Showing papers in "Genome Announcements in 2014"
TL;DR: The complete coding sequence of a Zika virus strain belonging to the Asian lineage is reported, isolated from an infected patient returning from French Polynesia, an epidemic area in 2013/2014.
Abstract: Zika virus is an arthropod-borne Flavivirus member of the Spondweni serocomplex, transmitted by Aedes mosquitoes. We report here the complete coding sequence of a Zika virus strain belonging to the Asian lineage, isolated from an infected patient returning from French Polynesia, an epidemic area in 2013/2014.
232 citations
TL;DR: The complete 4,631,469-bp genome sequence of this strain and the key variations from the type strain E. coli MG1655 are reported.
Abstract: Escherichia coli BW25113 is the parent strain of the Keio collection comprising nearly 4,000 single-gene deletion mutants. We report the complete 4,631,469-bp genome sequence of this strain and the key variations from the type strain E. coli MG1655.
157 citations
TL;DR: The complete genome of the Korean PDCoV strain, KOR/KNU14-04/2014, was sequenced and analyzed to characterizePDCoV circulating in South Korea.
Abstract: In April 2014, porcine deltacoronavirus (PDCoV) was first identified in feces from diarrheic piglets in South Korea and found to be closely related to other PDCoV strains. The complete genome of the Korean PDCoV strain, KOR/KNU14-04/2014, was sequenced and analyzed to characterize PDCoV circulating in South Korea.
143 citations
TL;DR: In this article, the authors sequenced four Vibrio parahaemolyticus strains, three of which caused serious acute hepatopancreatic necrosis disease and revealed genes related to cholera toxin and the type IV pilus/type IV secretion system, and a unique, previously unreported, large extrachromosomal plasmid that encodes a homolog to the insecticidal Photorhabdus insect-related binary toxin PirAB.
Abstract: We sequenced four Vibrio parahaemolyticus strains, three of which caused serious acute hepatopancreatic necrosis disease. Sequence analysis of the virulent strains revealed not only genes related to cholera toxin and the type IV pilus/type IV secretion system but also a unique, previously unreported, large extrachromosomal plasmid that encodes a homolog to the insecticidal Photorhabdus insect-related binary toxin PirAB.
130 citations
TL;DR: Using ANI, this work detected mislabeled genomes and recommends verifying with ANI and multilocus phylogenetic analysis the species affiliations of the announced genomes.
Abstract: The average nucleotide identity (ANI) determines if two genomes belong to the same species. Using ANI, we detected mislabeled genomes and recommend verifying with ANI and multilocus phylogenetic analysis the species affiliations of the announced genomes. The slightly different results obtained with different ANI calculation software can potentially mislead taxonomic inferences.
128 citations
TL;DR: Porcine deltacoronavirus (PDCoV) was detected in feces from diarrheic sows during an epidemic of acute and transmissible diarrhea and the PDCoV USA/IA/2014/8734 from the herd was sequenced for full-length genomic RNA to further characterize PD CoV in U.S. swine.
Abstract: Porcine deltacoronavirus (PDCoV) was detected in feces from diarrheic sows during an epidemic of acute and transmissible diarrhea. No transmissible gastroenteritis virus or porcine epidemic diarrhea virus was detected. The PDCoV USA/IA/2014/8734 from the herd was sequenced for full-length genomic RNA to further characterize PDCoV in U.S. swine.
103 citations
TL;DR: A unique sequence encoding a type IV pilus/type IV secretion system was found in 3 AHPND strains and all of them lacked the pathogenicity island relevant to human infection.
Abstract: Some strains of Vibrio parahaemolyticus cause acute hepatopancreatic necrosis disease (AHPND) in shrimp. We sequenced 3 AHPND and 3 non-AHPND strains and found that all of them lacked the pathogenicity island relevant to human infection. A unique sequence encoding a type IV pilus/type IV secretion system was found in 3 AHPND strains.
102 citations
TL;DR: The draft genome sequence of one Mexican strain of Vibrio parahaemolyticus that causes similar clinical signs in diseased shrimps is reported.
Abstract: Acute hepatopancreatic necrosis disease (AHPND), also known as early mortality syndrome (EMS), causes high mortalities in cultured shrimps in Asia (L. Tran et al., Dis. Aquat. Organ. 105:45-55, 2013, http://dx.doi.org/10.3354/dao02621). Here, we report the draft genome sequence of one Mexican strain of Vibrio parahaemolyticus that causes similar clinical signs in diseased shrimps.
91 citations
TL;DR: The isolation of 3 complete genome sequences of gemycircularvirus-related viruses from healthy bovine serum and human brain and serum samples from patients with multiple sclerosis are reported.
Abstract: Myco-like viruses have been isolated from fungi, feces of various animals, and plant leaves. We report here the isolation of 3 complete genome sequences of gemycircularvirus-related viruses from healthy bovine serum and human brain and serum samples from patients with multiple sclerosis (MS). Their putative capsid proteins share similarity to Torque teno virus (TTV) open reading frame 1 (ORF1) proteins.
83 citations
TL;DR: Phylogenetic analysis showed that the isolate was a novel reassortant virus with a neuraminidase (NA) gene from H6N6 viruses and the other seven genes from H5N1 viruses, which may pose a potential threat to human and animal health.
Abstract: An avian influenza virus, A/environment/Zhenjiang/C13/2013(H5N6), was isolated from a live poultry market in eastern China. Phylogenetic analysis showed that the isolate was a novel reassortant virus with a neuraminidase (NA) gene from H6N6 viruses and the other seven genes from H5N1 viruses, which may pose a potential threat to human and animal health.
82 citations
TL;DR: To investigate the causative agent of swine diarrhea, next-generation sequencing was performed on a porcine fecal sample and generated a complete swine Deltacoronavirus genome sequence, that of strain SDCV/USA/Illinois121/2014.
Abstract: To investigate the causative agent of swine diarrhea, next-generation sequencing (NGS) was performed on a porcine fecal sample. The NGS reads were assembled, which generated a complete swine Deltacoronavirus genome sequence, that of strain SDCV/USA/Illinois121/2014.
TL;DR: Seven EV-D68 genomes from the outbreak are reported, and it is confirmed that enterovirus D68 was identified from 83% (30/36) of initial severe cases.
Abstract: Clusters of severe respiratory disease in the United States were reported to the CDC beginning in August 2014. Enterovirus D68 (EV-D68) was identified from 83% (30/36) of initial severe cases. Investigations in August and September found severe EV-D68 cases to be widespread across the United States. We report seven EV-D68 genomes from the outbreak.
TL;DR: The approximately 20.3-Mb genome sequence of PO1f will greatly facilitate research efforts in metabolic engineering of Yarrowia lipolytica for value-added chemical production.
Abstract: The draft genome sequence of the oleaginous yeast Yarrowia lipolytica stain PO1f, a commonly used metabolic engineering host, is presented here. The approximately 20.3-Mb genome sequence of PO1f will greatly facilitate research efforts in metabolic engineering of Yarrowia lipolytica for value-added chemical production.
TL;DR: The whole-genome sequencing, assembly, and annotation of three Endozoicomonas type strains are reported on, which will assist in exploring interactions between Endozoicsomonas organisms and their hosts, and it will aid in the assembly of genomes from uncultivated EndozoIComonas spp.
Abstract: Members of the genus Endozoicomonas associate with a wide range of marine organisms. Here, we report on the whole-genome sequencing, assembly, and annotation of three Endozoicomonas type strains. These data will assist in exploring interactions between Endozoicomonas organisms and their hosts, and it will aid in the assembly of genomes from uncultivated Endozoicomonas spp.
TL;DR: The completed genome sequence for the strain Staphylococcus aureus ATCC 25923 is presented, consisting of the chromosome and a 27.5-kb plasmid.
Abstract: Staphylococcus aureus subsp. aureus ATCC 25923 is commonly used as a control strain for susceptibility testing to antibiotics and as a quality control strain for commercial products. We present the completed genome sequence for the strain, consisting of the chromosome and a 27.5-kb plasmid.
TL;DR: The draft genome sequences of the 8 bacteria that comprise the altered Schaedler flora, a bacterial community that supports normal growth and development of gnotobiotic mice, are reported on.
Abstract: The altered Schaedler flora (ASF) is a bacterial community that supports normal growth and development of gnotobiotic mice. We report here the draft genome sequences of the 8 bacteria that comprise the ASF.
TL;DR: The complete genome sequence of the free-living bacterium Pseudomonas protegens (formerly PseUDomonas fluorescens) CHA0 is reported, a model organism used in plant-microbe interactions, biological control of phytopathogens, and bacterial genetics.
Abstract: We report the complete genome sequence of the free-living bacterium Pseudomonas protegens (formerly Pseudomonas fluorescens) CHA0, a model organism used in plant-microbe interactions, biological control of phytopathogens, and bacterial genetics.
TL;DR: The draft genome sequence of Shiraia sp.
Abstract: Here, we report the draft genome sequence of Shiraia sp. strain Slf14 (China Center for Type Culture Collection [CCTCC] no. 209294), which is used to produce huperzine A and hypocrellin A. The genome sequence will allow for the characterization of the molecular mechanisms underlying its beneficial properties.
TL;DR: The draft genome sequence of a heterothallic reference isolate of C. fioriniae (strain PJ7) is reported, providing a range of new resources that serve as a useful platform for further research in the field.
Abstract: In addition to its economic impact, Colletotrichum acutatum sensu lato is an interesting model for molecular investigations due to the diversity of host-determined specialization and reproductive lifestyles within the species complex. The pathogen Colletotrichum fioriniae forms part of this species complex and causes anthracnose in a wide range of crops and wild plants worldwide. Some members of this species have also been reported to be entomopathogenic. Here, we report the draft genome sequence of a heterothallic reference isolate of C. fioriniae (strain PJ7). This sequence provides a range of new resources that serve as a useful platform for further research in the field.
TL;DR: The complete genome assembly of Escherichia coli ATCC 25922 is presented as submitted to NCBI under accession no.
Abstract: We present the complete genome assembly of Escherichia coli ATCC 25922 as submitted to NCBI under accession no. CP009072. This strain was originally isolated from a clinical sample in Seattle, Washington (1946), and is often used in quality control testing. The assembled genome is 5.20 Mb (50.4% G+C content) and includes two plasmids.
TL;DR: The complete chromosomal sequence of a genetically tractable, prototypical strain of Klebsiella pneumoniae used in animal models is reported to facilitate genetic, molecular, and immunological studies of this pathogen.
Abstract: Klebsiella pneumoniae is an urgent public health threat due to the spread of carbapenem-resistant strains causing serious, and frequently fatal, infections. To facilitate genetic, molecular, and immunological studies of this pathogen, we report the complete chromosomal sequence of a genetically tractable, prototypical strain used in animal models.
TL;DR: The genome sequence and a brief analysis of strain GB03 are presented and it is shown that this strain has been used for biological control against a broad spectrum of plant pathogens and as a bio-fertilizer to promote growth and yield of field crops for more than two decades.
Abstract: Bacillus amyloliquefaciens GB03 has been used as a representative commercialized strain of the bacilli for biological control against a broad spectrum of plant pathogens and as a bio-fertilizer to promote growth and yield of field crops for more than two decades. Herein, we present the genome sequence and a brief analysis of strain GB03.
TL;DR: An updated high-quality, unambiguous genome sequence with no assembly gaps is presented for E. coli serotype O157:H7, associated with deadly food-borne outbreaks.
Abstract: Escherichia coli EDL933 is the prototypic strain for enterohemorrhagic E. coli serotype O157:H7, associated with deadly food-borne outbreaks. Because the publicly available sequence of the EDL933 genome has gaps and >6,000 ambiguous base calls, we here present an updated high-quality, unambiguous genome sequence with no assembly gaps.
TL;DR: This work reports on the 51,705,945 bp draft consensus genome sequence of R. solani strain Rhs1AP, a pathogen of agricultural crops that may provide insight into the plant disease ecology and adaptive behavior of the fungus.
Abstract: The soil fungus Rhizoctonia solani is a pathogen of agricultural crops. Here, we report on the 51,705,945 bp draft consensus genome sequence of R. solani strain Rhs1AP. A comprehensive understanding of the heterokaryotic genome complexity and organization of R. solani may provide insight into the plant disease ecology and adaptive behavior of the fungus.
TL;DR: The draft genome sequence of “Candidatus Liberibacter asiaticus” strain A4, isolated from a mandarin citrus in Guangdong, People's Republic of China, is reported.
Abstract: The draft genome sequence of “Candidatus Liberibacter asiaticus” strain A4, isolated from a mandarin citrus in Guangdong, People9s Republic of China, is reported. The A4 strain has a genome size of 1,208,625 bp, G+C content of 36.4%, 1,107 predicted open reading frames, and 53 RNA genes.
TL;DR: The complete genomic sequences of strain AG174, the stock of the commonly used strain JH642, and strain AG1839, a derivative that contains a mutation in the replication initiation gene dnaB and a linked Tn917 are announced.
Abstract: The Gram-positive bacterium Bacillus subtilis is widely used for studies of cellular and molecular processes. We announce the complete genomic sequences of strain AG174, our stock of the commonly used strain JH642, and strain AG1839, a derivative that contains a mutation in the replication initiation gene dnaB and a linked Tn917.
TL;DR: The genome sequence of the T. cruzi Dm28c clone (TcI), a strain related to the sylvatic cycle of the parasite, is reported, suggesting that clinical variability of Chagas disease can be due to the genetic variability of this parasite.
Abstract: Trypanosoma cruzi affects millions of people worldwide. Clinical variability of Chagas disease can be due to the genetic variability of this parasite, requiring further genome studies. Here we report the genome sequence of the T. cruzi Dm28c clone (TcI), a strain related to the sylvatic cycle of the parasite.
TL;DR: Bacteria associated with the Eastern oysters native to Apalachicola Bay, FL, were investigated using 16S rRNA gene amplicon metagenomic sequencing which revealed that the oyster microbiome was predominated by Cyanobacteria and Proteobacteria.
Abstract: Bacteria associated with the Eastern oysters (Crassostrea virginica) native to Apalachicola Bay, FL, were investigated using 16S rRNA gene amplicon metagenomic sequencing which revealed that the oyster microbiome was predominated by Cyanobacteria and Proteobacteria. We also found that the oyster tissues were predominated by the pathogenic and symbiotic Photobacterium spp. (formerly known as Vibrio damselae).
TL;DR: The complete genome sequence of Azospirillum brasilense Az39, isolated from wheat roots in the central region of Argentina and used as inoculant in extensive and intensive agriculture during the last four decades is presented.
Abstract: We present the complete genome sequence of Azospirillum brasilense Az39, isolated from wheat roots in the central region of Argentina and used as inoculant in extensive and intensive agriculture during the last four decades. The genome consists of 7.39 Mb, distributed in six replicons: one chromosome, three chromids, and two plasmids.
TL;DR: Empirical data point to the involvement of a cow milk factor in the etiology of multiple sclerosis.
Abstract: Epidemiological data point to the involvement of a cow milk factor in the etiology of multiple sclerosis (MS). Eleven circular DNA molecules closely related to transmissible spongiform encephalopathy (TSE)-associated isolate Sphinx 1.76 were isolated from healthy cattle serum, cow milk, and serum and brain tissue from MS patients.