Abstract:
:Legionella pneumophila is an environmental bacterium and the leading cause of Legionnaires' disease. Just five sequence types (ST), from more than 2000 currently described, cause nearly half of disease cases in northwest Europe. Here, we report the sequence and analyses of 364 L. pneumophila genomes, including 337 from the five disease-associated STs and 27 representative of the species diversity. Phylogenetic analyses revealed that the five STs have independent origins within a highly diverse species. The number of de novo mutations is extremely low with maximum pairwise single-nucleotide polymorphisms (SNPs) ranging from 19 (ST47) to 127 (ST1), which suggests emergences within the last century. Isolates sampled geographically far apart differ by only a few SNPs, demonstrating rapid dissemination. These five STs have been recombining recently, leading to a shared pool of allelic variants potentially contributing to their increased disease propensity. The oldest clone, ST1, has spread globally; between 1940 and 2000, four new clones have emerged in Europe, which show long-distance, rapid dispersal. That a large proportion of clinical cases is caused by recently emerged and internationally dispersed clones, linked by convergent evolution, is surprising for an environmental bacterium traditionally considered to be an opportunistic pathogen. To simultaneously explain recent emergence, rapid spread and increased disease association, we hypothesize that these STs have adapted to new man-made environmental niches, which may be linked by human infection and transmission.
journal_name
Genome Resjournal_title
Genome researchauthors
David S,Rusniok C,Mentasti M,Gomez-Valero L,Harris SR,Lechat P,Lees J,Ginevra C,Glaser P,Ma L,Bouchier C,Underwood A,Jarraud S,Harrison TG,Parkhill J,Buchrieser Cdoi
10.1101/gr.209536.116subject
Has Abstractpub_date
2016-11-01 00:00:00pages
1555-1564issue
11eissn
1088-9051issn
1549-5469pii
gr.209536.116journal_volume
26pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of ORFans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. The uni...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2231904
更新日期:2004-06-01 00:00:00
abstract::Biophysical, chemical, and nanoscience approaches to the study of nuclear structure and activity have been developing recently and hold considerable promise. A selection of fundamental problems in genome organization and function are reviewed and discussed in the context of these new perspectives and approaches. Advan...
journal_title:Genome research
pub_type: 杂志文章,评审
doi:10.1101/gr.946403
更新日期:2003-06-01 00:00:00
abstract::Recent computational and experimental work suggests that functional modules underlie much of cellular physiology and are a useful unit of cellular organization from the perspective of systems biology. Because interactions among modules can give rise to higher-level properties that are essential to cellular function, a...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3847105
更新日期:2005-09-01 00:00:00
abstract::Fish-mammal genomic comparisons have proved powerful in identifying conserved noncoding elements likely to be cis-regulatory in nature, and the majority of those tested in vivo have been shown to act as tissue-specific enhancers associated with genes involved in transcriptional regulation of development. Although most...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4143406
更新日期:2006-04-01 00:00:00
abstract::Essential genes refer to those whose null mutation leads to lethality or sterility. Theoretical reasoning and empirical data both suggest that the fatal effect of inactivating an essential gene can be attributed to either the loss of indispensable core cellular function (Type I), or the gain of fatal side effects afte...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.205955.116
更新日期:2016-10-01 00:00:00
abstract::The reported human genome sequence includes about 400 gaps of unknown sequence that were not found in the bacterial artificial chromosome (BAC) and cosmid libraries used for sequencing of the genome. These missing sequences correspond to approximately 1% of euchromatic regions of the human genome. Gap filling is a lab...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1929904
更新日期:2004-02-01 00:00:00
abstract::ClinSeq is a pilot project to investigate the use of whole-genome sequencing as a tool for clinical research. By piloting the acquisition of large amounts of DNA sequence data from individual human subjects, we are fostering the development of hypothesis-generating approaches for performing research in genomic medicin...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.092841.109
更新日期:2009-09-01 00:00:00
abstract::Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has limited our understanding of the evolutionary dynamics of gene persistence and loss, our ability to identify conserved regulatory elements, as well our knowledge of the extent to which...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.154286.112
更新日期:2013-09-01 00:00:00
abstract::To elucidate the role of exon shuffling in shaping the complexity of the human genome/proteome, we have systematically analyzed intron phase distributions in the coding sequence of human protein domains. We found that introns at the boundaries of domains show high excess of symmetrical phase combinations (i.e., 0-0, 1...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.520702
更新日期:2002-11-01 00:00:00
abstract::Epigenetic mechanisms are believed to play key roles in the establishment of cell-specific transcription programs. Accordingly, the modified bases 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been observed in DNA of genomic regulatory regions such as enhancers, and oxidation of 5mC into 5hmC by Ten-e...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.211466.116
更新日期:2017-06-01 00:00:00
abstract::We find that the degree of impairment of protein function by missense variants is predictable by comparative sequence analysis alone. The applicable range of impairment is not confined to binary predictions that distinguish normal from deleterious variants, but extends continuously from mild to severe effects. The acc...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3804205
更新日期:2005-07-01 00:00:00
abstract::A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of 107 known nuclear domain families used for the analysis. Most of the novel domains are present in all major eukaryotic l...
journal_title:Genome research
pub_type: 信件
doi:10.1101/gr.203201
更新日期:2002-01-01 00:00:00
abstract::Despite considerable genetic heterogeneity underlying neurodevelopmental diseases, there is compelling evidence that many disease genes will map to a much smaller number of biological subnetworks. We developed a computational method, termed MAGI (merging affected genes into integrated networks), that simultaneously in...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.178855.114
更新日期:2015-01-01 00:00:00
abstract::The genetics of aging in the yeast Saccharomyces cerevisiae has involved the manipulation of individual genes in laboratory strains. We have instituted a quantitative genetic analysis of the yeast replicative lifespan by sampling the natural genetic variation in a wild yeast isolate. Haploid segregants from a cross be...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.136549.111
更新日期:2012-10-01 00:00:00
abstract::Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.109678.110
更新日期:2011-04-01 00:00:00
abstract::An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such "localizome" maps should provide information on where (in what cells or tissues) and when (at what stage of development or under wha...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2497604
更新日期:2004-10-01 00:00:00
abstract::The prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single exon of a single-copy chromosomal gene. In addition to the protein-coding exon, PrP genes in mammals contain one or two 5'-noncoding exons. To learn more about the genomic organization of regions surrounding the PrP exons, we...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.10.1022
更新日期:1998-10-01 00:00:00
abstract::We have conducted a phylogenetic analysis of the Ribonuclease HI (RNH) domains present in Eubacteria, Eukarya, all long-term repeat (LTR)-bearing retrotransposons, and several late-branching clades of non-LTR retrotransposons. Analysis of this simple yet highly conserved enzymatic domain from these disparate sources p...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.185101
更新日期:2001-07-01 00:00:00
abstract::Lemurs and the other strepsirrhine primates are of great interest to the primate genomics community due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships po...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7265208
更新日期:2008-03-01 00:00:00
abstract::To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the "2-n-way" software suite to provide a fundamental and innovative processing framework for revealing and compar...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.262261.120
更新日期:2020-10-01 00:00:00
abstract::Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important compone...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7.5.551
更新日期:1997-05-01 00:00:00
abstract::How pathogens evolve their virulence to humans in nature is a scientific issue of great medical and biological importance. Shiga toxin (Stx)-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are the major foodborne pathogens that can cause hemolytic uremic syndrome and infantile diarrhea, respectiv...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.249268.119
更新日期:2019-09-01 00:00:00
abstract::Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of post-transcriptional gene regulatory evolution are largely unknown. Here we used ri...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.164996.113
更新日期:2014-03-01 00:00:00
abstract::The lack of long-term evolutionary conservation of microRNA (miRNA) target sites appears to contradict many analyses of their functions. Several hypotheses have been offered, but an attractive one-that the conservation may be a function of taxonomic hierarchy (vertebrates, mammals, primates, etc.)-has rarely been disc...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.148916.112
更新日期:2013-11-01 00:00:00
abstract::Chicken B cells create their immunoglobulin repertoire within the Bursa of Fabricius by gene conversion. The high homologous recombination activity is shared by the bursal B-cell-derived DT40 cell line, which integrates transfected DNA constructs at high rates into its endogenous loci. Targeted integration in DT40 is ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.12.2062
更新日期:2000-12-01 00:00:00
abstract::Mouse chromosome 7F4/F5, where the imprinting domain is located, is syntenic to human 11p15.5, the locus for Beckwith-Wiedemann syndrome. The domain is thought to consist of the two subdomains Kip2 (p57(kip2))/Lit1 and Igf2/H19. Because DNA methylation is believed to be a key factor in genomic imprinting, we performed...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.110702
更新日期:2002-12-01 00:00:00
abstract::Nucleosomes containing the CenH3 (CENPA or CENP-A) histone variant replace H3 nucleosomes at centromeres to provide a foundation for kinetochore assembly. CENPA nucleosomes are part of the constitutive centromere associated network (CCAN) that forms the inner kinetochore on which outer kinetochore proteins assemble. T...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.204784.116
更新日期:2016-09-01 00:00:00
abstract::Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation kinetics with high-throughput sequencing. CBCS was used to generate sequence libraries representing the high, middle, an...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2438004
更新日期:2005-01-01 00:00:00
abstract::Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences overlooked by previous Arabidopsis genome annotation methods. A total of 454,274 whole genome shotgun sequences covering ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3176505
更新日期:2005-04-01 00:00:00
abstract::Obesity is reaching epidemic proportions in developed countries and represents a significant risk factor for hypertension, heart disease, diabetes, and dyslipidemia. Splicing mutations constitute at least 14% of disease-causing mutations, thus implicating polymorphisms that affect splicing as likely candidates for dis...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6661308
更新日期:2008-02-01 00:00:00