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At least 703 records · Page 39Linked to original sources
PubMed2005

Genome sequence, comparative analysis and haplotype structure of the domestic dog.

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

Animals↗
PubMed2005

Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences.

Molecular phylogenetic analyses were conducted using the whole mitochondrial genome sequences of all 18 species/subspecies of the freshwater eels genus Anguilla to infer their phylogenetic relationships and to evaluate hypotheses about the possible dispersal routes of this genus. The Bayesian and maximum likelihood analyses using a total of 15,187 sites of mitochondrial DNA sequences suggested that A. mossambica was the most basal species of anguillid eel, and that the other species (except for A. borneensis) formed three geographic clades: Atlantic (two species), Oceania (three species), and Indo-Pacific (11 species). The present study clearly indicated a sister relationship between the Atlantic and Oceanian species, which now have distantly separated geographic distributions. This suggests that the previous hypotheses to estimate the dispersal route of anguillid eels into the Atlantic Ocean based on the current geographic distribution of species are unsupported by the present more complete analysis. Alternatively, the unique geographic distribution of the present day species in the genus Anguilla appears to have resulted from multiple dispersal events. Although the age of the beginning of speciation among anguillid eels was tentatively estimated as 20 million years ago using a calibration for bony fishes of 7.3x10(-4) substitutions/site/million years, it is possible that this divergence time was underestimated because of the ecological characteristics of these fishes. The results of the present study suggest that the hypotheses for the dispersal route and divergence time of the genus Anguilla should be reconsidered.

Anguilla↗
PubMed2026

Microbiological analysis and whole-genome sequencing of Neisseria gonorrhoeae from the microbiological failures in the international, zoliflodacin, phase 3, clinical trial for treatment of uncomplicated urogenital gonorrhoea: a retrospective, genomic, observational study.

BACKGROUND: Zoliflodacin, a first-in-class oral bacterial, DNA gyrase (GyrB) inhibitor, showed non-inferiority to ceftriaxone combined with azithromycin in a recent large international, phase 3, randomised controlled trial for treatment of uncomplicated urogenital gonorrhoea. The aim of this study was to describe the microbiological and whole-genome sequencing (WGS) analyses of paired baseline (pre-treatment) and test-of-cure (TOC) gonococcal isolates from the zoliflodacin phase 3, randomised controlled trial to further characterise and evaluate the protocol-specified microbiological failures with zoliflodacin (n=22) or ceftriaxone and azithromycin (n=1). METHODS: In this retrospective, genomic, observational study, results from antimicrobial susceptibility testing (agar dilution method) of isolates (n=960; 936 baseline isolates from 763 participants and 24 TOC isolates [23 with a paired baseline isolate in the same anatomical site] from 20 participants) collected during the zoliflodacin phase 3, randomised controlled trial done in 16 outpatient clinics in Belgium, the Netherlands, South Africa, Thailand, and the USA (Nov 6, 2019-March 16, 2023) are described. WGS analysis was performed on paired baseline and TOC isolates from participants with microbiological failures (zoliflodacin 44 isolates [19 participants]; ceftriaxone and azithromycin two isolates [one participant]), and the three baseline isolates with highest zoliflodacin minimum inhibitory concentration (MIC 0·5 mg/L). FINDINGS: All isolates were inhibited by the same zoliflodacin concentrations (MICs ≤0·008 to 0·5 mg/L) as wild-type strains cultured internationally in 2013-23. In participants with a microbiological failure after zoliflodacin treatment (n=22, 19 participants), zoliflodacin MIC values for baseline and TOC isolates were similar, and resistance selection was lacking. WGS showed that five (23%) of 22 infections (95% CI 10-43 [in four participants]) of zoliflodacin microbiological failures had different strains at TOC versus baseline. In 17 zoliflodacin microbiological failures (15 participants), isolates at baseline and TOC were indistinguishable. 13 of these 17 microbiological failures, corresponding to 59% (95% CI 39-77; 13 of 22) of all zoliflodacin microbiological failures, were in urogenital or rectal sites in 11 participants and the isolates had zoliflodacin MICs less than or equal to 0·008 to 0·25 mg/L. The single microbiological failure after ceftriaxone and azithromycin treatment had different strains at TOC versus at baseline. No sequenced isolates had mutations associated with elevated zoliflodacin MICs. INTERPRETATION: In the zoliflodacin phase 3, randomised controlled trial, 23% of the zoliflodacin microbiological failures and the single ceftriaxone and azithromycin microbiological failure had different gonococcal strains at TOC versus baseline, which suggests reinfections and not treatment failures. In addition, 59% of the zoliflodacin microbiological failures, all in anogenital sites, had no obvious microbiological explanation based on the low zoliflodacin MICs, previous pharmacodynamic studies, and no evidence of resistance selection after zoliflodacin therapy. A reinfection as the cause for these microbiological failures could not be excluded. We recommend that WGS is implemented in future randomised controlled trials for gonorrhoea treatment to further evaluate possible microbiological failures, exclude reinfections (to avoid underestimating the cure rates), and characterise antimicrobial resistance determinants. FUNDING: GARDP through grants from Germany BMFTR (03KA1831), UK DHSC as part of GAMRIF, Japan MHLW, the Netherlands' Ministry of Health, Welfare and Sport and Directorate-General for International Cooperation, the Federal Office of Public Health of Switzerland, the Canton of Geneva, Switzerland, and Örebro University Hospital, Sweden.

Humans↗
PubMed2002

[Plant genome sequencing: a prelude to the study of its expression].

This report illustrates development of plant sequencing programmes. So far Arabidopsis genome has been completely sequenced and a draft of the rice genome is available. The Arabidopsis programmes stimulated sequencing of EST (expressed sequence tags) from numerous cultivated species thus creating an enormous resource. The major challenge is now to correctly annotate all the genes in Arabidopsis and find out a biological and biochemical function for each one. The availability of EST and genome sequence now allows one to analyse the expression of genes at the level of the whole genome.

Arabidopsis↗
PubMed1997

A tool for analyzing and annotating genomic sequences.

We describe a tool for analyzing and annotating large genomic sequences containing introns. The analysis and annotation tool (AAT) includes two sets of programs, one for comparing the query sequence with a protein database and the other for comparing the query with a cDNA database. Each set contains a fast database search program and a rigorous alignment program. The database search program quickly identifies regions of the query sequence that are similar to a database sequence. Then the alignment program constructs an optimal alignment for each region and the database sequence. The alignment program also reports the coordinates of exons in the query sequence. Pairwise alignments of the query sequence with protein and cDNA database sequences are combined into multiple sequence alignments, which provide a view of all protein and cDNA sequences matching a query region. On a data set of 570 DNA sequences, AAT identified 94% of coding nucleotides correctly and 74% of exons exactly. Results of analyzing a human BAC sequence with the AAT tool are also presented. The AAT tool reduces the labor-intensive work of locating the exons of the query sequence and improves the process of defining intron-exon boundaries by using the wealth of available protein and cDNA data.

Amino Acid Sequence↗
PubMed1998

DNA methylation in mouse A-repeats in DNA methyltransferase-knockout ES cells and in normal cells determined by bisulfite genomic sequencing.

Mouse ES cells with a null mutation of the known DNA methyltransferase retain some residual DNA methylation and can methylate foreign sequences de novo. We have used bisulfite genomic sequencing to examine the sequence specificity and distributions of methylation of a hypermethylated CG island sequence, mouse A-repeats. There were 13 CG dinucleotides in the region examined, 12 of which were methylated to variable extents in all DNAs. We found that: (1) there is considerable residual DNA methylation in ES cells lacking the known DNA methyltransferase (29% of normal methylation in the complete knockout ES DNA); (2) this other activity methylates at exactly the same CG sites as the major methyltransferase; and (3) differences in the distribution of methylated sites between A-repeats in these DNAs are consistent with this other activity methylating in a random de novo fashion. Also, the lack of any methylation in non-CG sites argues that, in other studies where non-CG methylation sites have been found by bisulfite sequencing, detection of such sites of non-CG methylation is not an inherent artifact in this methodology.

Animals↗
PubMed2006

Genome sequence of the bioplastic-producing "Knallgas" bacterium Ralstonia eutropha H16.

The H(2)-oxidizing lithoautotrophic bacterium Ralstonia eutropha H16 is a metabolically versatile organism capable of subsisting, in the absence of organic growth substrates, on H(2) and CO(2) as its sole sources of energy and carbon. R. eutropha H16 first attracted biotechnological interest nearly 50 years ago with the realization that the organism's ability to produce and store large amounts of poly[R-(-)-3-hydroxybutyrate] and other polyesters could be harnessed to make biodegradable plastics. Here we report the complete genome sequence of the two chromosomes of R. eutropha H16. Together, chromosome 1 (4,052,032 base pairs (bp)) and chromosome 2 (2,912,490 bp) encode 6,116 putative genes. Analysis of the genome sequence offers the genetic basis for exploiting the biotechnological potential of this organism and provides insights into its remarkable metabolic versatility.

Aerobiosis↗
PubMed2002

Complete genome sequence of garlic latent virus, a member of the carlavirus family.

The complete genome sequence of the garlic latent virus (GLV) has been determined. The whole GLV genome consists of 8,353 nucleotides, excluding the 3'-end poly(A)+ tail, and contains six open-reading frames (ORFs). Putative proteins that were encoded by the reading frames contain the motifs that were conserved in carlavirus-specific RNA replicases, NTP-dependent DNA helicases, two viral membrane-bound proteins, a viral coat protein, and a zinc-finger. Overall, the GLV genome shows structural features that are common in carlaviruses. An in vitro translation analysis revealed that the zinc-finger protein is not produced as a transframe protein with the coat protein by ribosomal frameshifting. A Northern blot analysis showed that GLV-specific probes hybridized to garlic leaf RNA fragments of about 2.6 and 1.5 kb long, in addition to the 8.5 kb whole genome. The two subgenomic RNAs might be encapsidated into smaller viral particles. In garlic plants, 700 nm long flexuous rod-shaped virus particles were observed in the immunoelectron microscopy using polyclonal antibodies against the GLV coat proteins.

Amino Acid Sequence↗
PubMed2002

The multidrug resistance transporters of the major facilitator superfamily, 6 years after disclosure of Saccharomyces cerevisiae genome sequence.

The emergence of multidrug resistance (MDR) plays a crucial role in the failure of treatments of tumors and infectious diseases and in the control of plant pathogens, weeds and food-poisoning and food-spoilage microorganisms. Among the mechanisms underlying the MDR phenomenon in various organisms is the action of transmembrane transport proteins that presumably catalyse the active expulsion of structurally and functionally unrelated cytotoxic compounds out of the cell or their intracellular partitioning. On the basis of the complete genome sequence of Saccharomyces cerevisiae, numerous established and putative multidrug transporters were identified in this non-pathogenic, easy to manipulate eukaryotic model system. In yeast, the putative drug:H(+)-antiporters belong to the major facilitator superfamily; they comprise at least 23 proteins that have largely escaped characterisation by classical approaches. Other MDR determinants are membrane transporters belonging to the ATP binding cassette (ABC) superfamily, that utilize the energy of ATP hydrolysis for activity, and factors for transcriptional regulation of all the MDR transporters. This work reviews the current status of knowledge on the poorly characterized H(+)-antiporters, with 12 and 14 predicted spans, DHA12 and DHA14, drug efflux families. Consideration is given to the inventory and phylogenetic characterization, role as MDR determinants, regulation of gene expression, subcellular localisation and activity as solute transporters. Most of the present knowledge on these putative drug:H(+)-antiporters was driven by disclosure of S. cerevisiae genome sequence, in April 1996, being a paradigm of post-genomic research.

Drug Resistance, Multiple, Fungal↗
PubMed2005

Identification of Chlamydia trachomatis genomic sequences recognized by chlamydial divalent cation-dependent regulator A (DcrA).

The Chlamydia trachomatis divalent cation-dependent regulator (DcrA), encoded by open reading frame CT296, is a distant relative of the ferric uptake regulator (Fur) family of iron-responsive regulators. Chlamydial DcrA specifically binds to a consensus Escherichia coli Fur box and is able to complement an E. coli Fur mutant. In this report, the E. coli Fur titration assay (FURTA) was used to locate chlamydial genomic sequences that are recognized by E. coli Fur. The predictive regulatory regions of 28 C. trachomatis open reading frames contained sequences functionally recognized by E. coli Fur; targets include components of the type III secretion pathway, elements involved in envelope and cell wall biogenesis, predicted transport proteins, oxidative defense enzymes, and components of metabolic pathways. Selected FURTA-positive sequences were subsequently examined for recognition by C. trachomatis DcrA using an electrophoretic mobility shift assay. The resultant data show that C. trachomatis DcrA binds to native chlamydial genomic sequences and, overall, substantiate a functional relationship between chlamydial DcrA and the Fur family of regulators.

Bacterial Proteins↗
PubMed2026

The genome sequence of the brown tree ant, Lasius brunneus (Latreille, 1798) (Hymenoptera: Formicidae).

We present a genome assembly from an individual female Lasius brunneus (Brown Ant; Arthropoda; Insecta; Hymenoptera; Formicidae). The genome sequence has a total length of 264.94 megabases. Most of the assembly (97.62%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 18.03 kilobases. Gene annotation of this assembly on Ensembl identified 15 125 protein-coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Hymenoptera↗
PubMed1990

Amplification of Epstein-Barr virus genomic sequences in blood cells, lacrimal glands, and tears from primary Sjögren's syndrome patients.

Based on observations of primary Sjögren's syndrome (SS) following acute Epstein-Barr virus (EBV) infection, the authors hypothesized that EBV may play a role in the pathogenesis of SS. This hypothesis was tested by evaluating ten peripheral blood mononuclear (PBMN) cell specimens, ten lacrimal gland biopsies, and five tear specimens from 15 EBV-seropositive primary SS patients for EBV genomic sequences using polymerase chain reaction (PCR). Epstein-Barr virus DNA sequences were detected in 50% of SS PBMN cell specimens and 80% of SS lacrimal gland and tear specimens. In six SS patients, specimens were obtained from two or more sites (i.e., PBMN cell and lacrimal gland and/or tears), and EBV genomic sequences were amplified in the PBMN cells and the lacrimal gland or tears in three of these subjects. The authors previously detected EBV genomes in 32% (11/34) of normal human lacrimal glands from EBV-seropositive donors using PCR and concluded that the normal human lacrimal gland may be a site of EBV persistence; however, they were unable to amplify EBV sequences in DNA from PBMN cells or tear specimens from normal donors. Amplification of EBV DNA in PBMN cells, lacrimal glands, and tears of primary SS patients at a greater frequency (P less than 0.01) than normal controls suggests that EBV may be a risk factor in the pathogenesis of SS.

Antibodies↗
PubMed2026

Genome sequences of fungi isolated from retail ground beef.

Studies on fungi in meat products are very limited. In our previous study, we recovered 10 fungal strains from aerobically packaged ground beef collected from retail stores. We conducted whole-genome sequencing on these strains. This genomic information may help to inform more effective interventions to extend meat shelf life.

fungi↗
PubMed2003

The 2R hypothesis and the human genome sequence.

One theory formalised in 1970 proposes that the complexity of vertebrate genomes originated by means of genome duplication at the base of the vertebrate lineage. Since then, the theory has remained both popular and controversial. Here we review the theory, and present preliminary results from our analysis of duplications in the draft human genome sequence. We find evidence for extensive duplication of parts of the genome. We also question the validity of the 'parsimony test' that has been used in other analyses.

Animals↗
PubMed2024

The genome sequence of the black-footed limpet, Patella depressa (Pennant, 1777).

We present a genome assembly from an individual Patella depressa (the black-footed limpet; Mollusca; Gastropoda; Patellogastropoda; Patellidae). The genome sequence is 683.7 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl identified 20,502 protein coding genes.

Patella depressa↗
PubMed2005

Genome sequence of Chrysodeixis chalcites nucleopolyhedrovirus, a baculovirus with two DNA photolyase genes.

The complete genome sequence of a single nucleocapsid nucleopolyhedrovirus recently isolated from Chrysodeixis chalcites (ChchNPV) was determined. The viral genome has a size of 149 622 bp and an overall G+C content of 39.1 mol%. The sequence contains 151 predicted open reading frames (ORFs) with a minimal size of 50 codons. The similarity of these ORFs with those of other completely sequenced baculoviruses was calculated using a newly developed database, named GECCO. Phylogenetic analysis of the whole genome confirmed the evolutionary relationship of ChchNPV with group II NPVs, as did the absence of the NPV group I-specific gp64 gene. It is the first group II NPV to encode proliferating cell nuclear antigen. Most noteworthy is the presence of two ORFs encoding a class II cyclobutane pyrimidine dimer DNA photolyase. These two ORFs share only 45 % amino acid identity and have different promoter motifs. Twenty-two additional unique baculovirus genes were identified, including a gene encoding a novel putative RING finger protein with a possible homologue in poxviruses.

Animals↗