BASys: a web server for automated bacterial genome annotation

Domselaar, Gary H. Van; Stothard, Paul; Shrivastava, Savita; Cruz, Joseph A.; Guo, Anchi; Dong, Xiaoli; Lu, Paul; Szafron, Duane; Greiner, Russell; Wishart, David S.

doi:10.1093/nar/gki593

Cited by 293 publications

(246 citation statements)

References 26 publications

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“…Annotation of the bacterial genes was performed using the free automated web server BASys (Bacterial Annotation System, www.basys.ca) (Van Domselaar et al 2005). The annotation was run on aligned sequences, removing multiply hit loci.…”

Section: Gene Annotation and Biological Interpretation Of The Resultsmentioning

confidence: 99%

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

et al. 2015

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Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g., transcription elongation factor NusA and tumor necrosis factor alpha-inducing protein Tipa) and hitherto unknown functional genes.KEYWORDS adaptation; neutral evolution; human pathogens H ELICOBACTER pylori is a Gram-negative bacterium that infects the mucosa of the human stomach. It was first described in the 1980s, when it was initially identified in association with chronic gastritis and later causally linked to serious gastric pathologies such as gastric cancer and ulcers (Marshall and Warren 1984;Suerbaum and Michetti 2002). It infects .80% of humans in developing countries and, although its prevalence is lower in developed countries, nearly 50% of the worldwide human population is infected (Ghose et al. 2005;Salih 2009;Salama et al. 2013).Due to its clinical and evolutionary importance, there has been considerable research on mechanisms of H. pylori transmission, as well as on the population genetics and phylogenetic relationships among global isolates. Thus far, population genetic analyses have mainly focused on seven housekeeping genes (usually referred to as multilocus sequence typing or MLST), with the primary conclusions being that H. pylori strains appear highly structured, and their phylogeographic patterns correlate consistently with that of their human hosts. Given that the H. pylori-humans association is at least 100,000 years old (Moodley et al. 2012), the current population structure of H. pylori may be regarded as mirroring past human expansions and migrations Linz et al. 2007;Breurec et al. 2011) and thus help us shed light on yet unknown dynamics of local demographic processes in human evolution. However, despite the knowledge gained thus far, the long-term global demographic history of H. pylori has never been directly inferred. The long, intimate association of H. pylori with humans suggests a history of bacterial adaptation. Considerable attention has focused on specific genes involved in modulating adaptive immunity of the host (for a review see Yamaoka 2010 andSalama et al. 2013) and on genomic changes occurring during acute and chronic H. pylori infection (Kennemann et al. 2011;Linz et a...

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Section: Gene Annotation and Biological Interpretation Of The Resultsmentioning

confidence: 99%

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

et al. 2015

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“…Automated annotation of the bacterial sequences was done using the BASys web server (29). Anti-SMASH was used to analyze the potential secondary metabolite biosynthesis gene clusters present in the genomes (30).…”

Section: Methodsmentioning

confidence: 99%

Bacterial Biosynthetic Gene Clusters Encoding the Anti-cancer Haterumalide Class of Molecules

Matilla

Stöckmann

Leeper

et al. 2012

Journal of Biological Chemistry

121

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Background: Oocydin A is an anticancer haterumalide with strong antimicrobial activity against agriculturally important plant pathogenic fungi and oomycetes. Results: The oocydin A gene cluster has been identified and characterized in four plant-associated enterobacteria. Conclusion:The ooc gene cluster is organized in three transcriptional units encoding enzymes that belong to a growing class of trans-acyltransferase polyketide synthases. Significance: Oocydin A has potential agricultural, pharmacological, and chemotherapeutic applications.

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“…A first round of open reading frame prediction was performed using Prodigal v.2.5 (Hyatt et al, 2010) and the predicted open reading frames were annotated using the BASys server (Van Domselaar et al, 2005). tRNAs were predicted using the 'COVE-only' algorithm of tRNAscan-SE v.1.3.1 (Lowe and Eddy, 1997), and checked with TFAM v.1.4 (Tåquist et al, 2007).…”

Section: Westeberhardia Detection and Phylogenomic Analysesmentioning

confidence: 99%

A novel intracellular mutualistic bacterium in the invasive antCardiocondyla obscurior

et al. 2015

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The evolution of eukaryotic organisms is often strongly influenced by microbial symbionts that confer novel traits to their hosts. Here we describe the intracellular Enterobacteriaceae symbiont of the invasive ant Cardiocondyla obscurior, 'Candidatus Westeberhardia cardiocondylae'. Upon metamorphosis, Westeberhardia is found in gut-associated bacteriomes that deteriorate following eclosion. Only queens maintain Westeberhardia in the ovarian nurse cells from where the symbionts are transmitted to late-stage oocytes during nurse cell depletion. Functional analyses of the streamlined genome of Westeberhardia (533 kb, 23.41% GC content) indicate that neither vitamins nor essential amino acids are provided for the host. However, the genome encodes for an almost complete shikimate pathway leading to 4-hydroxyphenylpyruvate, which could be converted into tyrosine by the host. Taken together with increasing titers of Westeberhardia during pupal stage, this suggests a contribution of Westeberhardia to cuticle formation. Despite a widespread occurrence of Westeberhardia across host populations, one ant lineage was found to be naturally symbiont-free, pointing to the loss of an otherwise prevalent endosymbiont. This study yields insights into a novel intracellular mutualist that could play a role in the invasive success of C. obscurior.

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BASys: a web server for automated bacterial genome annotation

Cited by 293 publications

References 26 publications

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

Bacterial Biosynthetic Gene Clusters Encoding the Anti-cancer Haterumalide Class of Molecules

A novel intracellular mutualistic bacterium in the invasive antCardiocondyla obscurior

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