute pyelonephritis, fever, and bacteremia. Most notoriously, this pathogen uses urease to catalyze the formation of kidney and bladder stones or to encrust or obstruct indwelling urinary catheters. Here we report the complete genome sequence of P. mirabilis HI4320, a representative strain cultured in our laboratory from the urine of a nursing home patient with a long-term ([greater than or equal to] 30 days) indwelling urinary catheter. The genome is 4.063 Mb long and has a G + C content of 38.88%. There is a single plasmid consisting of 36,289 nucleotides. Annotation of the genome identified 3,685 coding sequences and seven rRNA loci. Analysis of the sequence confirmed the presence of previously identified virulence determinants, as well as a contiguous 54-kb flagellar regulon and 17 types of fimbriae. Genes encoding a potential type III secretion system were identified on a low-G+C-content genomic island containing 24 intact genes that appear to encode all components necessary to assemble a type III secretion system needle complex. In addition, the P. mirabilis HI4320 genome possesses four tandem copies of the zapE metalloprotease gene, genes encoding six putative autotransporters, an extension of the atf fimbrial operon to six genes, including an mrpJ homolog, and genes encoding at least five iron uptake mechanisms, two potential type IV secretion systems, and 16 two-component regulators.

Published
2008

5. Complete genome of acute rheumatic fever-associated serotype M5 Streptococcus pyogenes strain Manfredo

Author

Holden, Matthew T.G., Scott, Annabel, Cherevach, Inna, Chillingworth, Tracey, Churcher, Carol, Cronin, Ann, Dowd, Linda, Feltwell, Theresa, Hamlin, Nancy, Holroyd, Simon, Jagels, Kay, Moule, Sharon, Mungall, Karen, Quail, Michael A., Price, Claire, Rabbinowitsch, Ester, Sharp, Sarah, Skelton, Jason, Whitehead, Sally, Barrell, Bart G., Kehoe, Michael, and Parkhill, Julian

Subjects
Rheumatic fever -- Genetic aspects, Rheumatic fever -- Research, Streptococcus pyogenes -- Genetic aspects, Streptococcus pyogenes -- Research, Genomes -- Research, Biological sciences
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 or S. pyogenes and the close relationship between strain Manfredo and MGAS8232, another acute rheumatic fever-associated strain.

Published
2007

6. The genome of the protist parasite Entamoeba histolytica

Author

Loftus, Brendan, Anderson, Iain, Davies, Rob, Alsmark, U. Cecilia M., Samuelson, John, Amedeo, Paolo, Roncaglia, Paola, Berriman, Matt, Hirt, Robert P., Mann, Barbara J., Nozaki, Tomo, Suh, Bernard, Pop, Mihai, Duchene, Michael, Ackers, John, Tannich, Egbert, Leippe, Matthias, Hofer, Margit, Bruchhaus, Iris, Willhoeft, Ute, Bhattacharya, Alok, Chillingworth, Tracey, Churcher, Carol, Hance, Zahra, Harris, Barbara, Harris, David, Jagels, Kay, Moule, Sharon, Mungall, Karen, Ormond, Doug, Squares, Rob, Whitehead, Sally, Quail, Michael A., Rabbinowitsch, Ester, Norbertczak, Halina, Price, Claire, Wang, Zheng, Guillen, Nancy, Gilchrist, Carol, Stroup, Suzanne E., Bhattacharya, Sudha, Lohia, Anuradha, Foster, Peter G., Sicheritz-Ponten, Thomas, Weber, Christian, Singh, Upinder, Mukherjee, Chandrama, El-Sayed, Najib M., Petri, Jr, William A., Clark, C. Graham, Embley, T. Martin, Barrell, Bart, Fraser, Claire M., and Hall, Neil

Abstract

Author(s): Brendan Loftus (corresponding author) [1]; Iain Anderson [1]; Rob Davies [2]; U. Cecilia M. Alsmark [3]; John Samuelson [4]; Paolo Amedeo [1]; Paola Roncaglia [1]; Matt Berriman [2]; Robert [...]

Published
2005
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7. Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei

Author

Holden, Matthew T.G., Titball, Richard W., Peacock, Sharon J., Cerdeno-Tarraga, Ana M., Atkins, Timothy, Crossman, Lisa C., Pitt, Tyrone, Churcher, Carol, Mungall, Karen, Bentley, Stephen D., Sebaihia, Mohammed, Thomson, Nicholas R., Bason, Nathalie, Beacham, Ifor R., Brooks, Karen, Brown, Katherine A., Brown, Nat F., Challis, Greg L., Cherevach, Inna, Chillingworth, Tracy, Cronin, Ann, Crossett, Ben, Davis, Paul, DeShazer, David, Feltwell, Theresa, Fraser, Audrey, Hance, Zahra, Hauser, Heidi, Holroyd, Simon, Jagels, Kay, Keith, Karen E., Maddison, Mark, Moule, Sharon, Price, Claire, Quail, Michael A., Rabbinowitsch, Ester, Rutherford, Kim, Sanders, Mandy, Simmonds, Mark, Songsivilai, Sirirurg, Stevens, Kim, Tumapa, Sarinna, Vesaratchavest, Monkgol, Whitehead, Sally, Yeats, Corin, Barrell, Bart G., Oyston, Petra C.F., and Parkhill, Julian

Subjects
Pseudomonas infections -- Research, Science and technology
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.

Published
2004

8. Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance

Author

Holden, Matthew T.G., Feil, Edward J., Lindsay, Jodi A., Peacock, Sharon J., Day, Nicholas P.J., Enright, Mark C., Foster, Tim J., Moore, Catrin E., Hurst, Laurence, Atkin, Rebecca, Barron, Andrew, Bason, Nathalie, Bentley, Stephen D., Chillingworth, Carol, Chillingworth, Tracey, Churcher, Carol, Clark, Louise, Corton, Craig, Cronin, Ann, Doggett, Jon, Dowd, Linda, Feltwell, Theresa, Hance, Zahra, Harris, Barbara C., Bishop, Hauser, Heidi, Holroyd, Simon, Jagels, Kay, James, Keith D., Lennard, Nicola, Line, Alexandra, Mayes, Rebecca, Moule, Sharon, Mungall, Karen, Ormond, Douglas, Quail, Michael A., Rabbinowitsch, Ester, Rutherford, Kim, Sanders, Mandy, Sharp, Sarah, Simmonds, Mark, Stevens, Kim, Whitehead, Sally, Barrell, Bart G., Spratt, Brian G., and Parkhill, Julian

Subjects
Drug resistance in microorganisms -- Research, Staphylococcus aureus -- Research, Staphylococcus aureus -- Genetic aspects, Science and technology, National Academy of Sciences -- Research
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 equal to] 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 equal to] 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 SC[C.sub.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.

Published
2004

9. Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

Author

Thomson, Nicholas R., Clayton, Debra J., Windhorst, Daniel, Vernikos, Georgios, Davidson, Susanne, Churcher, Carol, Quail, Michael A., Stevens, Mark, Jones, Michael A., Watson, Michael, Barron, Andy, Layton, Abigail, Pickard, Derek, Kingsley, Robert A., Bignell, Alex, Clark, Louise, Harris, Barbara, Ormond, Doug, Abdellah, Zahra, Brooks, Karen, Cherevach, Inna, Chillingworth, Tracey, Woodward, John, Norberczak, Halina, Lord, Angela, Arrowsmith, Claire, Jagels, Kay, Moule, Sharon, Mungall, Karen, Sanders, Mandy, Whitehead, Sally, Chabalogoity, Jose A., Maskell, Duncan, Humphrey, Tom, Roberts, Mark, Barrow, Paul A., Dougan, Gordon, and Parkhill, Julian

Subjects
Salmonella enteritidis -- Genetic aspects, Nucleotide sequence -- Comparative analysis, Pathogenic microorganisms -- Research, Health
Abstract

Several genome analyses are conducted to study the compare the genome sequences of Salmonella enterica serovar Enteritidis PT4 isolate and Salmonella Gallinarum 287/91 isolate. The various evolution and host adaptation pathways involved in the formation of these pathogens are also discussed.

Published
2008

10. Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis

Author

Stinear, Timothy P., Seemann, Torsten, Harrison, Paul F., Jenkin, Grant A., Davies, John K., Johnson, Paul D.R., Abdellah, Zahra, Arrowsmith, Claire, Chillingworth, Tracey, Churcher, Carol, Clarke, Kay, Cronin, Ann, Davis, Paul, Goodhead, Ian, Holroyd, Nancy, Jagels, Kay, Lord, Angela, Moule, Sharon, Mungall, Karen, Norbertczak, Halina, Quail, Michael A., Rabbinowitsch, Ester, Walker, Danielle, White, Brian, Whitehead, Sally, Small, Pamela L.C., Brosch, Roland, Ramakrishnan, Lalita, Fischbach, Michael A., Parkhill, Julian, and Cole, Stewart T.

Subjects
Genomics -- Analysis, Mycobacteria -- Genetic aspects, Mycobacterium -- Genetic aspects, Tuberculosis -- Genetic aspects, Tuberculosis -- Causes of, Health
Abstract

The genome sequence of Mycobacterium marnium is determined and it's very close genetic relationship with Mycobacterium tuberculosis is exploited to provide further insight into the multiple changes that shapes Mycobacterium tuberculosis into a major human pathogen from environmental origins. The study provides a foundation for using Mycobacterium marinum to better understand the determinants of pathogenesis of tuberculosis.

Published
2008

11. Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii

Author

Khan, Asis, Bohme, Ulrike, Kelly, Krystyna A., Adlem, Ellen, Brooks, Karen, Simmonds, Mark, Mungall, Karen, Quail, Michael A., Arrowsmith, Claire, Chillingworth, Tracey, Churcher, Carol, Harris, David, Collins, Matthew, Fosker, Nigel, Fraser, Audrey, Hance, Zahra, Jagels, Kay, Moule, Sharon, Murphy, Lee, O'Neil, Susan, Rajandream, Marie-Adele, Saunders, David, Seeger, Kathy, Whitehead, Sally, Mayr, Thomas, Xuenan Xuan, Watanabe, Junichi, Suzuki, Yutaka, Wakaguri, Hiroyuki, Sugano, Sumio, Sugimoto, Chihiro, Paulsen, Ian, Mackey, Aaron J., Roos, David S., Hall, Neil, Berriman, Matthew, Barrell, Bart, Sibley, L. David, and Ajioka, James W.

Subjects
Chromosome mapping -- Analysis, Genetic polymorphisms -- Analysis, Toxoplasma -- Genetic aspects, Toxoplasma -- Physiological aspects, Health
Published
2006

12. The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081

Author

Thomson, Nicholas R, Howard, Sarah, Wren, Brendan W, Holden, Matthew TG, Crossman, Lisa, Challis, Gregory L, Churcher, Carol, Mungall, Karen, Brooks, Karen, Chillingworth, Tracey, Feltwell, Theresa, Abdellah, Zahra, Hauser, Heidi, Jagels, Kay, Maddison, Mark, Moule, Sharon, Sanders, Mandy, Whitehead, Sally, Quail, Michael A, Dougan, Gordon, Parkhill, Julian, and Prentice, Michael B

Subjects
bacteria
Abstract

The human enteropathogen, Yersinia enterocolitica, is a significant link in the range of Yersinia pathologies extending from mild gastroenteritis to bubonic plague. Comparison at the genomic level is a key step in our understanding of the genetic basis for this pathogenicity spectrum. Here we report the genome of Y. enterocolitica strain 8081 (serotype 0:8; biotype 1B) and extensive microarray data relating to the genetic diversity of the Y. enterocolitica species. Our analysis reveals that the genome of Y. enterocolitica strain 8081 is a patchwork of horizontally acquired genetic loci, including a plasticity zone of 199 kb containing an extraordinarily high density of virulence genes. Microarray analysis has provided insights into species-specific Y. enterocolitica gene functions and the intraspecies differences between the high, low, and nonpathogenic Y. enterocolitica biotypes. Through comparative genome sequence analysis we provide new information on the evolution of the Yersinia. We identify numerous loci that represent ancestral clusters of genes potentially important in enteric survival and pathogenesis, which have been lost or are in the process of being lost, in the other sequenced Yersinia lineages. Our analysis also highlights large metabolic operons in Y. enterocolitica that are absent in the related enteropathogen, Yersinia pseudotuberculosis, indicating major differences in niche and nutrients used within the mammalian gut. These include clusters directing, the production of hydrogenases, tetrathionate respiration, cobalamin synthesis, and propanediol utilisation. Along with ancestral gene clusters, the genome of Y. enterocolitica has revealed species-specific and enteropathogen-specific loci. This has provided important insights into the pathology of this bacterium and, more broadly, into the evolution of the genus. Moreover, wider investigations looking at the patterns of gene loss and gain in the Yersinia have highlighted common themes in the genome evolution of other human enteropathogens.

Published
2006

13. Comparative genomic analysis of three Leishmania species that cause diverse human disease.

Author

Peacock, Christopher S, Seeger, Kathy, Harris, David, Murphy, Lee, Ruiz, Jeronimo C, Quail, Michael A, Peters, Nick, Adlem, Ellen, Tivey, Adrian, Aslett, Martin, Kerhornou, Arnaud, Ivens, Alasdair, Fraser, Audrey, Rajandream, Marie-Adele, Carver, Tim, Norbertczak, Halina, Chillingworth, Tracey, Hance, Zahra, Jagels, Kay, Moule, Sharon, Ormond, Doug, Rutter, Simon, Squares, Rob, Whitehead, Sally, Rabbinowitsch, Ester, Arrowsmith, Claire, White, Brian, Thurston, Scott, Bringaud, Frédéric, Baldauf, Sandra L, Faulconbridge, Adam, Jeffares, Daniel, Depledge, Daniel P, Oyola, Samuel O, Hilley, James D, Brito, Loislene O, Tosi, Luiz R O, Barrell, Barclay, Cruz, Angela K, Mottram, Jeremy C, Smith, Deborah F, Berriman, Matthew, Peacock, Christopher S, Seeger, Kathy, Harris, David, Murphy, Lee, Ruiz, Jeronimo C, Quail, Michael A, Peters, Nick, Adlem, Ellen, Tivey, Adrian, Aslett, Martin, Kerhornou, Arnaud, Ivens, Alasdair, Fraser, Audrey, Rajandream, Marie-Adele, Carver, Tim, Norbertczak, Halina, Chillingworth, Tracey, Hance, Zahra, Jagels, Kay, Moule, Sharon, Ormond, Doug, Rutter, Simon, Squares, Rob, Whitehead, Sally, Rabbinowitsch, Ester, Arrowsmith, Claire, White, Brian, Thurston, Scott, Bringaud, Frédéric, Baldauf, Sandra L, Faulconbridge, Adam, Jeffares, Daniel, Depledge, Daniel P, Oyola, Samuel O, Hilley, James D, Brito, Loislene O, Tosi, Luiz R O, Barrell, Barclay, Cruz, Angela K, Mottram, Jeremy C, Smith, Deborah F, and Berriman, Matthew

Abstract

Leishmania parasites cause a broad spectrum of clinical disease. Here we report the sequencing of the genomes of two species of Leishmania: Leishmania infantum and Leishmania braziliensis. The comparison of these sequences with the published genome of Leishmania major reveals marked conservation of synteny and identifies only 200 genes with a differential distribution between the three species. L. braziliensis, contrary to Leishmania species examined so far, possesses components of a putative RNA-mediated interference pathway, telomere-associated transposable elements and spliced leader–associated SLACS retrotransposons. We show that pseudogene formation and gene loss are the principal forces shaping the different genomes. Genes that are differentially distributed between the species encode proteins implicated in host-pathogen interactions and parasite survival in the macrophage.

Published
2007
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14. Intra- and Interhost Evolutionary Dynamics of Equine Influenza Virus

Author

Murcia, Pablo R., primary, Baillie, Gregory J., additional, Daly, Janet, additional, Elton, Debra, additional, Jervis, Carley, additional, Mumford, Jennifer A., additional, Newton, Richard, additional, Parrish, Colin R., additional, Hoelzer, Karin, additional, Dougan, Gordon, additional, Parkhill, Julian, additional, Lennard, Nicola, additional, Ormond, Doug, additional, Moule, Sharon, additional, Whitwham, Andrew, additional, McCauley, John W., additional, McKinley, Trevelyan J., additional, Holmes, Edward C., additional, Grenfell, Bryan T., additional, and Wood, James L. N., additional

Published
2010
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15. Comparative genomic analysis of three Leishmania species that cause diverse human disease

Author

Peacock, Christopher S, primary, Seeger, Kathy, additional, Harris, David, additional, Murphy, Lee, additional, Ruiz, Jeronimo C, additional, Quail, Michael A, additional, Peters, Nick, additional, Adlem, Ellen, additional, Tivey, Adrian, additional, Aslett, Martin, additional, Kerhornou, Arnaud, additional, Ivens, Alasdair, additional, Fraser, Audrey, additional, Rajandream, Marie-Adele, additional, Carver, Tim, additional, Norbertczak, Halina, additional, Chillingworth, Tracey, additional, Hance, Zahra, additional, Jagels, Kay, additional, Moule, Sharon, additional, Ormond, Doug, additional, Rutter, Simon, additional, Squares, Rob, additional, Whitehead, Sally, additional, Rabbinowitsch, Ester, additional, Arrowsmith, Claire, additional, White, Brian, additional, Thurston, Scott, additional, Bringaud, Frédéric, additional, Baldauf, Sandra L, additional, Faulconbridge, Adam, additional, Jeffares, Daniel, additional, Depledge, Daniel P, additional, Oyola, Samuel O, additional, Hilley, James D, additional, Brito, Loislene O, additional, Tosi, Luiz R O, additional, Barrell, Barclay, additional, Cruz, Angela K, additional, Mottram, Jeremy C, additional, Smith, Deborah F, additional, and Berriman, Matthew, additional

Published
2007
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16. Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes

Author

Sebaihia, Mohammed, primary, Peck, Michael W., additional, Minton, Nigel P., additional, Thomson, Nicholas R., additional, Holden, Matthew T.G., additional, Mitchell, Wilfrid J., additional, Carter, Andrew T., additional, Bentley, Stephen D., additional, Mason, David R., additional, Crossman, Lisa, additional, Paul, Catherine J., additional, Ivens, Alasdair, additional, Wells-Bennik, Marjon H.J., additional, Davis, Ian J., additional, Cerdeño-Tárraga, Ana M., additional, Churcher, Carol, additional, Quail, Michael A., additional, Chillingworth, Tracey, additional, Feltwell, Theresa, additional, Fraser, Audrey, additional, Goodhead, Ian, additional, Hance, Zahra, additional, Jagels, Kay, additional, Larke, Natasha, additional, Maddison, Mark, additional, Moule, Sharon, additional, Mungall, Karen, additional, Norbertczak, Halina, additional, Rabbinowitsch, Ester, additional, Sanders, Mandy, additional, Simmonds, Mark, additional, White, Brian, additional, Whithead, Sally, additional, and Parkhill, Julian, additional

Published
2007
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17. Meningococcal Genetic Variation Mechanisms Viewed through Comparative Analysis of Serogroup C Strain FAM18

Author

Bentley, Stephen D, primary, Vernikos, George S, additional, Snyder, Lori A. S, additional, Churcher, Carol, additional, Arrowsmith, Claire, additional, Chillingworth, Tracey, additional, Cronin, Ann, additional, Davis, Paul H, additional, Holroyd, Nancy E, additional, Jagels, Kay, additional, Maddison, Mark, additional, Moule, Sharon, additional, Rabbinowitsch, Ester, additional, Sharp, Sarah, additional, Unwin, Louise, additional, Whitehead, Sally, additional, Quail, Michael A, additional, Achtman, Mark, additional, Barrell, Bart, additional, Saunders, Nigel J, additional, and Parkhill, Julian, additional

Published
2007
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18. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome

Author

Sebaihia, Mohammed, primary, Wren, Brendan W, additional, Mullany, Peter, additional, Fairweather, Neil F, additional, Minton, Nigel, additional, Stabler, Richard, additional, Thomson, Nicholas R, additional, Roberts, Adam P, additional, Cerdeño-Tárraga, Ana M, additional, Wang, Hongmei, additional, Holden, Matthew TG, additional, Wright, Anne, additional, Churcher, Carol, additional, Quail, Michael A, additional, Baker, Stephen, additional, Bason, Nathalie, additional, Brooks, Karen, additional, Chillingworth, Tracey, additional, Cronin, Ann, additional, Davis, Paul, additional, Dowd, Linda, additional, Fraser, Audrey, additional, Feltwell, Theresa, additional, Hance, Zahra, additional, Holroyd, Simon, additional, Jagels, Kay, additional, Moule, Sharon, additional, Mungall, Karen, additional, Price, Claire, additional, Rabbinowitsch, Ester, additional, Sharp, Sarah, additional, Simmonds, Mark, additional, Stevens, Kim, additional, Unwin, Louise, additional, Whithead, Sally, additional, Dupuy, Bruno, additional, Dougan, Gordon, additional, Barrell, Bart, additional, and Parkhill, Julian, additional

Published
2006
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19. The Complete Genome Sequence and Comparative Genome Analysis of the High Pathogenicity Yersinia enterocolitica Strain 8081

Author

Thomson, Nicholas R., primary, Howard, Sarah, additional, Wren, Brendan W., additional, Holden, Matthew T. G., additional, Crossman, Lisa, additional, Challis, Gregory L., additional, Churcher, Carol, additional, Mungall, Karen, additional, Brooks, Karen, additional, Chillingworth, Tracey, additional, Feltwell, Theresa, additional, Abdellah, Zahra, additional, Hauser, Heidi, additional, Jagels, Kay, additional, Maddison, Mark, additional, Moule, Sharon, additional, Sanders, Mandy, additional, Whitehead, Sally, additional, Quail, Michael A., additional, Dougan, Gordon, additional, Parkhill, Julian, additional, and Prentice, Michael B., additional

Published
2006
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20. Comparative genomic view of mechanisms of variation in Neisseria meningitidis through sequencing and analysis of a third meningococcal genome from serogroup C strain FAM18

Author

Bentley, Stephen D., primary, Vernikos, George, additional, Snyder, Lori A. S., additional, Churcher, Carol, additional, Arrowsmith, Claire, additional, Chillingworth, Tracey, additional, Cronin, Ann, additional, Davis, Paul H, additional, Holroyd, Nancy E., additional, Jagels, Kay, additional, Maddison, Mark, additional, Moule, Sharon, additional, Rabbinowitsch, Ester, additional, Sharp, Sarah, additional, Unwin, Louise, additional, Whitehead, Sally, additional, Quail, Michael A., additional, Achtman, Mark, additional, Barrell, Bart, additional, Saunders, Nigel J., additional, and Parkhill, Julian, additional

Published
2005
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21. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica

Author

Parkhill, Julian, primary, Sebaihia, Mohammed, additional, Preston, Andrew, additional, Murphy, Lee D, additional, Thomson, Nicholas, additional, Harris, David E, additional, Holden, Matthew T G, additional, Churcher, Carol M, additional, Bentley, Stephen D, additional, Mungall, Karen L, additional, Cerdeño-Tárraga, Ana M, additional, Temple, Louise, additional, James, Keith, additional, Harris, Barbara, additional, Quail, Michael A, additional, Achtman, Mark, additional, Atkin, Rebecca, additional, Baker, Steven, additional, Basham, David, additional, Bason, Nathalie, additional, Cherevach, Inna, additional, Chillingworth, Tracey, additional, Collins, Matthew, additional, Cronin, Anne, additional, Davis, Paul, additional, Doggett, Jonathan, additional, Feltwell, Theresa, additional, Goble, Arlette, additional, Hamlin, Nancy, additional, Hauser, Heidi, additional, Holroyd, Simon, additional, Jagels, Kay, additional, Leather, Sampsa, additional, Moule, Sharon, additional, Norberczak, Halina, additional, O'Neil, Susan, additional, Ormond, Doug, additional, Price, Claire, additional, Rabbinowitsch, Ester, additional, Rutter, Simon, additional, Sanders, Mandy, additional, Saunders, David, additional, Seeger, Katherine, additional, Sharp, Sarah, additional, Simmonds, Mark, additional, Skelton, Jason, additional, Squares, Robert, additional, Squares, Steven, additional, Stevens, Kim, additional, Unwin, Louise, additional, Whitehead, Sally, additional, Barrell, Bart G, additional, and Maskell, Duncan J, additional

Published
2003
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22. The genome of Rhizobium leguminosarum has recognizable core and accessory components

Author

Young, J Peter, Crossman, Lisa, Johnston, Andrew, Thomson, Nicholas, Ghazoui, Zara, Hull, Katherine, Wexler, Margaret, Curson, Andrew, Todd, Jonathan, Poole, Philip, Mauchline, Tim, East, Alison, Quail, Michael, Churcher, Carol, Arrowsmith, Claire, Cherevach, Inna, Chillingworth, Tracey, Clarke, Kay, Cronin, Ann, Davis, Paul, Fraser, Audrey, Hance, Zahra, Hauser, Heidi, Jagels, Kay, Moule, Sharon, Mungall, Karen, Norbertczak, Halina, Rabbinowitsch, Ester, Sanders, Mandy, Simmonds, Mark, Whitehead, Sally, and Parkhill, Julian

Abstract

Background Rhizobium leguminosarum is an α-proteobacterial N2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841.Results The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes (Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were over-represented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens.Conclusion Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.

Published
2006

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