scholarly journals Genomic Characteristics and Evolutionary Analysis of a Rare GI.1 Norovirus Isolate From Beijing, China

2021 ◽  
Author(s):  
Weishan Zhang ◽  
Wei Zhang ◽  
Xinling Hu ◽  
Xintong Zhou ◽  
Guobao Tian ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Large Scale ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Evolutionary Analysis ◽  
And Control ◽  
Beijing China ◽  
Strain Genome ◽  
Reading Frames

Abstract Noroviruses are one of the main pathogens of acute gastroenteritis, causing frequent outbreaks worldwide every year that seriously affect human health. The GII.4 genotype causes most norovirus (NoV) infections and large-scale outbreaks. By contrast, the GI genotype is relatively rare. In this study, the whole genome sequence of a newly isolated ZD strain from a patient in Beijing, China, was sequenced and analyzed. The ZD strain genome consisted of 7,597 nucleotides and contained three open reading frames. Whole-genomic analysis indicated the strain was a GI.1 genotype, and no recombination site was detected in the genome. The histo-blood group antigen (HBGA)binding site associated with invasion of the GI genotype did not change, implying relatively conservative evolution. Phylogenetic analysis indicated the VP1 sequence of GI.1 strains could be divided into three clusters according to time of appearance: older (1968-2011), earlier (2011-2015), and new (2017-2018). Each cluster showed distinctive amino acid substitution characteristics, and the number of substitutions increased with time. The isolated ZD strain was in the new cluster. This study is the first to conduct a phylogenetic analysis of a GI genotype NoV isolated from Beijing. The results improve understanding of NoV diversity in China and can be a reference for further study of nondominant epidemic strains of NoVs as well as epidemic prevention and control.

scholarly journals Characterization and Genome Analysis of Staphylococcus aureus Podovirus CSA13 and Its Anti-Biofilm Capacity

Viruses ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 54 ◽  
Author(s):  
Yoyeon Cha ◽  
Jihwan Chun ◽  
Bokyung Son ◽  
Sangryeol Ryu
Keyword(s):  
Staphylococcus Aureus ◽  
Biocontrol Agent ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Experimental Setting ◽  
Human Pathogens ◽  
Bacteriophage Therapy ◽  
Chromosomal Structure ◽  
Inhibition Effect ◽  
Reading Frames

Staphylococcus aureus is one of the notable human pathogens that can be easily encountered in both dietary and clinical surroundings. Among various countermeasures, bacteriophage therapy is recognized as an alternative method for resolving the issue of antibiotic resistance. In the current study, bacteriophage CSA13 was isolated from a chicken, and subsequently, its morphology, physiology, and genomics were characterized. This Podoviridae phage displayed an extended host inhibition effect of up to 23 hours of persistence. Its broad host spectrum included methicillin susceptible S. aureus (MSSA), methicillin resistant S. aureus (MRSA), local S. aureus isolates, as well as non-aureus staphylococci strains. Moreover, phage CSA13 could successfully remove over 78% and 93% of MSSA and MRSA biofilms in an experimental setting, respectively. Genomic analysis revealed a 17,034 bp chromosome containing 18 predicted open reading frames (ORFs) without tRNAs, representing a typical chromosomal structure of the staphylococcal Podoviridae family. The results presented here suggest that phage CSA13 can be applicable as an effective biocontrol agent against S. aureus.

An Umbra-related Virus Found in Vasconcellea X Heilbornii (Caricaceae)

2021 ◽  
Author(s):  
Juan F Cornejo-Franco ◽  
Francisco Flores ◽  
Dimitre Mollov ◽  
diego fernando quito-avila
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Rna Dependent Rna Polymerase ◽  
Sequence Comparisons ◽  
Genomic Features ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Abstract The complete sequence of a new viral RNA from babaco (Vasconcellea x heilbornii) was determined. The genome consisted of 4,584 nucleotides organized in two non-overlapping open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5’ terminus and a 1,843 -nt-long NCR at the 3’ terminus. Sequence comparisons of ORF 2 revealed homology to the RNA-dependent-RNA-polymerase (RdRp) of several umbra- and umbra-related viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported from papaya, citrus, opuntia, maize and sugarcane hosts. This clade shares a most recent ancestor with the umbraviruses but has different genomic features. The creation of a new genus, within the Tombusviridae, is proposed for the classification of these novel viruses.

scholarly journals A Chemogenomic Screening of Sulfanilamide-Hypersensitive Saccharomyces cerevisiae Mutants Uncovers ABZ2, the Gene Encoding a Fungal Aminodeoxychorismate Lyase

2007 ◽  
Vol 6 (11) ◽  
pp. 2102-2111 ◽  
Author(s):  
Javier Botet ◽  
Laura Mateos ◽  
José L. Revuelta ◽  
María A. Santos
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Cellular Processes ◽  
Founder Member ◽  
Yeast Genes ◽  
Vacuole Biogenesis ◽  
Reading Frames

ABSTRACT Large-scale phenotypic analyses have proved to be useful strategies in providing functional clues about the uncharacterized yeast genes. We used here a chemogenomic profiling of yeast deletion collections to identify the core of cellular processes challenged by treatment with the p-aminobenzoate/folate antimetabolite sulfanilamide. In addition to sulfanilamide-hypersensitive mutants whose deleted genes can be categorized into a number of groups, including one-carbon related metabolism, vacuole biogenesis and vesicular transport, DNA metabolic and cell cycle processes, and lipid and amino acid metabolism, two uncharacterized open reading frames (YHI9 and YMR289w) were also identified. A detailed characterization of YMR289w revealed that this gene was required for growth in media lacking p-aminobenzoic or folic acid and encoded a 4-amino-4-deoxychorismate lyase, which is the last of the three enzymatic activities required for p-aminobenzoic acid biosynthesis. In light of these results, YMR289w was designated ABZ2, in accordance with the accepted nomenclature. ABZ2 was able to rescue the p-aminobenzoate auxotrophy of an Escherichia coli pabC mutant, thus demonstrating that ABZ2 and pabC are functional homologues. Phylogenetic analyses revealed that Abz2p is the founder member of a new group of fungal 4-amino-4-deoxychorismate lyases that have no significant homology to its bacterial or plant counterparts. Abz2p appeared to form homodimers and dimerization was indispensable for its catalytic activity.

scholarly journals Whole-Genome Sequence Analysis of Pseudomonas syringae pv. phaseolicola 1448A Reveals Divergence among Pathovars in Genes Involved in Virulence and Transposition

2005 ◽  
Vol 187 (18) ◽  
pp. 6488-6498 ◽  
Author(s):  
Vinita Joardar ◽  
Magdalen Lindeberg ◽  
Robert W. Jackson ◽  
Jeremy Selengut ◽  
Robert Dodson ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Genome Sequence ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Circular Chromosome ◽  
Physiological Level ◽  
Halo Blight ◽  
Bacterial Plant Pathogen ◽  
Reciprocal Best Hit ◽  
Reading Frames

ABSTRACT Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific.

scholarly journals Genomic Characterization of a New Enamovirus Infecting Common Bean

2021 ◽  
Author(s):  
Ruo-bin Lu ◽  
Ping-xiu Lan ◽  
Ru-jing Kang ◽  
Guan-lin Tan ◽  
Xiao-jiao Chen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Novel Species ◽  
Open Reading Frames ◽  
Amino Acid Sequence Level ◽  
Disease Symptoms ◽  
Bean Plants ◽  
Genomic Characterization ◽  
Pea Enation Mosaic Virus ◽  
Reading Frames

Abstract A novel enamovirus was identified from bean plants with disease symptoms. Its genome of 5,781 nucleotides (nt) encodes five open reading frames. The virus and other species of the genus Enamovirus share identities of 50.4%-68.4% at the complete genome, and 19.9%-51.9% of P0, 24.9%-52.5% of P1, 33.4%-62.9% of P1-P2, 30.6%-81.1% of P3, 32.3%-74.2% of P3-P5 at amino acid sequence level, respectively. Phylogenetic analysis showed that the virus is most closely related to Alfalfa enamovirus 1 and Pea enation mosaic virus 1 in the genus Enamovirus within family Solemoviridae. These results suggest that the virus should be considered as a novel species in the genus Enamovirus and tentatively named as “bean enamovirus 1”.

scholarly journals Evolutionary divergence of novel open reading frames in cichlids speciation

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shraddha Puntambekar ◽  
Rachel Newhouse ◽  
Jaime San Miguel Navas ◽  
Ruchi Chauhan ◽  
Grégoire Vernaz ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Potential Role ◽  
Open Reading Frames ◽  
Evolutionary Divergence ◽  
Evolutionary Analysis ◽  
Noncoding Dna ◽  
Phenotypic Diversification ◽  
Genomic Regions ◽  
Coding Potential ◽  
Reading Frames

AbstractNovel open reading frames (nORFs) with coding potential may arise from noncoding DNA. Not much is known about their emergence, functional role, fixation in a population or contribution to adaptive radiation. Cichlids fishes exhibit extensive phenotypic diversification and speciation. Encounters with new environments alone are not sufficient to explain this striking diversity of cichlid radiation because other taxa coexistent with the Cichlidae demonstrate lower species richness. Wagner et al. analyzed cichlid diversification in 46 African lakes and reported that both extrinsic environmental factors and intrinsic lineage-specific traits related to sexual selection have strongly influenced the cichlid radiation, which indicates the existence of unknown molecular mechanisms responsible for rapid phenotypic diversification, such as emergence of novel open reading frames (nORFs). In this study, we integrated transcriptomic and proteomic signatures from two tissues of two cichlids species, identified nORFs and performed evolutionary analysis on these nORF regions. Our results suggest that the time scale of speciation of the two species and evolutionary divergence of these nORF genomic regions are similar and indicate a potential role for these nORFs in speciation of the cichlid fishes.

scholarly journals Draft Whole-Genome Sequence of “Candidatus Liberibacter asiaticus” Strain TX2351 Isolated from Asian Citrus Psyllids in Texas, USA

2017 ◽  
Vol 5 (15) ◽  
Author(s):  
Madhurababu Kunta ◽  
Zheng Zheng ◽  
Fengnian Wu ◽  
John V. da Graca ◽  
Jong-Won Park ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
South Texas ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Candidatus Liberibacter Asiaticus ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Rna Genes ◽  
Reading Frames

ABSTRACT We report here the draft genome sequence of “Candidatus Liberibacter asiaticus” strain TX2351, collected from Asian citrus psyllids in south Texas, USA. The TX2351 genome has a size of 1,252,043 bp, a G+C content of 36.5%, 1,184 predicted open reading frames, and 52 RNA genes.

scholarly journals Complete nucleotide sequence and genome organization of Grapevine leafroll-associated virus 3, type member of the genus Ampelovirus

2004 ◽  
Vol 85 (7) ◽  
pp. 2099-2102 ◽  
Author(s):  
Kai-Shu Ling ◽  
Hai-Ying Zhu ◽  
Dennis Gonsalves
Keyword(s):  
Phylogenetic Analysis ◽  
Nucleotide Sequence ◽  
Fusion Protein ◽  
Complete Genome Sequence ◽  
Genome Organization ◽  
Complete Nucleotide Sequence ◽  
Open Reading Frames ◽  
The Family ◽  
Mealy Bug ◽  
Reading Frames

This study reports on the complete genome sequence of Grapevine leafroll-associated virus 3, the type member of the genus Ampelovirus. The genome is 17 919 nt in size and contains 13 open reading frames (ORFs). Previously, the sequence of 13 154 nt of the 3′-terminal of the genome was reported. The newly sequenced portion contains a 158 nt 5′ UTR, a single papain-like protease and a methyltransferase-like (MT) domain. ORF1a encodes a large polypeptide with a molecular mass of 245 kDa. With a predicted +1 frameshift, the large fusion protein generated from ORF1a/1b would produce a 306 kDa polypeptide. Phylogenetic analysis using MT domains further supports the creation of the genus Ampelovirus for mealy-bug-transmitted viruses in the family Closteroviridae.

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