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Christopher A Desjardins,
Gustavo C Cerqueira,
Jonathan M Goldberg,
Julie C Dunning Hotopp, Brian J Haas,
Jeremy Zucker,
José M C Ribeiro,
Sakina Saif,
Joshua Z Levin,
Lin Fan,
Qiandong Zeng,
Carsten Russ,
Jennifer R Wortman,
Doran L Fink,
Bruce W Birren,
Thomas B Nutman
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ABSTRACT: Loa loa, the African eyeworm, is a major filarial pathogen of humans. Unlike most filariae, L. loa does not contain the obligate intracellular Wolbachia endosymbiont. We describe the 91.4-Mb genome of L. loa and that of the related filarial parasite Wuchereria bancrofti and predict 14,907 L. loa genes on the basis of microfilarial RNA sequencing. By comparing these genomes to that of another filarial parasite, Brugia malayi, and to those of several other nematodes, we demonstrate synteny among filariae but not with nonparasitic nematodes. The L. loa genome encodes many immunologically relevant genes, as well as protein kinases targeted by drugs currently approved for use in humans. Despite lacking Wolbachia, L. loa shows no new metabolic synthesis or transport capabilities compared to other filariae. These results suggest that the role of Wolbachia in filarial biology is more subtle than previously thought and reveal marked differences between parasitic and nonparasitic nematodes.
Nature Genetics 03/2013; · 35.53 Impact Factor
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Yonatan H Grad,
Marc Lipsitch,
Michael Feldgarden,
Harindra M Arachchi,
Gustavo C Cerqueira,
Michael Fitzgerald,
Paul Godfrey, Brian J Haas,
Cheryl I Murphy,
Carsten Russ, [......],
Andreas M Petersen,
Carsten Struve,
Karen A Krogfelt,
Edouard Bingen,
François-Xavier Weill,
Eric S Lander,
Chad Nusbaum,
Bruce W Birren,
Deborah T Hung,
William P Hanage
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Yonatan H Grad,
Paul Godfrey,
Gustavo C Cerquiera,
Patricia Mariani-Kurkdjian,
Malika Gouali,
Edouard Bingen,
Terrence P Shea, Brian J Haas,
Allison Griggs,
Sarah Young,
Qiandong Zeng,
Marc Lipsitch,
Matthew K Waldor,
François-Xavier Weill,
Jennifer R Wortman,
William P Hanage
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ABSTRACT: ABSTRACT The large outbreak of diarrhea and hemolytic uremic syndrome (HUS) caused by Shiga toxin-producing Escherichia coli O104:H4 in Europe from May to July 2011 highlighted the potential of a rarely identified E. coli serogroup to cause severe disease. Prior to the outbreak, there were very few reports of disease caused by this pathogen and thus little known of its diversity and evolution. The identification of cases of HUS caused by E. coli O104:H4 in France and Turkey after the outbreak and with no clear epidemiological links raises questions about whether these sporadic cases are derived from the outbreak. Here, we report genome sequences of five independent isolates from these cases and results of a comparative analysis with historical and 2011 outbreak isolates. These analyses revealed that the five isolates are not derived from the outbreak strain; however, they are more closely related to the outbreak strain and each other than to isolates identified prior to the 2011 outbreak. Over the short time scale represented by these closely related organisms, the majority of genome variation is found within their mobile genetic elements: none of the nine O104:H4 isolates compared here contain the same set of plasmids, and their prophages and genomic islands also differ. Moreover, the presence of closely related HUS-associated E. coli O104:H4 isolates supports the contention that fully virulent O104:H4 isolates are widespread and emphasizes the possibility of future food-borne E. coli O104:H4 outbreaks. IMPORTANCE In the summer of 2011, a large outbreak of bloody diarrhea with a high rate of severe complications took place in Europe, caused by a previously rarely seen Escherichia coli strain of serogroup O104:H4. Identification of subsequent infections caused by E. coli O104:H4 raised questions about whether these new cases represented ongoing transmission of the outbreak strain. In this study, we sequenced the genomes of isolates from five recent cases and compared them with historical isolates. The analyses reveal that, in the very short term, evolution of the bacterial genome takes place in parts of the genome that are exchanged among bacteria, and these regions contain genes involved in adaptation to local environments. We show that these recent isolates are not derived from the outbreak strain but are very closely related and share many of the same disease-causing genes, emphasizing the concern that these bacteria may cause future severe outbreaks.
mBio 01/2013; 4(1). · 5.31 Impact Factor
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ABSTRACT: BACKGROUND: High-throughput sequencing of cDNA libraries (RNA-Seq) has proven to be a highly effective approach for studying bacterial transcriptomes. A central challenge in designing RNA-Seq-based experiments is estimating a priori the number of reads per sample needed to detect and quantify thousands of individual transcripts with a large dynamic range of abundance. RESULTS: We have conducted a systematic examination of how changes in the number of RNA-Seq reads per sample influences both profiling of a single bacterial transcriptome and the comparison of gene expression among samples. Our findings suggest that the number of reads typically produced in a single lane of the Illumina HiSeq sequencer far exceeds the number needed to saturate the annotated transcriptomes of diverse bacteria growing in monoculture. Moreover, as sequencing depth increases, so too does the detection of cDNAs that likely correspond to spurious transcripts or genomic DNA contamination. Finally, even when dozens of barcoded individual cDNA libraries are sequenced in a single lane, the vast majority of transcripts in each sample can be detected and numerous genes differentially expressed between samples can be identified. CONCLUSIONS: Our analysis provides a guide for the many researchers seeking to determine the appropriate sequencing depth for RNA-Seq-based studies of diverse bacterial species.
BMC Genomics 12/2012; 13(1):734. · 4.07 Impact Factor
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Yonatan H Grad,
Marc Lipsitch,
Allison D Griggs, Brian J Haas,
Terrance P Shea,
Caryn McCowan,
Anna Montmayeur,
Michael FitzGerald,
Jennifer R Wortman,
Karen A Krogfelt,
Edouard Bingen,
François-Xavier Weill,
Erhard Tietze,
Antje Flieger,
Eric S Lander,
Chad Nusbaum,
Bruce W Birren,
Deborah T Hung,
William P Hanage
Proceedings of the National Academy of Sciences 12/2012; 109(52):E3629-30. · 9.68 Impact Factor
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Georgia Giannoukos,
Dawn M Ciulla,
Katherine Huang, Brian J Haas,
Jacques Izard,
Joshua Z Levin,
Jonathan Livny,
Ashlee M Earl,
Dirk Gevers,
Doyle V Ward,
Chad Nusbaum,
Bruce W Birren,
Andreas Gnirke
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ABSTRACT: We have developed a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq. We applied this approach to an RNA mixture derived from three diverse cultured bacterial species and to RNA isolated from clinical stool samples. The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA.
Genome biology 03/2012; 13(3):R23. · 6.63 Impact Factor
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Yonatan H Grad,
Marc Lipsitch,
Michael Feldgarden,
Harindra M Arachchi,
Gustavo C Cerqueira,
Michael Fitzgerald,
Paul Godfrey, Brian J Haas,
Cheryl I Murphy,
Carsten Russ, [......],
Andreas M Petersen,
Carsten Struve,
Karen A Krogfelt,
Edouard Bingen,
François-Xavier Weill,
Eric S Lander,
Chad Nusbaum,
Bruce W Birren,
Deborah T Hung,
William P Hanage
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ABSTRACT: The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May-July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak.
Proceedings of the National Academy of Sciences 02/2012; 109(8):3065-70. · 9.68 Impact Factor
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Veronica N Kos,
Christopher A Desjardins,
Allison Griggs,
Gustavo Cerqueira,
Andries Van Tonder,
Matthew T G Holden,
Paul Godfrey,
Kelli L Palmer,
Kip Bodi,
Emmanuel F Mongodin,
Jennifer Wortman,
Michael Feldgarden,
Trevor Lawley,
Steven R Gill, Brian J Haas,
Bruce Birren,
Michael S Gilmore
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ABSTRACT: Methicillin-resistant Staphylococcus aureus (MRSA) strains are leading causes of hospital-acquired infections in the United States, and clonal cluster 5 (CC5) is the predominant lineage responsible for these infections. Since 2002, there have been 12 cases of vancomycin-resistant S. aureus (VRSA) infection in the United States-all CC5 strains. To understand this genetic background and what distinguishes it from other lineages, we generated and analyzed high-quality draft genome sequences for all available VRSA strains. Sequence comparisons show unambiguously that each strain independently acquired Tn1546 and that all VRSA strains last shared a common ancestor over 50 years ago, well before the occurrence of vancomycin resistance in this species. In contrast to existing hypotheses on what predisposes this lineage to acquire Tn1546, the barrier posed by restriction systems appears to be intact in most VRSA strains. However, VRSA (and other CC5) strains were found to possess a constellation of traits that appears to be optimized for proliferation in precisely the types of polymicrobic infection where transfer could occur. They lack a bacteriocin operon that would be predicted to limit the occurrence of non-CC5 strains in mixed infection and harbor a cluster of unique superantigens and lipoproteins to confound host immunity. A frameshift in dprA, which in other microbes influences uptake of foreign DNA, may also make this lineage conducive to foreign DNA acquisition. IMPORTANCE: Invasive methicillin-resistant Staphylococcus aureus (MRSA) infection now ranks among the leading causes of death in the United States. Vancomycin is a key last-line bactericidal drug for treating these infections. However, since 2002, vancomycin resistance has entered this species. Of the now 12 cases of vancomycin-resistant S. aureus (VRSA), each was believed to represent a new acquisition of the vancomycin-resistant transposon Tn1546 from enterococcal donors. All acquisitions of Tn1546 so far have occurred in MRSA strains of the clonal cluster 5 genetic background, the most common hospital lineage causing hospital-acquired MRSA infection. To understand the nature of these strains, we determined and examined the nucleotide sequences of the genomes of all available VRSA. Genome comparison identified candidate features that position strains of this lineage well for acquiring resistance to antibiotics in mixed infection.
mBio 01/2012; 3(3). · 5.31 Impact Factor
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ABSTRACT: Fungal genome annotation is the starting point for analysis of genome content. This generally involves the application of diverse methods to identify features on a genome assembly such as protein-coding and non-coding genes, repeats and transposable elements, and pseudogenes. Here we describe tools and methods leveraged for eukaryotic genome annotation with a focus on the annotation of fungal nuclear and mitochondrial genomes. We highlight the application of the latest technologies and tools to improve the quality of predicted gene sets. The Broad Institute eukaryotic genome annotation pipeline is described as one example of how such methods and tools are integrated into a sequencing center's production genome annotation environment.
Mycology. 10/2011; 2(3):118-141.
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Christopher A Desjardins,
Mia D Champion,
Jason W Holder,
Anna Muszewska,
Jonathan Goldberg,
Alexandre M Bailão,
Marcelo Macedo Brigido,
Márcia Eliana da Silva Ferreira,
Ana Maria Garcia,
Marcin Grynberg, [......],
Maria Sueli Felipe,
Gustavo H Goldman, Brian J Haas,
Juan G McEwen,
Gustavo Nino-Vega,
Rosana Puccia,
Gioconda San-Blas,
Celia Maria de Almeida Soares,
Bruce W Birren,
Christina A Cuomo
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ABSTRACT: Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, is coupled with a thermally regulated transition from a soil-dwelling filamentous form to a yeast-like pathogenic form. To better understand the genetic basis of growth and pathogenicity in Paracoccidioides, we sequenced the genomes of two strains of Paracoccidioides brasiliensis (Pb03 and Pb18) and one strain of Paracoccidioides lutzii (Pb01). These genomes range in size from 29.1 Mb to 32.9 Mb and encode 7,610 to 8,130 genes. To enable genetic studies, we mapped 94% of the P. brasiliensis Pb18 assembly onto five chromosomes. We characterized gene family content across Onygenales and related fungi, and within Paracoccidioides we found expansions of the fungal-specific kinase family FunK1. Additionally, the Onygenales have lost many genes involved in carbohydrate metabolism and fewer genes involved in protein metabolism, resulting in a higher ratio of proteases to carbohydrate active enzymes in the Onygenales than their relatives. To determine if gene content correlated with growth on different substrates, we screened the non-pathogenic onygenale Uncinocarpus reesii, which has orthologs for 91% of Paracoccidioides metabolic genes, for growth on 190 carbon sources. U. reesii showed growth on a limited range of carbohydrates, primarily basic plant sugars and cell wall components; this suggests that Onygenales, including dimorphic fungi, can degrade cellulosic plant material in the soil. In addition, U. reesii grew on gelatin and a wide range of dipeptides and amino acids, indicating a preference for proteinaceous growth substrates over carbohydrates, which may enable these fungi to also degrade animal biomass. These capabilities for degrading plant and animal substrates suggest a duality in lifestyle that could enable pathogenic species of Onygenales to transfer from soil to animal hosts.
PLoS Genetics 10/2011; 7(10):e1002345. · 8.69 Impact Factor
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Nicholas Rhind,
Zehua Chen,
Moran Yassour,
Dawn A Thompson, Brian J Haas,
Naomi Habib,
Ilan Wapinski,
Sushmita Roy,
Michael F Lin,
David I Heiman, [......],
Hanah Margalit,
Rob Martienssen,
Conrad A Nieduszynski,
Joseph W Spatafora,
Nir Friedman,
Jacob Z Dalgaard,
Peter Baumann,
Hironori Niki,
Aviv Regev,
Chad Nusbaum
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ABSTRACT: The fission yeast clade--comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus--occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.
Science 05/2011; 332(6032):930-6. · 31.20 Impact Factor
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Manfred G Grabherr, Brian J Haas,
Moran Yassour,
Joshua Z Levin,
Dawn A Thompson,
Ido Amit,
Xian Adiconis,
Lin Fan,
Raktima Raychowdhury,
Qiandong Zeng, [......],
Evan Mauceli,
Nir Hacohen,
Andreas Gnirke,
Nicholas Rhind,
Federica di Palma,
Bruce W Birren,
Chad Nusbaum,
Kerstin Lindblad-Toh,
Nir Friedman,
Aviv Regev
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ABSTRACT: Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.
Nature Biotechnology 05/2011; 29(7):644-52. · 29.50 Impact Factor
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Brian J Haas,
Dirk Gevers,
Ashlee M Earl,
Mike Feldgarden,
Doyle V Ward,
Georgia Giannoukos,
Dawn Ciulla,
Diana Tabbaa,
Sarah K Highlander,
Erica Sodergren,
Barbara Methé,
Todd Z DeSantis,
Joseph F Petrosino,
Rob Knight,
Bruce W Birren
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ABSTRACT: Bacterial diversity among environmental samples is commonly assessed with PCR-amplified 16S rRNA gene (16S) sequences. Perceived diversity, however, can be influenced by sample preparation, primer selection, and formation of chimeric 16S amplification products. Chimeras are hybrid products between multiple parent sequences that can be falsely interpreted as novel organisms, thus inflating apparent diversity. We developed a new chimera detection tool called Chimera Slayer (CS). CS detects chimeras with greater sensitivity than previous methods, performs well on short sequences such as those produced by the 454 Life Sciences (Roche) Genome Sequencer, and can scale to large data sets. By benchmarking CS performance against sequences derived from a controlled DNA mixture of known organisms and a simulated chimera set, we provide insights into the factors that affect chimera formation such as sequence abundance, the extent of similarity between 16S genes, and PCR conditions. Chimeras were found to reproducibly form among independent amplifications and contributed to false perceptions of sample diversity and the false identification of novel taxa, with less-abundant species exhibiting chimera rates exceeding 70%. Shotgun metagenomic sequences of our mock community appear to be devoid of 16S chimeras, supporting a role for shotgun metagenomics in validating novel organisms discovered in targeted sequence surveys.
Genome Research 02/2011; 21(3):494-504. · 13.61 Impact Factor
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Agnes P Chan,
Jonathan Crabtree,
Qi Zhao,
Hernan Lorenzi,
Joshua Orvis,
Daniela Puiu,
Admasu Melake-Berhan,
Kristine M Jones,
Julia Redman,
Grace Chen,
Edgar B Cahoon,
Melaku Gedil,
Mario Stanke, Brian J Haas,
Jennifer R Wortman,
Claire M Fraser-Liggett,
Jacques Ravel,
Pablo D Rabinowicz
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ABSTRACT: Castor bean (Ricinus communis) is an oilseed crop that belongs to the spurge (Euphorbiaceae) family, which comprises approximately 6,300 species that include cassava (Manihot esculenta), rubber tree (Hevea brasiliensis) and physic nut (Jatropha curcas). It is primarily of economic interest as a source of castor oil, used for the production of high-quality lubricants because of its high proportion of the unusual fatty acid ricinoleic acid. However, castor bean genomics is also relevant to biosecurity as the seeds contain high levels of ricin, a highly toxic, ribosome-inactivating protein. Here we report the draft genome sequence of castor bean (4.6-fold coverage), the first for a member of the Euphorbiaceae. Whereas most of the key genes involved in oil synthesis and turnover are single copy, the number of members of the ricin gene family is larger than previously thought. Comparative genomics analysis suggests the presence of an ancient hexaploidization event that is conserved across the dicotyledonous lineage.
Nature Biotechnology 09/2010; 28(9):951-6. · 29.50 Impact Factor
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Agnes P Chan,
Jonathan Crabtree,
Qi Zhao,
Hernan Lorenzi,
Joshua Orvis,
Daniela Puiu,
Admasu Melake-Berhan,
Kristine M Jones,
Julia Redman,
Grace Chen,
Edgar B Cahoon,
Melaku Gedil,
Mario Stanke, Brian J Haas,
Jennifer R Wortman,
Claire M Fraser-Liggett,
Jacques Ravel,
Pablo D Rabinowicz
Nature Biotechnology 08/2010; 28(9):951-956. · 23.27 Impact Factor
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Karen E Nelson,
George M Weinstock,
Sarah K Highlander,
Kim C Worley,
Heather Huot Creasy,
Jennifer Russo Wortman,
Douglas B Rusch,
Makedonka Mitreva,
Erica Sodergren,
Asif T Chinwalla, [......],
Sandra W Clifton,
Emma Allen-Vercoe,
Ashlee M Earl,
Candace N Farmer,
Konstantinos Liolios,
Michael G Surette,
Qiang Xu,
Craig Pohl,
Katarzyna Wilczek-Boney,
Dianhui Zhu
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ABSTRACT: The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.
Science 05/2010; 328(5981):994-9. · 31.20 Impact Factor
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Nature Biotechnology 05/2010; 28(5):421-3. · 29.50 Impact Factor
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Ewen F Kirkness, Brian J Haas,
Weilin Sun,
Henk R Braig,
M Alejandra Perotti,
John M Clark,
Si Hyeock Lee,
Hugh M Robertson,
Ryan C Kennedy,
Eran Elhaik, [......],
Terry R Utterback,
Granger G Sutton,
Daniel Lawson,
Robert M Waterhouse,
J Craig Venter,
Robert L Strausberg,
May R Berenbaum,
Frank H Collins,
Evgeny M Zdobnov,
Barry R Pittendrigh
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ABSTRACT: As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is an important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences of the body louse and its primary bacterial endosymbiont Candidatus Riesia pediculicola. The body louse has the smallest known insect genome, spanning 108 Mb. Despite its status as an obligate parasite, it retains a remarkably complete basal insect repertoire of 10,773 protein-coding genes and 57 microRNAs. Representing hemimetabolous insects, the genome of the body louse thus provides a reference for studies of holometabolous insects. Compared with other insect genomes, the body louse genome contains significantly fewer genes associated with environmental sensing and response, including odorant and gustatory receptors and detoxifying enzymes. The unique architecture of the 18 minicircular mitochondrial chromosomes of the body louse may be linked to the loss of the gene encoding the mitochondrial single-stranded DNA binding protein. The genome of the obligatory louse endosymbiont Candidatus Riesia pediculicola encodes less than 600 genes on a short, linear chromosome and a circular plasmid. The plasmid harbors a unique arrangement of genes required for the synthesis of pantothenate, an essential vitamin deficient in the louse diet. The human body louse, its primary endosymbiont, and the bacterial pathogens that it vectors all possess genomes reduced in size compared with their free-living close relatives. Thus, the body louse genome project offers unique information and tools to use in advancing understanding of coevolution among vectors, symbionts, and pathogens.
Proceedings of the National Academy of Sciences 01/2010; 107(27):12168-12173. · 9.68 Impact Factor
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Sebastian Schornack,
Edgar Huitema,
Liliana M Cano,
Tolga O Bozkurt,
Ricardo Oliva,
Mireille Van Damme,
Simon Schwizer,
Sylvain Raffaele,
Angela Chaparro-Garcia,
Rhys Farrer,
Maria Eugenia Segretin,
Jorunn Bos, Brian J Haas,
Michael C Zody,
Chad Nusbaum,
Joe Win,
Marco Thines,
Sophien Kamoun
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ABSTRACT: Long considered intractable organisms by fungal genetic research standards, the oomycetes have recently moved to the centre stage of research on plant-microbe interactions. Recent work on oomycete effector evolution, trafficking and function has led to major conceptual advances in the science of plant pathology. In this review, we provide a historical perspective on oomycete genetic research and summarize the state of the art in effector biology of plant pathogenic oomycetes by describing what we consider to be the 10 most important concepts about oomycete effectors.
Molecular Plant Pathology 11/2009; 10(6):795-803. · 3.90 Impact Factor
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Brian J Haas,
Sophien Kamoun,
Michael C Zody,
Rays H Y Jiang,
Robert E Handsaker,
Liliana M Cano,
Manfred Grabherr,
Chinnappa D Kodira,
Sylvain Raffaele,
Trudy Torto-Alalibo, [......],
Shiguo Zhou,
William Fry,
Blake C Meyers,
Pieter van West,
Jean Ristaino,
Francine Govers,
Paul R J Birch,
Stephen C Whisson,
Howard S Judelson,
Chad Nusbaum
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ABSTRACT: Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars. Here we report the sequence of the P. infestans genome, which at approximately 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for approximately 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
Nature 10/2009; 461(7262):393-8. · 36.28 Impact Factor
