The NCBI Taxonomy database

Federhen, Scott

doi:10.1093/nar/gkr1178

Cited by 1,273 publications

(1,082 citation statements)

References 11 publications

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“…All GFF3 files are curated prior to loading into Chado to ensure accuracy and kept in a file repository for future reference. To record distributions of genes among pathogens, the CARD additionally uses a pruned form of NCBI's taxonomy system (16) in the form of a custom NCBI Taxonomy ontology as described below. The CARD's GFF3 loader script tags all new sequences with terms from the CARD's NCBI Taxonomy ontology to provide organismal context and similarly loads any associated PubMed publications into the CARD Publication module.…”

Section: Methodsmentioning

confidence: 99%

The Comprehensive Antibiotic Resistance Database

McArthur¹,

Waglechner

Nizam

et al. 2013

Antimicrob Agents Chemother

1,699

1,325

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The field of antibiotic drug discovery and the monitoring of new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. Despite the fact that the first genomes sequenced of free living organisms were those of bacteria, there have been few specialized bioinformatic tools developed to mine the growing amount of genomic data associated with pathogens. In particular, there are few tools to study the genetics and genomics of antibiotic resistance and how it impacts bacterial populations, ecology, and the clinic. We have initiated development of such tools in the form of the Comprehensive Antibiotic Research Database (CARD; http://arpcard.mcmaster.ca). The CARD integrates disparate molecular and sequence data, provides a unique organizing principle in the form of the Antibiotic Resistance Ontology (ARO), and can quickly identify putative antibiotic resistance genes in new unannotated genome sequences. This unique platform provides an informatic tool that bridges antibiotic resistance concerns in health care, agriculture, and the environment.A ntibiotic resistance is an increasing crisis as both the range of microbial antibiotic resistance in clinical settings expands and the pipeline for development of new antibiotics contracts (1). This problem is compounded by the global genomic scope of the antibiotic resistome, such that antibiotic resistance spans a continuum from genes in pathogens found in the clinic to those of benign environmental microbes along with their proto-resistance gene progenitors (2, 3). The recent emergence of New Delhi metallo-ß-lactamase (NDM-1) in Gram-negative organisms (4), which can hydrolyze all ␤-lactams with the exception of monobactams, illustrates the capacity of new antibiotic resistance genes to emerge rapidly from as-yet-undetermined reservoirs. Surveys of genes originating from both clinical and environmental sources (microbes and metagenomes) will provide increasing insight into these reservoirs and offer predictive capacity for the emergence and epidemiology of antibiotic resistance.The increasing opportunity to prepare a broader and comprehensive antibiotic resistance gene census is facilitated by the power and falling costs of next-generation DNA sequencing. For example, whole-genome sequencing (WGS) is being increasingly used to examine new antibiotic-resistant isolates discovered in clinical settings (5). Additionally, culture-independent metagenomic surveys are adding tremendously to the pool of known genes and their distribution outside clinical settings (6, 7). These approaches have the advantage of providing a rapid survey of the antibiotic resistome of new strains, the discovery of newly emergent antibiotic resistance genes, the epidemiology of antibiotic resistance genes, and the horizontal gene transfer (HGT) of known antibiotic resistance genes through plasmids and transposable elements. However, despite the existence of tools for general annotation of prokaryotic genomes (see, e.g., reference 8), prediction of an antibiotic resista...

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Section: Methodsmentioning

confidence: 99%

The Comprehensive Antibiotic Resistance Database

McArthur¹,

Waglechner

Nizam

et al. 2013

Antimicrob Agents Chemother

1,699

1,325

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“…Species with a sequencing project are shown in bold. The tree was generated with data from NCBI Taxonomy (Federhen 2012). disease resistance, and adaptations to climate change.…”

Section: Future Of Solanaceae Researchmentioning

confidence: 99%

Advances in tomato research in the post-genome era

Menda

Strickler

Mueller

2013

Plant Biotechnology

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The tomato (Solanum lycopersicum) draft genome, along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012, almost a decade after the International Tomato Genome project was initiated. Tomato is an important domesticated crop species, as well as a model organism for many aspects of plant biology such as fleshy fruit development, ripening, disease resistance, plant architecture, and compound leaf development. For these reasons, there has been a substantial effort for producing a high quality reference genome that will serve as an anchor for tomato species, and for closely related Solanaceae plants. The utility of this genome has already been demonstrated by a relatively large number of studies that have been published since the release of the sequence, covering a wide range of topics including gene expression, genetic diversity, phylogeny, comparative genomics, and epigenetics. With the availability of the potato genome, it is now possible to perform detailed comparative genomic analysis of gene families in the Solanaceae, facilitated by conservation and synteny between their genomes. A large number of ongoing efforts will result in the sequencing of hundreds of wild and domesticated tomato accessions from various populations, uncovering the breeding history of tomatoes and introducing new genomic technologies to accelerate breeding processes. In this review, we provide an overview of the origins of tomato and its position in the wider Solanaceae, and demonstrate the impact of the tomato genome sequence on Solanaceae research on the basis of recent literature that has made use of this new resource.

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“…The phyletic distribution figure was produced using the Aquerium tool (30), which uses NCBI taxonomic ranks (75) to build the tree. Eukaryotes and Archaea were excluded from the tree, because no HKIIIs were identified in these domains of life.…”

Section: Methodsmentioning

confidence: 99%

Class III Histidine Kinases: a Recently Accessorized Kinase Domain in Putative Modulators of Type IV Pilus-Based Motility

et al. 2017

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Histidine kinases are key components of regulatory systems that enable bacteria to respond to environmental changes. Two major classes of histidine kinases are recognized on the basis of their modular design: classical (HKI) and chemotaxis specific (HKII). Recently, a new type of histidine kinase that appeared to have features of both HKIs and HKIIs was identified and termed HKIII; however, the details of HKIII's relationship to other two classes of histidine kinases, their function, and evolutionary history remain unknown. Here, we carried out genomic, phylogenetic, and protein sequence analyses that allowed us to reveal the unusual evolutionary history of this protein family, formalize its distinctive features, and propose its putative function. HKIIIs are characterized by the presence of sensory domains and the lack of a dimerization domain, which is typically present in all histidine kinases. In addition to a single-domain response regulator, HKIII signal transduction systems utilize CheX phosphatase and, in many instances, an unorthodox soluble chemoreceptor that are usual components of chemotaxis signal transduction systems. However, many HKIII genes are found in genomes completely lacking chemotaxis genes, thus decoupling their function from chemotaxis. By contrast, all HKIIIcontaining genomes also contain pilT, a marker gene for bacterial type IV pilus-based motility, whose regulation is proposed as a putative function for HKIII. These signal transduction systems have a narrow phyletic distribution but are present in many emerging and opportunistic pathogens, thus offering an attractive potential target for future antimicrobial drug design.IMPORTANCE Bacteria adapt to their environment and their hosts by detecting signals and regulating their cellular functions accordingly. Here, we describe a largely unexplored family of signal transduction histidine kinases, called HKIII, that have a unique modular design. While they are currently identified in a relatively short list of bacterial species, this list contains many emerging pathogens. We show that HKIIIs likely control bacterial motility across solid surfaces, which is a key virulence factor in many bacteria, including those causing severe infections. Full understanding of this putative function may help in designing effective drugs against pathogens that will not affect the majority of the beneficial human microbiome.KEYWORDS chemotaxis, evolution, genomics, histidine kinase, motility, pathogens, signal transduction, type IV pili T he transmission of molecular signals in prokaryotes is carried out by the specialized cellular machinery. The simplest signal transduction systems consist of a single protein that is capable of both sensing a signal and directly affecting a cellular

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The NCBI Taxonomy database

Cited by 1,273 publications

References 11 publications

The Comprehensive Antibiotic Resistance Database

The Comprehensive Antibiotic Resistance Database

Advances in tomato research in the post-genome era

Class III Histidine Kinases: a Recently Accessorized Kinase Domain in Putative Modulators of Type IV Pilus-Based Motility

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