-
Kerstin Svensson,
Andreas Sjödin,
Mona Byström,
Malin Granberg,
Mitchell J Brittnacher,
Laurence Rohmer,
Michael A Jacobs,
Elizabeth H Sims-Day,
Ruth Levy,
Yang Zhou, [......],
Regina Lim,
Jean Chang,
Donald Guenthener,
Allison Kang,
Eric Haugen, Will Gillett,
Rajinder Kaul,
Mats Forsman,
Pär Larsson,
Anders Johansson
[show abstract]
[hide abstract]
ABSTRACT: Here we report the complete, accurate 1.89-Mb genome sequence of Francisella tularensis subsp. holarctica strain FSC200, isolated in 1998 in the Swedish municipality Ljusdal, which is in an area where tularemia is highly endemic. This genome is important because strain FSC200 has been extensively used for functional and genetic studies of Francisella and is well-characterized.
Journal of bacteriology 12/2012; 194(24):6965-6. · 3.94 Impact Factor
-
Hillary S Hayden,
Regina Lim,
Mitchell J Brittnacher,
Elizabeth H Sims,
Elizabeth R Ramage,
Christine Fong,
Zaining Wu,
Eva Crist,
Jean Chang,
Yang Zhou,
Matthew Radey,
Laurence Rohmer,
Eric Haugen, Will Gillett,
Vanaporn Wuthiekanun,
Sharon J Peacock,
Rajinder Kaul,
Samuel I Miller,
Colin Manoil,
Michael A Jacobs
[show abstract]
[hide abstract]
ABSTRACT: Burkholderia pseudomallei, the etiologic agent of human melioidosis, is capable of causing severe acute infection with overwhelming septicemia leading to death. A high rate of recurrent disease occurs in adult patients, most often due to recrudescence of the initial infecting strain. Pathogen persistence and evolution during such relapsing infections are not well understood. Bacterial cells present in the primary inoculum and in late infections may differ greatly, as has been observed in chronic disease, or they may be genetically similar. To test these alternative models, we conducted whole-genome comparisons of clonal primary and relapse B. pseudomallei isolates recovered six months to six years apart from four adult Thai patients. We found differences within each of the four pairs, and some, including a 330 Kb deletion, affected substantial portions of the genome. Many of the changes were associated with increased antibiotic resistance. We also found evidence of positive selection for deleterious mutations in a TetR family transcriptional regulator from a set of 107 additional B. pseudomallei strains. As part of the study, we sequenced to base-pair accuracy the genome of B. pseudomallei strain 1026b, the model used for genetic studies of B. pseudomallei pathogenesis and antibiotic resistance. Our findings provide new insights into pathogen evolution during long-term infections and have important implications for the development of intervention strategies to combat recurrent melioidosis.
PLoS ONE 01/2012; 7(5):e36507. · 4.09 Impact Factor
-
Bridget R Kulasekara,
Michael Jacobs,
Yang Zhou,
Zaining Wu,
Elizabeth Sims,
Channakhone Saenphimmachak,
Laurence Rohmer,
Jennifer M Ritchie,
Matthew Radey,
Matthew McKevitt, [......], Will Gillett,
Christine Fong,
Jean Chang,
Viktoriya Beskhlebnaya,
Matthew K Waldor,
Mansour Samadpour,
Thomas S Whittam,
Rajinder Kaul,
Mitchell Brittnacher,
Samuel I Miller
[show abstract]
[hide abstract]
ABSTRACT: In addition to causing diarrhea, Escherichia coli O157:H7 infection can lead to hemolytic-uremic syndrome (HUS), a severe disease characterized by hemolysis and renal failure. Differences in HUS frequency among E. coli O157:H7 outbreaks have been noted, but our understanding of bacterial factors that promote HUS is incomplete. In 2006, in an outbreak of E. coli O157:H7 caused by consumption of contaminated spinach, there was a notably high frequency of HUS. We sequenced the genome of the strain responsible (TW14359) with the goal of identifying candidate genetic factors that contribute to an enhanced ability to cause HUS. The TW14359 genome contains 70 kb of DNA segments not present in either of the two reference O157:H7 genomes. We identified seven putative virulence determinants, including two putative type III secretion system effector proteins, candidate genes that could result in increased pathogenicity or, alternatively, adaptation to plants, and an intact anaerobic nitric oxide reductase gene, norV. We surveyed 100 O157:H7 isolates for the presence of these putative virulence determinants. A norV deletion was found in over one-half of the strains surveyed and correlated strikingly with the absence of stx(1). The other putative virulence factors were found in 8 to 35% of the O157:H7 isolates surveyed, and their presence also correlated with the presence of norV and the absence of stx(1), indicating that the presence of norV may serve as a marker of a greater propensity for HUS, similar to the correlation between the absence of stx(1) and a propensity for HUS.
Infection and immunity 07/2009; 77(9):3713-21. · 4.21 Impact Factor
-
Stéphane Vuilleumier,
Ludmila Chistoserdova,
Ming-Chun Lee,
Françoise Bringel,
Aurélie Lajus,
Yang Zhou,
Benjamin Gourion,
Valérie Barbe,
Jean Chang,
Stéphane Cruveiller, [......],
Grégory Salvignol,
David Vallenet,
Zaining Wu,
Christopher J Marx,
Julia A Vorholt,
Maynard V Olson,
Rajinder Kaul,
Jean Weissenbach,
Claudine Médigue,
Mary E Lidstrom
[show abstract]
[hide abstract]
ABSTRACT: Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared.
The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name "island integration determinant" (iid).
These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.
PLoS ONE 02/2009; 4(5):e5584. · 4.09 Impact Factor
-
Hillary S Hayden, Will Gillett,
Channakhone Saenphimmachak,
Regina Lim,
Yang Zhou,
Michael A Jacobs,
Jean Chang,
Laurence Rohmer,
David A D'Argenio,
Anthony Palmieri,
Ruth Levy,
Eric Haugen,
Gane K S Wong,
Mitch J Brittnacher,
Jane L Burns,
Samuel I Miller,
Maynard V Olson,
Rajinder Kaul
[show abstract]
[hide abstract]
ABSTRACT: Large-insert genome analysis (LIGAN) is a broadly applicable, high-throughput technology designed to characterize genome-scale structural variation. Fosmid paired-end sequences and DNA fingerprints from a query genome are compared to a reference sequence using the Genomic Variation Analysis (GenVal) suite of software tools to pinpoint locations of insertions, deletions, and rearrangements. Fosmids spanning regions that contain new structural variants can then be sequenced. Clonal pairs of Pseudomonas aeruginosa isolates from four cystic fibrosis patients were used to validate the LIGAN technology. Approximately 1.5 Mb of inserted sequences were identified, including 743 kb containing 615 ORFs that are absent from published P. aeruginosa genomes. Six rearrangement breakpoints and 220 kb of deleted sequences were also identified. Our study expands the "genome universe" of P. aeruginosa and validates a technology that complements emerging, short-read sequencing methods that are better suited to characterizing single-nucleotide polymorphisms than structural variation.
Genomics 07/2008; 91(6):530-7. · 3.02 Impact Factor
-
Jeffrey M. Kidd,
Gregory M. Cooper,
William F. Donahue,
Hillary S. Hayden,
Nick Sampas,
Tina Graves,
Nancy Hansen,
Brian Teague,
Can Alkan,
Francesca Antonacci, [......],
John Stamatoyannopoulos,
David Schwartz,
Deborah A. Nickerson,
James C. Mullikin,
Richard K. Wilson,
Laurakay Bruhn,
Maynard V. Olson,
Rajinder Kaul,
Douglas R. Smith,
Evan E. Eichler
[show abstract]
[hide abstract]
ABSTRACT: Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale—particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation—a standard for genotyping platforms and a prelude to future individual genome sequencing projects.
Nature 04/2008; 453(7191):56-64. · 36.28 Impact Factor
-
Donald Bovee,
Yang Zhou,
Eric Haugen,
Zaining Wu,
Hillary S Hayden, Will Gillett,
Eray Tuzun,
Gregory M Cooper,
Nick Sampas,
Karen Phelps, [......],
V Anne Morrison,
James Sprague,
Donald Jewett,
Danielle Buckley,
Sandhya Subramaniam,
Jean Chang,
Douglas R Smith,
Maynard V Olson,
Evan E Eichler,
Rajinder Kaul
[show abstract]
[hide abstract]
ABSTRACT: The human genome sequence has been finished to very high standards; however, more than 340 gaps remained when the finished genome was published by the International Human Genome Sequencing Consortium in 2004. Using fosmid resources generated from multiple individuals, we targeted gaps in the euchromatic part of the human genome. Here we report 2,488,842 bp of previously unknown euchromatic sequence, 363,114 bp of which close 26 of 250 euchromatic gaps, or 10%, including two remaining euchromatic gaps on chromosome 19. Eight (30.7%) of the closed gaps were found to be polymorphic. These sequences allow complete annotation of several human genes as well as the assignment of mRNAs. The gap sequences are 2.3-fold enriched in segmentally duplicated sequences compared to the whole genome. Our analysis confirms that not all gaps within 'finished' genomes are recalcitrant to subcloning and suggests that the paired-end-sequenced fosmid libraries could prove to be a rich resource for completion of the human euchromatic genome.
Nature Genetics 02/2008; 40(1):96-101. · 35.53 Impact Factor
-
Laurence Rohmer,
Christine Fong,
Simone Abmayr,
Michael Wasnick,
Theodore J Larson Freeman,
Matthew Radey,
Tina Guina,
Kerstin Svensson,
Hillary S Hayden,
Michael Jacobs, [......],
Greg Taylor,
Jinzhi Chen,
Byron Gallis,
David A D'Argenio,
Mats Forsman,
Maynard V Olson,
David R Goodlett,
Rajinder Kaul,
Samuel I Miller,
Mitchell J Brittnacher
[show abstract]
[hide abstract]
ABSTRACT: Francisella tularensis subspecies tularensis and holarctica are pathogenic to humans, whereas the two other subspecies, novicida and mediasiatica, rarely cause disease. To uncover the factors that allow subspecies tularensis and holarctica to be pathogenic to humans, we compared their genome sequences with the genome sequence of Francisella tularensis subspecies novicida U112, which is nonpathogenic to humans.
Comparison of the genomes of human pathogenic Francisella strains with the genome of U112 identifies genes specific to the human pathogenic strains and reveals pseudogenes that previously were unidentified. In addition, this analysis provides a coarse chronology of the evolutionary events that took place during the emergence of the human pathogenic strains. Genomic rearrangements at the level of insertion sequences (IS elements), point mutations, and small indels took place in the human pathogenic strains during and after differentiation from the nonpathogenic strain, resulting in gene inactivation.
The chronology of events suggests a substantial role for genetic drift in the formation of pseudogenes in Francisella genomes. Mutations that occurred early in the evolution, however, might have been fixed in the population either because of evolutionary bottlenecks or because they were pathoadaptive (beneficial in the context of infection). Because the structure of Francisella genomes is similar to that of the genomes of other emerging or highly pathogenic bacteria, this evolutionary scenario may be shared by pathogens from other species.
Genome biology 02/2007; 8(6):R102. · 6.63 Impact Factor
-
Donna M Muzny,
Steven E Scherer,
Rajinder Kaul,
Jing Wang,
Jun Yu,
Ralf Sudbrak,
Christian J Buhay,
Rui Chen,
Andrew Cree,
Yan Ding, [......],
Jianling Zhou,
Yang Zhou,
David Nelson,
Hans Lehrach,
Richard Reinhardt,
Susan L Naylor,
Huanming Yang,
Maynard Olson,
George Weinstock,
Richard A Gibbs
[show abstract]
[hide abstract]
ABSTRACT: After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.
Nature 05/2006; 440(7088):1194-8. · 36.28 Impact Factor
-
Donna M. Muzny,
Steven E. Scherer,
Rajinder Kaul,
Jing Wang,
Jun Yu,
Ralf Sudbrak,
Christian J. Buhay,
Rui Chen,
Andrew Cree,
Yan Ding, [......],
Yang Zhou,
further contributors,
David Nelson,
Hans Lehrach,
Richard Reinhardt,
Susan L. Naylor,
Huanming Yang,
Maynard Olson,
George Weinstock,
Richard A. Gibbs
[show abstract]
[hide abstract]
ABSTRACT: After the completion of a draft human genome sequence1, the International Human Genome Sequencing Consortium has proceeded to finish2 and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B3. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.
Nature 04/2006; 440(7088):1194-1198. · 36.28 Impact Factor
-
Ladeana W Hillier,
Robert S Fulton,
Lucinda A Fulton,
Tina A Graves,
Kymberlie H Pepin,
Caryn Wagner-McPherson,
Dan Layman,
Jason Maas,
Sara Jaeger,
Rebecca Walker, [......],
David Torrents,
Asif T Chinwalla,
Warren R Gish,
Sean R Eddy,
John D McPherson,
Maynard V Olson,
Evan E Eichler,
Eric D Green,
Robert H Waterston,
Richard K Wilson
[show abstract]
[hide abstract]
ABSTRACT: Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame.
Nature 08/2003; 424(6945):157-64. · 36.28 Impact Factor
