Genome Sequence of Brevundimonas sp., an Arsenic Resistant Soil Bacterium

Brevundimonas sp. is a bacteria able to grow in metal(loid) contaminated soil from Puchuncaví Valley, central Chile. This study has isolated a bacterial strain capable of growth under high doses of arsenic (As) (6000 mg L−1), and a draft genome sequence was generated. Additionally, real-time PCR was performed to examine the effect of As on some genes related to As resistance. Results demonstrated a total of 3275 predicted annotated genes with several genes related to the ars operon, metal(loid) resistance-related genes, metal efflux pumps, and detoxifying enzymes. Real-time PCR showed that the arsB involved in the efflux of As was down-regulated, whereas arsR, arsH, and ACR3 did not show differences with the addition of As. Our study provides novel evidence of diverse As regulating systems in tolerant bacteria that will lead to a better understanding of how microorganisms overcome toxic elements and colonize As contaminated soils and to the possible use of their specific properties in bioremediation.

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Genome Analysis and Development of a Multiplex TaqMan Real-Time PCR for Specific Identification and Detection of Clavibacter michiganensis subsp. nebraskensis

Phytopathology ◽

10.1094/phyto-05-16-0188-r ◽

2016 ◽

Vol 106 (12) ◽

pp. 1473-1485 ◽

Cited By ~ 7

Author(s):

James T. Tambong ◽

Renlin Xu ◽

Fouad Daayf ◽

Stephan Brière ◽

Guillaume J. Bilodeau ◽

...

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Type Strain ◽

Draft Genome ◽

Protein Sequences ◽

The United States ◽

Infected Leaf ◽

Clavibacter Michiganensis ◽

Blind Test ◽

Clavibacter Michiganensis Subsp

The reemergence of the Goss’s bacterial wilt and blight disease in corn in the United States and Canada has prompted investigative research to better understand the genome organization. In this study, we generated a draft genome sequence of Clavibacter michiganensis subsp. nebraskensis strain DOAB 395 and performed genome and proteome analysis of C. michiganensis subsp. nebraskensis strains isolated in 2014 (DOAB 397 and DOAB 395) compared with the type strain, NCPPB 2581 (isolated over 40 years ago). The proteomes of strains DOAB 395 and DOAB 397 exhibited a 99.2% homology but had 92.1 and 91.8% homology, respectively, with strain NCPPB 2581. The majority (99.9%) of the protein sequences had a 99.6 to 100% homology between C. michiganensis subsp. nebraskensis strains DOAB 395 and DOAB 397, with only four protein sequences (0.1%) exhibiting a similarity <70%. In contrast, 3.0% of the protein sequences of strain DOAB 395 or DOAB 397 showed low homologies (<70%) with the type strain NCPPB 2581. The genome data were exploited for the development of a multiplex TaqMan real-time polymerase chain reaction (PCR) tool for rapid detection of C. michiganensis subsp. nebraskensis. The specificity of the assay was validated using 122 strains of Clavibacter and non-Clavibacter spp. A blind test and naturally infected leaf samples were used to confirm specificity. The sensitivity (0.1 to 1.0 pg) compared favorably with previously reported real-time PCR assays. This tool should fill the current gap for a reliable diagnostic technique.

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Draft Genome Sequence of the Wood-Decaying Fungus Xylaria sp. BCC 1067

Microbiology Resource Announcements ◽

10.1128/mra.00512-19 ◽

2019 ◽

Vol 8 (25) ◽

Author(s):

Sawannee Sutheeworapong ◽

Nuthatai Suteerapongpan ◽

Prasobsook Paenkaew ◽

Peerada Prommeenate ◽

Supapon Cheevadhanarak ◽

...

Keyword(s):

Real Time ◽

Genome Sequence ◽

Single Molecule ◽

Draft Genome ◽

Draft Genome Sequence ◽

Lignocellulolytic Enzymes ◽

Sequencing Technology ◽

Protein Coding ◽

Protein Coding Genes ◽

Technology Analysis

Xylaria sp. BCC 1067 is a wood-decaying fungus which is capable of producing lignocellulolytic enzymes. Based on the results of a single-molecule real-time sequencing technology analysis, we present the first draft genome of Xylaria sp. BCC 1067, comprising 54.1 Mb with 12,112 protein-coding genes.

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Genome Sequence of a Minacovirus Strain from a Farmed Mink in The Netherlands

Microbiology Resource Announcements ◽

10.1128/mra.01451-20 ◽

2021 ◽

Vol 10 (8) ◽

Author(s):

Kirsty T. T. Kwok ◽

Myrna M. T. de Rooij ◽

Felisita F. Sinartio ◽

Lidwien A. M. Smit ◽

Marion P. G. Koopmans ◽

...

Keyword(s):

Severe Acute Respiratory Syndrome ◽

The Netherlands ◽

Real Time ◽

Genome Sequence ◽

Deep Sequencing ◽

Real Time Pcr ◽

Fecal Sample ◽

Viral Genome ◽

Rt Pcr ◽

Content Type

ABSTRACT We report the genome sequence of a Minacovirus strain identified from a fecal sample from a farmed mink (Neovison vison) in The Netherlands that was tested negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using real-time PCR (RT-PCR). The viral genome sequence was obtained using agnostic deep sequencing.

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Identification of DNA Signatures Suitable for Use in Development of Real-Time PCR Assays by Whole-Genome Sequence Approaches: Use of Streptococcus pyogenes in a Pilot Study

Journal of Clinical Microbiology ◽

10.1128/jcm.01155-12 ◽

2012 ◽

Vol 50 (8) ◽

pp. 2770-2773 ◽

Cited By ~ 11

Author(s):

G.-C. Hung ◽

K. Nagamine ◽

B. Li ◽

S.-C. Lo

Keyword(s):

Pilot Study ◽

Real Time ◽

Genome Sequence ◽

Streptococcus Pyogenes ◽

Real Time Pcr ◽

Whole Genome Sequence ◽

Whole Genome ◽

Pcr Assays

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Draft Genome Sequence of Leishmania tarentolae Parrot Tar II, Obtained by Single-Molecule Real-Time Sequencing

Microbiology Resource Announcements ◽

10.1128/mra.00050-20 ◽

2020 ◽

Vol 9 (21) ◽

Author(s):

Yasuyuki Goto ◽

Akihiro Kuroki ◽

Kengo Suzuki ◽

Junya Yamagishi

Keyword(s):

Real Time ◽

Genome Sequence ◽

Single Molecule ◽

Genome Assembly ◽

Complete Genome ◽

Draft Genome ◽

Protozoan Parasite ◽

Leishmania Tarentolae ◽

Content Type ◽

Genome Information

ABSTRACT Leishmania tarentolae is a protozoan parasite of lizards and is nonpathogenic to mammals. Genome information for the nonpathogenic species will facilitate an understanding of the pathology caused by species pathogenic to mammals. Here, we report resequencing of the L. tarentolae genome with a single-molecule real-time (SMRT) sequencer to provide a more complete genome assembly.

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Draft Genome Sequence of a Metabolically Diverse Antarctic Supraglacial Stream Organism, Polaromonas sp. Strain CG9_12, Determined Using Pacific Biosciences Single-Molecule Real-Time Sequencing Technology

Genome Announcements ◽

10.1128/genomea.01242-14 ◽

2014 ◽

Vol 2 (6) ◽

Author(s):

H. J. Smith ◽

C. M. Foreman ◽

T. Ramaraj

Keyword(s):

Real Time ◽

Genome Sequence ◽

Single Molecule ◽

Draft Genome ◽

Draft Genome Sequence ◽

Sequencing Technology ◽

Pacific Biosciences

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Draft Genome Sequence of Bacillus cereus LCR12, a Plant Growth–Promoting Rhizobacterium Isolated from a Heavy Metal–Contaminated Environment

Genome Announcements ◽

10.1128/genomea.01041-16 ◽

2016 ◽

Vol 4 (5) ◽

Cited By ~ 3

Author(s):

Eleonora Egidi ◽

Jennifer L. Wood ◽

Elizabeth Mathews ◽

Edward Fox ◽

Wuxing Liu ◽

...

Keyword(s):

Heavy Metal ◽

Plant Growth ◽

Bacillus Cereus ◽

Genome Sequence ◽

Contaminated Soils ◽

Potential Application ◽

Genetic Basis ◽

Draft Genome ◽

Plant Growth Promoting ◽

Growth Promoting

Bacillus cereus LCR12 is a plant growth–promoting rhizobacterium, isolated from a heavy metal–contaminated environment. The 6.01-Mb annotated genome sequence provides the genetic basis for revealing its potential application to remediate contaminated soils in association with plants.

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Draft Genome Sequence of Pseudoalteromonas luteoviolacea HI1, Determined Using Roche 454 and PacBio Single-Molecule Real-Time Hybrid Sequencing

Genome Announcements ◽

10.1128/genomea.01590-14 ◽

2015 ◽

Vol 3 (1) ◽

Cited By ~ 4

Author(s):

Audrey Y. Asahina ◽

Michael G. Hadfield

Keyword(s):

Real Time ◽

Genome Sequence ◽

Single Molecule ◽

Draft Genome ◽

Draft Genome Sequence ◽

Roche 454

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Circovirus in Blood of a Febrile Horse with Hepatitis

Viruses ◽

10.3390/v13050944 ◽

2021 ◽

Vol 13 (5) ◽

pp. 944

Author(s):

Alvin Hui ◽

Eda Altan ◽

Nathan Slovis ◽

Caitlin Fletcher ◽

Xutao Deng ◽

...

Keyword(s):

New Species ◽

Real Time ◽

Genome Sequence ◽

Real Time Pcr ◽

Sanger Sequencing ◽

Viral Metagenomics ◽

Nucleotide Identity ◽

Wide Range ◽

Asymptomatic Infections ◽

A New Species

Circoviruses infect vertebrates where they can result in a wide range of disease signs or in asymptomatic infections. Using viral metagenomics we analyzed a pool of five sera from four healthy and one sick horse. Sequences from parvovirus-H, equus anellovirus, and distantly related to mammalian circoviruses were recognized. PCR identified the circovirus reads as originating from a pregnant mare with fever and hepatitis. That horse’s serum was also positive by real time PCR for equine parvovirus H and negative for the flavivirus equine hepacivirus. The complete circular genome of equine circovirus 1 strain Charaf (EqCV1-Charaf) was completed using PCR and Sanger sequencing. EqCV1 replicase showed 73–74% identity to those of their closest relatives, pig circoviruses 1/2, and elk circovirus. The closest capsid proteins were from the same ungulate circoviruses with 62–63% identity. The overall nucleotide identity of 72% to its closest relative indicates that EqCV1 is a new species in the Circovirus genus, the first reported in genus Equus. Whether EqCV1 alone or in co-infections can result in disease and its prevalence in different equine populations will require further studies now facilitated using EqCV1′s genome sequence.

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