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Ross Overbeek,
Niels Larsen,
Theresa Walunas,
Mark D'Souza,
Gordon Pusch, Eugene Selkov,
Konstantinos Liolios,
Viktor Joukov,
Denis Kaznadzey,
Iain Anderson, [......],
Warren Gardner,
Paul Hanke,
Vinayak Kapatral,
Natalia Mikhailova,
Olga Vasieva,
Andrei Osterman,
Veronika Vonstein,
Michael Fonstein,
Natalia Ivanova,
Nikos Kyrpides
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ABSTRACT: The ERGO (http://ergo.integratedgenomics.com/ERGO/) genome analysis and discovery suite is an integration of biological data from genomics, biochemistry, high-throughput expression profiling, genetics and peer-reviewed journals to achieve a comprehensive analysis of genes and genomes. Far beyond any conventional systems that facilitate functional assignments, ERGO combines pattern-based analysis with comparative genomics by visualizing genes within the context of regulation, expression profiling, phylogenetic clusters, fusion events, networked cellular pathways and chromosomal neighborhoods of other functionally related genes. The result of this multifaceted approach is to provide an extensively curated database of the largest available integration of genomes, with a vast collection of reconstructed cellular pathways spanning all domains of life. Although access to ERGO is provided only under subscription, it is already widely used by the academic community. The current version of the system integrates 500 genomes from all domains of life in various levels of completion, 403 of which are available for subscription.
Nucleic Acids Research 02/2003; 31(1):164-71. · 8.03 Impact Factor
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Anamitra Bhattacharyya,
Stephanie Stilwagen,
Gary Reznik,
Helene Feil,
William S Feil,
Iain Anderson,
Axel Bernal,
Mark D'Souza,
Natalia Ivanova,
Vinayak Kapatral, [......],
Athanasios Lykidis, Eugene Selkov,
Theresa L Walunas,
Alexander Purcell,
Rob A Edwards,
Trevor Hawkins,
Robert Haselkorn,
Ross Overbeek,
Nikos C Kyrpides,
Paul F Predki
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ABSTRACT: Draft sequencing is a rapid and efficient method for determining the near-complete sequence of microbial genomes. Here we report a comparative analysis of one complete and two draft genome sequences of the phytopathogenic bacterium, Xylella fastidiosa, which causes serious disease in plants, including citrus, almond, and oleander. We present highlights of an in silico analysis based on a comparison of reconstructions of core biological subsystems. Cellular pathway reconstructions have been used to identify a small number of genes, which are likely to reside within the draft genomes but are not captured in the draft assembly. These represented only a small fraction of all genes and were predominantly large and small ribosomal subunit protein components. By using this approach, some of the inherent limitations of draft sequence can be significantly reduced. Despite the incomplete nature of the draft genomes, it is possible to identify several phage-related genes, which appear to be absent from the draft genomes and not the result of insufficient sequence sampling. This region may therefore identify potential host-specific functions. Based on this first functional reconstruction of a phytopathogenic microbe, we spotlight an unusual respiration machinery as a potential target for biological control. We also predicted and developed a new defined growth medium for Xylella.
Genome Research 11/2002; 12(10):1556-63. · 13.61 Impact Factor
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Anamitra Bhattacharyya,
Stephanie Stilwagen,
Natalia Ivanova,
Mark D'Souza,
Axel Bernal,
Athanasios Lykidis,
Vinayak Kapatral,
Iain Anderson,
Niels Larsen,
Tamara Los, [......],
Theresa L Walunas,
Helene Feil,
William S Feil,
Alexander Purcell,
Jean-Louis Lassez,
Trevor L Hawkins,
Robert Haselkorn,
Ross Overbeek,
Paul F Predki,
Nikos C Kyrpides
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ABSTRACT: Xylella fastidiosa (Xf) causes wilt disease in plants and is responsible for major economic and crop losses globally. Owing to the public importance of this phytopathogen we embarked on a comparative analysis of the complete genome of Xf pv citrus and the partial genomes of two recently sequenced strains of this species: Xf pv almond and Xf pv oleander, which cause leaf scorch in almond and oleander plants, respectively. We report a reanalysis of the previously sequenced Xf 9a5c (CVC, citrus) strain and the two "gapped" Xf genomes revealing ORFs encoding critical functions in pathogenicity and conjugative transfer. Second, a detailed whole-genome functional comparison was based on the three sequenced Xf strains, identifying the unique genes present in each strain, in addition to those shared between strains. Third, an "in silico" cellular reconstruction of these organisms was made, based on a comparison of their core functional subsystems that led to a characterization of their conjugative transfer machinery, identification of potential differences in their adhesion mechanisms, and highlighting of the absence of a classical quorum-sensing mechanism. This study demonstrates the effectiveness of comparative analysis strategies in the interpretation of genomes that are closely related.
Proceedings of the National Academy of Sciences 10/2002; 99(19):12403-8. · 9.68 Impact Factor
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Vito G DelVecchio,
Vinayak Kapatral,
Rajendra J Redkar,
Guy Patra,
Cesar Mujer,
Tamara Los,
Natalia Ivanova,
Iain Anderson,
Anamitra Bhattacharyya,
Athanasios Lykidis, [......],
Mikhail Mazur,
Eugene Goltsman, Eugene Selkov,
Philip H Elzer,
Sue Hagius,
David O'Callaghan,
Jean-Jacques Letesson,
Robert Haselkorn,
Nikos Kyrpides,
Ross Overbeek
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ABSTRACT: Brucella melitensis is a facultative intracellular bacterial pathogen that causes abortion in goats and sheep and Malta fever in humans. The genome of B. melitensis strain 16M was sequenced and found to contain 3,294,935 bp distributed over two circular chromosomes of 2,117,144 bp and 1,177,787 bp encoding 3,197 ORFs. By using the bioinformatics suite ERGO, 2,487 (78%) ORFs were assigned functions. The origins of replication of the two chromosomes are similar to those of other alpha-proteobacteria. Housekeeping genes, including those involved in DNA replication, transcription, translation, core metabolism, and cell wall biosynthesis, are distributed on both chromosomes. Type I, II, and III secretion systems are absent, but genes encoding sec-dependent, sec-independent, and flagella-specific type III, type IV, and type V secretion systems as well as adhesins, invasins, and hemolysins were identified. Several features of the B. melitensis genome are similar to those of the symbiotic Sinorhizobium meliloti.
Proceedings of the National Academy of Sciences 02/2002; 99(1):443-8. · 9.68 Impact Factor
