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Results for “Genomic sequencing”

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At least 955 records · Page 53Linked to original sources
PubMed2004

Survey of the number of two-component response regulator genes in the complete and annotated genome sequences of prokaryotes.

The numbers of potential response regulator genes were determined from the complete and annotated genome sequences of Archaea and Bacteria. The numbers of each class of response regulators are shown for each organism, determined principally from BLASTP searches, but with reference to the gene category lists where available. The survey shows that for Bacteria there is a link between the total number of potential response regulator genes and both the genome complexity (number of potential protein-coding genes) and the organism's lifestyle/habitat. Increasingly complex lifestyles and genome complexities are matched by an increase in the average number of potential response regulator genes per genome, indicating that a higher degree of complexity requires a higher level of control of gene expression and cellular activity. Detailed results of this study are available online at and.

Data Collection↗
PubMedDate not supplied

Repeated sequences in bacterial chromosomes and plasmids: a glimpse from sequenced genomes.

To gain insight into the extent of exact DNA repeats in sequenced bacterial genomes and their plasmids, we analyzed the collection of completely sequenced bacterial genomes available at GenBank using the program Miropeats. This program draws graphical representations of exact DNA repeats in whole genomes. In this work, we present maps showing the extent and type (inverted or direct) of exact DNA repeats longer than 300 bp for the whole collection. These repeats may participate in a variety of events relevant for bacterial genome plasticity, such as amplifications, deletions, inversions, and translocations (via homologous recombination), as well as transposition. Additionally, we review recent data showing that high-frequency architectural variations in genomic structure occur at both the interspecies and interstrain levels.

Bacteria↗
PubMed2026

The complete genomic sequence of a novel member of the genus Caulimovirus isolated from Dregea volubilis.

A novel caulimovirus was identified from diseased leaves of Dregea volubilis exhibiting yellowing and vein-associated chlorosis in Yuanjiang County, Yunnan Province, China. The virus was tentatively named Dregea volubilis caulimovirus 1 (DVCaV1). The complete genome sequence of DVCaV1, determined by de novo assembly of high-throughput sequencing data, comprises 8,160 bp of circular double-stranded DNA containing two intergenic regions and seven open reading frames (ORFs). These ORFs encode (in order) a movement protein (MP), an aphid transmission factor (ATF), a virion-associated protein (VAP), a coat protein (CP), a polymerase polyprotein (Pol, containing protease, reverse transcriptase, and RNase H domains), a transactivator/viroplasmin (TAV) protein, and a hypothetical protein of unknown function. Sequence comparisons revealed the highest nucleotide similarity with strawberry vein banding virus (SVBV; NC_001725). Phylogenetic analysis confirmed DVCaV1 as a member of the genus Caulimovirus, with SVBV as its closest known relative. According to current ICTV species demarcation criteria for the genus Caulimovirus (host range and > 20% nucleotide sequence divergence in the polymerase region), DVCaV1 represents a novel species. This is, to our knowledge, the first report of a caulimovirus detected in naturally symptomatic Dregea volubilis.

Genome, Viral↗
PubMed2000

The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis.

Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically important plant diseases. Here we report the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis--a serious disease of orange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and two plasmids of 51,158 bp and 1,285 bp. We can assign putative functions to 47% of the 2,904 predicted coding regions. Efficient metabolic functions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylem sap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated by a range of proteins. Orthologues of some of these proteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis for bacterial pathogenicity is both conserved and independent of host. At least 83 genes are bacteriophage-derived and include virulence-associated genes from other bacteria, providing direct evidence of phage-mediated horizontal gene transfer.

Bacterial Adhesion↗
PubMed2004

High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence.

The laboratory rat is a major model organism for systems biology. To complement the cornucopia of physiological and pharmacological data generated in the rat, a large genomic toolset has been developed, culminating in the release of the rat draft genome sequence. The rat draft sequence used a variety of assembly packages, as well as data from the Radiation Hybrid (RH) map of the rat as part of their validation. As part of the Rat Genome Project, we have been building a high-density RH map to facilitate data integration from multiple maps and now to help validate the genome assembly. By incorporating vectors from our lab and several other labs, we have doubled the number of simple sequence length polymorphisms (SSLPs), genes, expressed sequence tags (ESTs), and sequence-tagged sites (STSs) compared to any other genome-wide rat map, a total of 24,437 elements. During the process, we also identified a novel approach for integrating the RH placement results from multiple maps. This new integrated RH map contains approximately 10 RH-mapped elements per Mb on the genome assembly, enabling the RH maps to serve as a scaffold for a variety of data visualization tools.

Animals↗
PubMed2026

Draft genome sequences of four bacterial isolates from the Indian Fort Nature Preserve in Geneseo, NY.

We report the genome sequences of four bacterial strains, Bacillus subtilis, Bacillus pumilus, Pseudomonas kermanshahensis, and Kocuria rhizophila, isolated from soil or plant material from Geneseo, NY. Bacterial strains were selected based on preliminary, qualitative screening for antimicrobial production via zones of clearing and/or inhibition against lab strains.

antimicrobial production↗
PubMed2001

A comparison of complete genome sequences of the attenuated RC-HL strain of rabies virus used for production of animal vaccine in Japan, and the parental Nishigahara strain.

In order to establish the molecular basis of the pathogenicity of the attenuated RC-HL strain of rabies virus used for the production of animal vaccine in Japan, the complete genome sequence of this strain was determined and compared with that of the parental Nishigahara strain which is virulent for adult mice. The viral genome of both strains was composed of 11,926 nucleotides. The nucleotide sequences of the two genomes showed a high homology of 98.9%. The homology of the G gene was lower than those of N, P, M and L genes at both nucleotide and deduced amino acid levels, and the percentage of radical amino acid substitutions on the G protein was the highest among the five proteins. These findings raise the possibility that the structure of the G protein is the most variable among the five proteins of the two strains. Furthermore, we found two clusters of amino acid substitutions on the G and L proteins. The relevance of these clusters to the difference in the pathogenicity between the two strains is discussed.

Amino Acid Sequence↗
PubMed2000

The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum.

Thermoplasma acidophilum is a thermoacidophilic archaeon that thrives at 59 degrees C and pH 2, which was isolated from self-heating coal refuse piles and solfatara fields. Species of the genus Thermoplasma do not possess a rigid cell wall, but are only delimited by a plasma membrane. Many macromolecular assemblies from Thermoplasma, primarily proteases and chaperones, have been pivotal in elucidating the structure and function of their more complex eukaryotic homologues. Our interest in protein folding and degradation led us to seek a more complete representation of the proteins involved in these pathways by determining the genome sequence of the organism. Here we have sequenced the 1,564,905-base-pair genome in just 7,855 sequencing reactions by using a new strategy. The 1,509 open reading frames identify Thermoplasma as a typical euryarchaeon with a substantial complement of bacteria-related genes; however, evidence indicates that there has been much lateral gene transfer between Thermoplasma and Sulfolobus solfataricus, a phylogenetically distant crenarchaeon inhabiting the same environment. At least 252 open reading frames, including a complete protein degradation pathway and various transport proteins, resemble Sulfolobus proteins most closely.

Archaeal Proteins↗
PubMed2026

Methods for cost-efficient, whole genome sequencing surveillance for enhanced detection of outbreaks in a hospital setting.

INTRODUCTION: Outbreaks of healthcare-associated infections (HAI) result in substantial patient morbidity and mortality; mitigation efforts by infection prevention teams have the potential to curb outbreaks and prevent transmission to additional patients. The incorporation of whole genome sequencing (WGS) surveillance of suspected high-risk pathogens often identifies outbreaks that are not detected by traditional infection prevention methods and provides evidence for transmission. Our approach to real-time WGS surveillance, the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT), has 1) identified serious outbreaks that were otherwise undetected and 2) shown the potential to be cost saving. METHODS: We describe our cost-efficient methods to perform WGS surveillance and data analysis of pathogens for institutions that are interested in expanding infection prevention surveillance. We provide an overview of the weekly workflow of EDS-HAT during two distinct phases over three years. RESULTS: In an average week at our tertiary healthcare system, we sequenced 60 samples at a cost of less than $100 each during Phase 1, and 80 samples for less than $70 each in Phase 2, inclusive of laboratory reagents and staff salaries. The average turnaround time, from sample collection to reporting data to infection prevention, was nine days. CONCLUSIONS: Performing EDS-HAT in real-time can be both feasible and time-efficient. Providing such timely information to aid in outbreak detection could identify transmission events sooner and thus could increase patient safety.

Disease Outbreaks↗
PubMed1998

Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.

Countless millions of people have died from tuberculosis, a chronic infectious disease caused by the tubercle bacillus. The complete genome sequence of the best-characterized strain of Mycobacterium tuberculosis, H37Rv, has been determined and analysed in order to improve our understanding of the biology of this slow-growing pathogen and to help the conception of new prophylactic and therapeutic interventions. The genome comprises 4,411,529 base pairs, contains around 4,000 genes, and has a very high guanine + cytosine content that is reflected in the biased amino-acid content of the proteins. M. tuberculosis differs radically from other bacteria in that a very large portion of its coding capacity is devoted to the production of enzymes involved in lipogenesis and lipolysis, and to two new families of glycine-rich proteins with a repetitive structure that may represent a source of antigenic variation.

Chromosome Mapping↗
PubMed2003

Maize genome sequencing by methylation filtration.

Gene enrichment strategies offer an alternative to sequencing large and repetitive genomes such as that of maize. We report the generation and analysis of nearly 100,000 undermethylated (or methylation filtration) maize sequences. Comparison with the rice genome reveals that methylation filtration results in a more comprehensive representation of maize genes than those that result from expressed sequence tags or transposon insertion sites sequences. About 7% of the repetitive DNA is unmethylated and thus selected in our libraries, but potentially active transposons and unmethylated organelle genomes can be identified. Reverse transcription polymerase chain reaction can be used to finish the maize transcriptome.

Algorithms↗
PubMed2004

Complete genome sequence of the apicomplexan, Cryptosporidium parvum.

The apicomplexan Cryptosporidium parvum is an intestinal parasite that affects healthy humans and animals, and causes an unrelenting infection in immunocompromised individuals such as AIDS patients. We report the complete genome sequence of C. parvum, type II isolate. Genome analysis identifies extremely streamlined metabolic pathways and a reliance on the host for nutrients. In contrast to Plasmodium and Toxoplasma, the parasite lacks an apicoplast and its genome, and possesses a degenerate mitochondrion that has lost its genome. Several novel classes of cell-surface and secreted proteins with a potential role in host interactions and pathogenesis were also detected. Elucidation of the core metabolism, including enzymes with high similarities to bacterial and plant counterparts, opens new avenues for drug development.

Animals↗
PubMed2002

Identification of G protein-coupled receptor genes from the human genome sequence.

We have identified novel G protein-coupled receptors (GPCRs) with no introns in the coding region from the human genome sequence: 322 olfactory receptors; 22 taste receptors; 128 registered GPCRs for endogenous ligands; 50 novel GPCR candidates homologous to registered GPCRs for endogenous ligands; and 59 novel GPCR candidates not homologous to registered GPCRs. The total number of GPCRs with and without introns in the human genome was estimated to be approximately 950, of which 500 are odorant or taste receptors and 450 are receptors for endogenous ligands.

Adult↗
PubMed2003

A genome sequence of novel SARS-CoV isolates: the genotype, GD-Ins29, leads to a hypothesis of viral transmission in South China.

We report a complete genomic sequence of rare isolates (minor genotype) of the SARS-CoV from SARS patients in Guangdong, China, where the first few cases emerged. The most striking discovery from the isolate is an extra 29-nucleotide sequence located at the nucleotide positions between 27,863 and 27,864 (referred to the complete sequence of BJ01) within an overlapped region composed of BGI-PUP5 (BGI-postulated uncharacterized protein 5) and BGI-PUP6 upstream of the N (nucleocapsid) protein. The discovery of this minor genotype, GD-Ins29, suggests a significant genetic event and differentiates it from the previously reported genotype, the dominant form among all sequenced SARS-CoV isolates. A 17-nt segment of this extra sequence is identical to a segment of the same size in two human mRNA sequences that may interfere with viral replication and transcription in the cytosol of the infected cells. It provides a new avenue for the exploration of the virus-host interaction in viral evolution, host pathogenesis, and vaccine development.

Base Sequence↗
PubMed2026

Whole genome sequencing reveals a specific microbiota in subglottic stenosis C. acnes may contribute to inflammation.

PURPOSE: Subglottic stenosis (SGS) progressively reduces the airway below the vocal folds. The cause is not known and there is a recurrent need of surgical treatment. Including all phenotypes, SGS affects 1/400 000/yr, with a female dominance. Previous studies have revealed a possible role of the Mycobacterium complex in SGS development. Our hypothesis is that microbiota is associated with the inflammation in SGS, if true it might affect the prevailing treatment options. METHODS: This prospective cross-sectional study included biopsies from 34 patients with subglottic stenosis, collected between 2020 and 2023. Nucleic acids were extracted from the tissue samples and analysed using whole genome sequencing. Microbial composition was characterized using taxonomic profiling of sequencing data. Species with sufficient read counts were selected for further validation using sequence alignment methods to ensure accuracy of identification. RESULTS: Using the most comprehensive form of genomic testing currently in clinical use, we present curated and stable data on the presence of Cutibacterium acnes in 28 out of the 34 cases. CONCLUSION: Cutibacterium acnes may serve as a driver of the inflammation characterizing SGS and should be considered in therapeutically oriented future studies.

Cutibacterium acnes↗
PubMed2004

e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences.

e2g is a web-based server which efficiently maps large expressed sequence tag (EST) and cDNA datasets to genomic DNA. It significantly extends the volume of data that can be mapped in reasonable time, and makes this improved efficiency available as a web service. Our server hosts large collections of EST sequences (e.g. 4.1 million mouse ESTs of 1.87 Gb) in precomputed indexed data structures for efficient sequence comparison. The user can upload a genomic DNA sequence of interest and rapidly compare this to the complete collection of ESTs on the server. This delivers a mapping of the ESTs on the genomic DNA. The e2g web interface provides a graphical overview of the mapping. Alignments of the mapped EST regions with parts of the genomic sequence are visualized. Zooming functions allow the user to interactively explore the results. Mapped sequences can be downloaded for further analysis. e2g is available on the Bielefeld University Bioinformatics Server at http://bibiserv.techfak.uni-bielefeld.de/e2g/.

Base Sequence↗