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At least 595 records · Page 33Linked to original sources
PubMed2005

Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis.

Brucellosis is a worldwide disease of humans and livestock that is caused by a number of very closely related classical Brucella species in the alpha-2 subdivision of the Proteobacteria. We report the complete genome sequence of Brucella abortus field isolate 9-941 and compare it to those of Brucella suis 1330 and Brucella melitensis 16 M. The genomes of these Brucella species are strikingly similar, with nearly identical genetic content and gene organization. However, a number of insertion-deletion events and several polymorphic regions encoding putative outer membrane proteins were identified among the genomes. Several fragments previously identified as unique to either B. suis or B. melitensis were present in the B. abortus genome. Even though several fragments were shared between only B. abortus and B. suis, B. abortus shared more fragments and had fewer nucleotide polymorphisms with B. melitensis than B. suis. The complete genomic sequence of B. abortus provides an important resource for further investigations into determinants of the pathogenicity and virulence phenotypes of these bacteria.

Bacterial Proteins↗
PubMed2003

Sequence mapping of the Californian MSW strain of Myxoma virus.

Partial sequence mapping of the MSW Californian strain of Myxoma virus was performed by cloning EcoRI and SalI restriction fragments of viral DNA and sequencing the ends of these. In this way, regions of 74 MSW open reading frames were sequenced and mapped onto the complete genome sequences of the related leporipoxviruses South American Myxoma virus and Rabbit fibroma virus to form a partial map of the MSW strain. In general, gene locations and sequences were conserved between the three viruses. However the Californian Myxoma virus was more closely related to South American myxoma virus than to Rabbit fibroma virus based on sequence comparisons and the presence of three genes that have been lost from the Rabbit fibroma virus genome. Compared to the other two viruses, the main difference found in the MSW genome was that the terminal inverted repeats were extended with the duplication of 5 complete open reading frames (M151R, M152R, M153R, M154L, M156R) and partial duplication of one open reading frame (M150R). This rearrangement was associated with the loss of the majority of the M009L open reading frame. Three known virulence genes, including the serine proteinase inhibitor (SERPIN) genes M151R and M152R and leukemia associated protein (LAP) gene M153R, and the potential virulence gene M156R are now present in two copies.

Animals↗
PubMed2004

GenePalette: a universal software tool for genome sequence visualization and analysis.

To make effective use of the growing host of complete genome sequences, biologists must have easy-to-use software tools that allow them to visualize, analyze, and modify genome data in an interactive and generalized manner. In an effort to bridge the gap between genome and researcher, we have created GenePalette (www.genepalette.org), a desktop application that can access any genome sequence and display the positions of various features [e.g., transcription factor binding sites (TFBSs)] relative to the introns and exons of annotated genes. Written in Java, GenePalette can run on all Java-supporting operating systems (Mac, PC, Unix, Linux). Annotated sequence encompassing the majority of public genome data is rapidly retrieved from GenBank or Ensembl. The software provides intuitive access to the selected genomic region through three interface components: a colorful graphical display showing a schematic of genes and features; an annotated sequence view in which features and genes are highlighted directly on the sequence; and the selectable raw sequence. The three interface components are fully integrated and presented on one page, permitting the user to move easily between representations at different levels of resolution, ranging from kilobases to individual nucleotides. GenePalette is a particularly powerful platform for analyzing the organization of cis-regulatory elements and designing wet-lab experiments to investigate them.

Computational Biology↗
PubMed2001

The meaning and impact of the human genome sequence for microbiology.

The characterization of life is immeasurably enhanced by determination of complete genome sequences. For organisms that engage in intimate interactions with others, the genome sequence from one participant, and associated tools, provide unique insight into its partner. We discuss how the human genome sequence will further our understanding of microbial pathogens and commensals, and vice versa. We also propose criteria for implicating a host gene in microbial pathogenesis, and urge consideration of a'second human genome project'.

Bacteria↗
PubMed2006

Genomic characterization of the unclassified bovine enteric virus Newbury agent-1 (Newbury1) endorses a new genus in the family Caliciviridae.

The pathogenic bovine enteric virus, Newbury agent-1 (Bo//Newbury1/1976/UK), first identified in 1976, was characterized as a possible calicivirus by morphology, buoyant density in CsCl and the presence of a single capsid protein but genomic sequence could not be obtained. In the present study, the complete genome sequence of Newbury1 was determined and classified Newbury1 in a new genus of the Caliciviridae. The Newbury1 genome, of 7454 nucleotides, had two predicted open reading frames (ORFs). ORF1 encoded the non-structural and contiguous capsid proteins. ORF2 encoded a basic protein characteristic of the family Caliciviridae. Compared to the 4 recognized Caliciviridae genera, Norovirus, Sapovirus, Lagovirus and Vesivirus, Newbury1 had less than 39% amino acid (47% nucleotide) identity in the complete 2C-helicase, 3C-protease, 3D-polymerase and capsid regions but had 89% to 98% amino acid (78% to 92% nucleotide) identity to the recently characterized NB virus in these regions. By phylogenetic analyses, Newbury1 and NB viruses formed a distinct clade independent of the 4 recognized genera. However, amino acid identities showed that Newbury1 and the NB virus were distinct polymerase types (90% amino acid identity), but their complete capsid proteins were almost identical (98% amino acid identity). Analyses of contemporary viruses showed that the two polymerase genotypes, Newbury1 and NB, were circulating in UK cattle and antibody to Newbury1-like viruses was common in cattle sera. The present study defined the existence of a new genus in the Caliciviridae that we propose be named Becovirus or Nabovirus to distinguish the new clade from bovine noroviruses.

Amino Acid Sequence↗
PubMed2026

Whole-genome sequencing of adenovirus 41 directly from wastewater using nested overlapping PCR and MinION.

Human adenovirus F41 (HAdV-F41) is one of the leading causes of children's acute gastroenteritis and was recently linked to an outbreak of severe acute hepatitis of unknown etiology among children during 2021 to 2022. While most evidence is based on clinical data, wastewater-based epidemiology offers a community-level approach to monitoring circulating strains and enhancing outbreak preparedness. In this study, we developed an overlapping amplicon-based whole-genome sequencing approach to directly detect HAdV-F41 from archived wastewater samples, using nested PCR with 13 primer sets. Archived wastewater samples were collected between 2021 and 2022 from three treatment plants in Seattle, USA. The viral load ranged from 1.2 × 103 to 8.4 × 103 genome copies per liter. The Oxford Nanopore platform was used for whole-genome sequencing. Complete or partial (>84%) HAdV-F41 genomes were recovered from wastewater samples, with mean coverage depths ranging from 10³ to 10⁵. The consensus sequences showed more than 99% similarity to reference genomes in the NCBI database. The phylogenetic analysis revealed that 2 sequences clustered within lineage 2a and 11 within lineage 2b, reflecting that at least two sub-lineages were circulating in the community at that time. Our results demonstrate that the overlapping amplicon-based whole-genome sequencing approach using the Oxford Nanopore platform reliably recovers HAdV-F41 genomes from wastewater. This method offers high-resolution genomic surveillance of circulating, clinically relevant HAdV-F41, supporting wastewater-based epidemiology as a valuable tool for detecting emerging variants and strengthening the early warning system for future disease outbreaks.IMPORTANCEHuman adenovirus F41 is a primary cause of childhood gastroenteritis and has been linked to recent outbreaks of severe acute hepatitis in children, yet community-level genomic surveillance of this virus remains limited. This study shows that wastewater can be used to recover nearly complete HAdV-F41 genomes through a targeted overlapping-amplicon sequencing strategy on the Oxford Nanopore platform. By applying this method to archived wastewater samples, we detected the simultaneous circulation of multiple viral lineages in a large city. These findings extend wastewater-based epidemiology beyond SARS-CoV-2 and emphasize its importance for monitoring clinically significant enteric viruses. The method described here offers a scalable tool for tracking viral evolution in communities and enhancing early warning systems for future outbreaks.

Wastewater↗
PubMed2000

Recent developments from the Leishmania genome project.

A first generation cosmid contig map of the Leishmania major Friedlin genome has been constructed, and genomic sequencing is well underway. Chromosome 1 (Chr1) and Chr3 have been completely sequenced, and Chr4 is virtually complete. Sequencing of several other chromosomes is in progress and the complete genome sequence may be available as soon as 2003. More than 600 completely sequenced new genes have been identified, representing approximately 8% of the total gene complement (approximately 8,600 genes) of Leishmania. Notably, a large proportion (approximately 69%) of the genes remain unclassified, with 40% of these being potentially Leishmania- (or kinetoplastid-) specific. Most interestingly, the genes are organized into large (>100-300 kb) polycistronic clusters of adjacent genes on the same DNA strand. Chr1 contains two such clusters organized in a 'divergent' manner, whereas Chr3 contains two 'convergent' clusters, with a single 'divergent' gene at one telomere, with the two large clusters separated by a tRNA gene. Statistical analyses of Chr1 show that the 'divergent junction' region between the two polycistronic gene clusters may be a candidate for an origin of DNA replication.

Animals↗
PubMed1997

The Bacillus subtilis genome from gerBC (311 degrees) to licR (334 degrees).

As part of the international project to sequence the Bacillus subtilis genome, the DNA region located between gerBC (311 degrees) and licR (334 degrees) was assigned to the institut Pasteur. In this paper, the cloning and sequencing of 176 kb of DNA and the analysis of the sequence of the entire 271 kb region (6.5% of the B. subtilis chromosome) is described; 273 putative coding sequences were identified. Although the complete genome sequences of seven other organisms (five bacteria, one archaeon and the yeast Saccharomyces cerevisiae) are available in public database, 65 genes from this region of the B. subtilis chromosome encode proteins without significant similarities to other known protein sequences. Among the 208 other genes, 115 have paralogues in the currently known B. subtilis DNA sequences and the products of 178 genes were found to display similarities to protein sequences from public databases for which a function is known. Classification of these genes shows a high proportion of them to be involved in the adaptation to various growth conditions (non-essential cell wall constituents, catabolic and bioenergetic pathways); a small number of the genes are essential or encode anabolic enzymes.

Amino Acid Sequence↗
PubMed2006

Genomic cartography of varicella-zoster virus: a complete genome-based analysis of strain variability with implications for attenuation and phenotypic differences.

In order to gain a better perspective on the true variability of varicella-zoster virus (VZV) and to catalogue the location and number of differences, 11 new complete genome sequences were compared with those previously in the public domain (18 complete genomes in total). Three of the newly sequenced genomes were derived from a single strain in order to assess variations that can occur during serial passage in cell culture. The analysis revealed that while VZV is relatively stable genetically it does posses a certain degree of variability. The reiteration regions, origins of replication and intergenic homopolymer regions were all found to be variable between strains as well as within a given strain. In addition, the terminal viral sequences were found to vary within and between strains specifically at the 3' end of the genome. Analysis of single nucleotide polymorphisms (SNPs) identified a total of 557 variable sites, 451 of which were found in coding regions and resulted in 187 different in amino acid substitutions. A comparison of the SNPs present in the two gE mutant strains, VZV-MSP and VZV-BC, suggested that the missense mutation in gE was primarily responsible for the accelerated cell spread phenotype. Some of the variations noted with high passage in cell culture are consistent with variations seen in the IE62 gene of the vaccine strains (S628G, R958G and I1260V) that may help in pinpointing variations essential for attenuation. Although VZV has been considered to be one of the most genetically stable human herpesviruses, this initial assessment of genomic VZV cartography provides insight into ORFs with previously unreported variations.

Base Sequence↗
PubMed2007

Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination.

Potyviruses have variable single-stranded RNA genomes and many show clear evidence of recombination. This report studied the distribution of recombination sites in the genomes of 92 isolates of the potyvirus Turnip mosaic virus (TuMV); 42 came from the international gene sequence databases and an additional 50 complete genomic sequences were generated from field samples collected in Europe and Asia. The sequences were examined for evidence of recombination using seven different sequence comparison methods and the exact position of each site was confirmed by sequence composition analysis. Recombination sites were found throughout the genomes, except in the small 6K1 protein gene, and only 24 of the genomes (26%) showed no evidence of recombination. Statistically significant clusters of recombination sites were found in the P1 gene and in the CI/6K2/VPg gene region. Most recombination sites were bordered by an upstream (5') region of GC-rich and downstream (3') region of AU-rich sequence of a similar length. Correlations between the presence and type of recombination site and provenance, host type and phylogenetic relationships are discussed, as is the role of recombination in TuMV evolution.

Genome, Viral↗
PubMed2003

Nontypeable Haemophilus influenzae gene expression induced in vivo in a chinchilla model of otitis media.

The gram-negative bacterium nontypeable Haemophilus influenzae (NTHI) is the predominant pathogen in chronic otitis media with effusion and, with Streptococcus pneumoniae and Moraxella catarrhalis, is a causative agent of acute otitis media. To identify potential virulence determinants, bacterial gene expression was monitored by differential fluorescence induction during early disease progression in one specific anatomical niche of a chinchilla model of NTHI-induced otitis media. Genomic DNA fragments from NTHI strain 86-028NP were cloned upstream of the promoterless gfpmut3 gene. NTHI strain 86-028NP served as the host for the promoter trap library. Pools of 2,000 transformants were inoculated into the left and right middle ear cavities of chinchillas. Middle ear effusions were recovered by epitympanic tap at 24 and 48 h, and clones containing promoter elements that were induced in vivo and producing green fluorescent protein were isolated by two-color fluorescence-activated cell sorting. Insert DNA was sequenced and compared to the complete genome sequence of H. influenzae strain Rd. In a screen of 16,000 clones, we have isolated 44 clones that contain unique gene fragments encoding biosynthetic enzymes, metabolic and regulatory proteins, and hypothetical proteins of unknown function. An additional eight clones contain gene fragments unique to our NTHI isolate. Using quantitative reverse transcription-PCR, we have confirmed that 26 clones demonstrated increased gene expression in vivo relative to expression in vitro. These data provide insight into the response of NTHI bacteria as they sense and respond to the middle ear microenvironment during early events of otitis media.

Acute Disease↗
PubMed1995

Sequence analysis of pothos latent virus genomic RNA.

The complete genomic sequence of pothos latent virus (PoLV) has been determined. The genome organization is very similar to that of tombusviruses. The genome is 4415 nucleotides long and contains five ORFs. The 5' ORF (ORF 1) encodes a protein with a predicted molecular mass of 25 kDa and readthrough of its amber stop codon results in an 84 kDa protein (ORF 2). ORF 3 encodes the 40 kDa capsid protein. Two nested ORFs (ORFs 4 and 5) in different reading frames encode 27 and 14 kDa proteins, respectively. Amino acid sequence alignments revealed significant similarities between the readthrough portion of ORF 2 and the coat protein (ORF 3) of PoLV and the corresponding proteins of several tombusviruses. Conversely, the predicted products of ORFs 1, 4 and 5 showed only limited similarity to the equivalent tombusvirus proteins. These results support the conclusion that PoLV is a new but atypical member of the family Tombusviridae.

Amino Acid Sequence↗
PubMed2004

The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis.

We present the complete genome sequence of Mycoplasma hyopneumoniae, an important member of the porcine respiratory disease complex. The genome is composed of 892,758 bp and has an average G+C content of 28.6 mol%. There are 692 predicted protein coding sequences, the average protein size is 388 amino acids, and the mean coding density is 91%. Functions have been assigned to 304 (44%) of the predicted protein coding sequences, while 261 (38%) of the proteins are conserved hypothetical proteins and 127 (18%) are unique hypothetical proteins. There is a single 16S-23S rRNA operon, and there are 30 tRNA coding sequences. The cilium adhesin gene has six paralogs in the genome, only one of which contains the cilium binding site. The companion gene, P102, also has six paralogs. Gene families constitute 26.3% of the total coding sequences, and the largest family is the 34-member ABC transporter family. Protein secretion occurs through a truncated pathway consisting of SecA, SecY, SecD, PrsA, DnaK, Tig, and LepA. Some highly conserved eubacterial proteins, such as GroEL and GroES, are notably absent. The DnaK-DnaJ-GrpR complex is intact, providing the only control over protein folding. There are several proteases that might serve as virulence factors, and there are 53 coding sequences with prokaryotic lipoprotein lipid attachment sites. Unlike other mycoplasmas, M. hyopneumoniae contains few genes with tandem repeat sequences that could be involved in phase switching or antigenic variation. Thus, it is not clear how M. hyopneumoniae evades the immune response and establishes a chronic infection.

Animals↗
PubMed2001

Genome sequence of a baculovirus pathogenic for Culex nigripalpus.

In this report we describe the complete genome sequence of a nucleopolyhedrovirus that infects larval stages of the mosquito Culex nigripalpus (CuniNPV). The CuniNPV genome is a circular double-stranded DNA molecule of 108,252 bp and is predicted to contain 109 genes. Although 36 of these genes show homology to genes from other baculoviruses, their orientation and order exhibit little conservation relative to the genomes of lepidopteran baculoviruses. CuniNPV genes homologous to those from other baculoviruses include genes involved in early and late gene expression (lef-4, lef-5, lef-8, lef-9, vlf-1, and p47), DNA replication (lef-1, lef-2, helicase-1, and dna-pol), and structural functions (vp39, vp91, odv-ec27, odv-e56, p6.9, gp41, p74, and vp1054). Auxiliary genes include homologues of genes encoding the p35 antiapoptosis protein and a novel insulin binding-related protein. In contrast to these conserved genes, CuniNPV lacks apparent homologues of baculovirus genes essential (ie-1 and lef-3) or stimulatory (ie-2, lef-7, pe38) for DNA replication. Also, baculovirus genes essential or stimulatory for early-late (ie-1, ie-2), early (ie-0 and pe-38), and late (lef-6, lef-11, and pp31) gene transcription are not identifiable. In addition, CuniNPV lacks homologues of genes involved in the formation of virogenic stroma (pp31), nucleocapsid (orf1629, p87, and p24), envelope of occluded virions (odv-e25, odv-e66, odv-e18), and polyhedra (polyhedrin/granulin, p10, pp34, and fp25k). A homologue of gp64, a budded virus envelope fusion protein, was also absent, although a gene related to the other category of baculovirus budded virus envelope proteins, Ld130, was present. The absence of homologues of occlusion-derived virion (ODV) envelope proteins and occlusion body (OB) protein (polyhedrin) suggests that both CuniNPV ODV and OB may be structurally and compositionally different from those found in terrestrial lepidopteran hosts. The striking difference in genome organization, the low level of conservation of homologous genes, and the lack of many genes conserved in other baculoviruses suggest a large evolutionary distance between CuniNPV and lepidopteran baculoviruses.

Animals↗
PubMed2004

Comparative genomics identifies genes shared by distantly related insect-transmitted plant pathogenic mollicutes.

Phytoplasmas and spiroplasmas are distantly related insect-transmitted plant pathogens within the class Mollicutes. Genome sequencing projects of phytoplasma strain Aster Yellows-Witches' Broom (AY-WB) and Spiroplasma kunkelii are near completion. Complete genome sequences of seven obligate animal and human pathogenic mollicutes (Mycoplasma and Ureaplasma spp.), and OY phytoplasma have been reported. Putative ORFs predicted from the genome sequences of AY-WB and S. kunkelii were compared to those of the completed genomes. This resulted in identification of at least three ORFs present in AY-WB, OY and S. kunkelii but not in the obligate animal and human pathogenic mollicutes. Moreover, we identified ORFs that seemed more closely related between AY-WB and S. kunkelii than to their mycoplasma counterparts. Phylogenetic analyses using parsimony were employed to study the origin of these genes, resulting in identification of one gene that may have undergone horizontal gene transfer. The possible involvement of these genes in plant pathogenicity is discussed.

Animals↗
PubMed2006

[Analysis of the secreted proteins encoded by genes in genome of filamental fungus (Neurospora crassa)].

The completed genome sequence of filamental fungus Neurospora crassa has completed and 10,082 open reading frames (ORFs) were predicted in whole genome. Among them, 437 proteins were secreted ones based on the combination of prediction algorithms SignalP v3.0 and PSORT, transmembrane domains prediction algorithms TMHMM v2.0 and THUMBUP, potential GPI-anchor sites prediction algorithm big-PI predictor and the subcellular protein location prediction algorithm TargetP v1.01. The minimum ORF length of the encoding sequences for 437 secreted proteins was 252 bp, the maximum ORF length was 6 604 bp and average was 1 433 bp. The length of signal peptide of secreted proteins ranged from 15 to 59 amino acids. Among the 437 secreted proteins, 205 were provided with function description. The function of secretory proteins were involved in kinds of enzyme, cell energy, transmission, cell recovered itself and defense mechanism et al. These results implied that processes catalyzed by these proteins probably occurred outside of cells, at least partially.

Amino Acid Sequence↗
PubMed2006

Identification and mapping of paralogous genes on a known genomic DNA sequence.

The completion of whole genome sequencing projects offers the opportunity to examine the organization of genes and the discovery of evolutionarily related genes in a given species. For the beginners in the field, through a specific example, this chapter provides a step-by-step procedure for identifying paralogous genes, using the genome browser at UCSC (http://genome.ucsc.edu/). The example describes identification and mapping in the human genome, the paralogs of TCF12/HTF4. The example identifies TCF3 and TCF4 as paralogs of the TCF12/HTF4 gene. The example also identifies a related sequence, corresponding to a pseudogene, in one of the introns of the JAK2 gene. The procedure described should be applicable to the discovery and creation of maps of paralogous genes in the genomic DNA sequences that are available at the genome browser at UCSC.

Amino Acid Sequence↗