scholarly journals Closed Genome Sequence of Salmonella enterica Serovar Richmond Strain CFSAN000191, Obtained with Nanopore Sequencing

2018 ◽  
Vol 7 (23) ◽  
Author(s):  
Narjol González-Escalona ◽  
Kuan Yao ◽  
Maria Hoffmann
Keyword(s):  
Genome Sequence ◽  
Salmonella Enterica ◽  
Nanopore Sequencing ◽  
Short Read ◽  
Content Type ◽  
Short Read Sequencing ◽  
Long Read

Here we report the genome sequence of Salmonella enterica serovar Richmond strain CFSAN000191, isolated from tilapia from Thailand in 2005. The genome was determined by a combination of long-read and short-read sequencing.

scholarly journals Closed Genome Sequences of Three Salmonella enterica Strains Belonging to Serovars Saintpaul, Weltevreden, and Thompson, Isolated from Mexico

2019 ◽  
Vol 8 (28) ◽  
Author(s):  
Narjol Gonzalez-Escalona ◽  
J. R. Aguirre-Sánchez ◽  
J. R. Ibarra-Rodríguez ◽  
C. Chaidez-Quiroz ◽  
Jaime Martinez-Urtaza
Keyword(s):  
River Water ◽  
Salmonella Enterica ◽  
Genome Sequences ◽  
Short Read ◽  
Content Type ◽  
Short Read Sequencing ◽  
Long Read ◽  
Sequence Types

Here, we report the genome sequences of three Salmonella enterica strains belonging to serovars Weltevreden (CFSAN047349), Saintpaul (CFSAN047351), and Thompson (CFSAN047352), isolated from river water in Sinaloa, Mexico. The genomes were closed by a combination of long-read and short-read sequencing. The strain sequence types (STs) are ST365, ST50, and ST26, respectively.

scholarly journals Complete Genome Sequence of Rubrobacter xylanophilus Strain AA3-22, Isolated from Arima Onsen in Japan

2019 ◽  
Vol 8 (34) ◽  
Author(s):  
Natsuki Tomariguchi ◽  
Kentaro Miyazaki
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Hot Spring ◽  
Sequencing Data ◽  
Short Read ◽  
Content Type ◽  
Short Read Sequencing ◽  
Oxford Nanopore ◽  
Long Read

Rubrobacter xylanophilus strain AA3-22, belonging to the phylum Actinobacteria, was isolated from nonvolcanic Arima Onsen (hot spring) in Japan. Here, we report the complete genome sequence of this organism, which was obtained by combining Oxford Nanopore long-read and Illumina short-read sequencing data.

scholarly journals Complete Genome Sequence of Vibrio rotiferianus Strain AM7

2020 ◽  
Vol 9 (21) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Apirak Wiseschart ◽  
Kusol Pootanakit ◽  
Kei Kitahara
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
The Novel ◽  
Sequencing Data ◽  
Short Read ◽  
Content Type ◽  
Short Read Sequencing ◽  
Oxford Nanopore ◽  
Long Read

ABSTRACT We isolated the novel strain Vibrio rotiferianus AM7 from the shell of an abalone. In this article, we report the complete genome sequence of this organism, which was obtained by combining Oxford Nanopore long-read and Illumina short-read sequencing data.

scholarly journals Closed Genome Sequences of Two Clostridium botulinum Strains Obtained by Nanopore Sequencing

2018 ◽  
Vol 7 (9) ◽  
Author(s):  
Narjol Gonzalez-Escalona ◽  
Julie Haendiges ◽  
Jesse D. Miller ◽  
Shashi K. Sharma
Keyword(s):  
Environmental Sample ◽  
Clostridium Botulinum ◽  
Clinical Sample ◽  
Nanopore Sequencing ◽  
Genome Sequences ◽  
Short Read ◽  
Content Type ◽  
Short Read Sequencing ◽  
Long Read

Here we report the genome sequences of two toxin-producing Clostridium botuli num strains, one environmental sample (83F) and one clinical sample (CDC51232). The genomes were closed by a combination of long-read and short-read sequencing.

scholarly journals Closed Genome Sequence of a Salmonella enterica Serotype Senftenberg Strain Carrying the mcr-9 Gene Isolated from Broken Chicken Eggshells in Trinidad and Tobago

2021 ◽  
Vol 10 (21) ◽  
Author(s):  
Meghan Maguire ◽  
Anisa S. Khan ◽  
Abiodun A. Adesiyun ◽  
Karla Georges ◽  
Narjol Gonzalez-Escalona
Keyword(s):  
Trinidad And Tobago ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Salmonella Enterica ◽  
Complete Genome ◽  
Foodborne Pathogen ◽  
Sequence Type ◽  
Short Read ◽  
Content Type ◽  
Short Read Sequencing

Salmonella enterica is a highly important foodborne pathogen worldwide. We report the complete genome sequence of a sequence type 14 Salmonella enterica serotype Senftenberg strain carrying the mcr-9 gene in a plasmid isolated from broken chicken eggshells in Trinidad and Tobago, obtained by using a combination of long- and short-read sequencing.

scholarly journals Complete Genome Sequence of Multidrug-Resistant Strain Nocardia wallacei FMUON74, Isolated from a Sputum Culture

2020 ◽  
Vol 9 (47) ◽  
Author(s):  
Masahiro Toyokawa ◽  
Makoto Taniguchi ◽  
Kazuma Uesaka ◽  
Keiko Nishimura
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Resistant Strain ◽  
Complete Genome ◽  
Hybrid Approach ◽  
Multidrug Resistant ◽  
Content Type ◽  
Short Read Sequencing ◽  
Long Read ◽  
Multidrug Resistant Strain

ABSTRACT Nocardia wallacei is one of the members of the N. transvalensis complex which possess a highly unique susceptibility pattern. Here, we describe the closed complete genome sequence of the multidrug-resistant strain N. wallacei FMUON74, which was obtained using a hybrid approach combining Nanopore long-read sequencing and Illumina and DNBseq short-read sequencing.

scholarly journals Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12

2021 ◽  
Vol 10 (27) ◽  
Author(s):  
Kristian Jensen ◽  
Kosai Al-Nakeeb ◽  
Anna Koza ◽  
Ahmad A. Zeidan
Keyword(s):  
Genome Sequence ◽  
Probiotic Bacterium ◽  
Content Type ◽  
Short Read Sequencing ◽  
Bifidobacterium Animalis ◽  
Oxford Nanopore ◽  
Hybrid Genome ◽  
Long Read ◽  
Sequencing Platforms ◽  
Oxford Nanopore Technologies

The genome of Bifidobacterium animalis subsp. lactis BB-12 was sequenced using Oxford Nanopore Technologies long-read and Illumina short-read sequencing platforms. A hybrid genome assembly approach was used to construct an updated complete genome sequence for BB-12 containing 1,944,152 bp, with a G+C content of 60.5% and 1,615 genes.

scholarly journals Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Kottbus Strain Kharkiv, Isolated from a Commercial Pork Production Facility in Ukraine

2020 ◽  
Vol 9 (49) ◽  
Author(s):  
Vasiliy Arefiev ◽  
Ganna Kovalenko ◽  
Maciej Frant ◽  
Tetiana Chumachenko ◽  
Yuliia Polyvianna ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Salmonella Enterica ◽  
Complete Genome ◽  
Human Infection ◽  
Production Facility ◽  
Content Type ◽  
Pork Production ◽  
Long Read

ABSTRACT The complete genome of Salmonella enterica subsp. enterica serovar Kottbus strain Kharkiv (serogroup C2-C3), which was isolated from a commercial pork production facility in Kharkiv, Ukraine, was assembled using long-read Nanopore sequences. A single circular contig (4,799,045 bp) comprised a complete chromosome encoding antibiotic resistance, highlighting the risk of cross-species livestock and human infection.

scholarly journals Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) orientalis, Isolate LSCM4, Strain LV768

2021 ◽  
Vol 10 (36) ◽  
Author(s):  
Hatim Almutairi ◽  
Michael D. Urbaniak ◽  
Michelle D. Bates ◽  
Narissara Jariyapan ◽  
Waleed S. Al-Salem ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Short Read ◽  
Content Type ◽  
Long Read ◽  
Kinetoplastid Parasite

Leishmania (Mundinia) orientalis is a kinetoplastid parasite first isolated in 2014 in Thailand. We report the complete genome sequence of L. ( M. ) orientalis , sequenced using combined short-read and long-read technologies. This will facilitate greater understanding of this novel pathogen and its relationship to other members of the subgenus Mundinia .

scholarly journals Long-Read Sequencing of the Zebrafish Genome Reorganizes Genomic Architecture

2021 ◽  
Author(s):  
Yelena Chernyavskaya ◽  
Xiaofei Zhang ◽  
Jinze Liu ◽  
Jessica S. Blackburn
Keyword(s):  
Low Complexity ◽  
Zebrafish Genome ◽  
Nanopore Sequencing ◽  
Sequencing Technology ◽  
Short Read ◽  
Short Read Sequencing ◽  
Genomic Landscape ◽  
Long Reads ◽  
Long Read ◽  
Sequencing Platforms

Nanopore sequencing technology has revolutionized the field of genome biology with its ability to generate extra-long reads that can resolve regions of the genome that were previously inaccessible to short-read sequencing platforms. Although long-read sequencing has been used to resolve several vertebrate genomes, a nanopore-based zebrafish assembly has not yet been released. Over 50% of the zebrafish genome consists of difficult to map, highly repetitive, low complexity elements that pose inherent problems for short-read sequencers and assemblers. We used nanopore sequencing to improve upon and resolve the issues plaguing the current zebrafish reference assembly (GRCz11). Our long-read assembly improved the current resolution of the reference genome by identifying 1,697 novel insertions and deletions over 1Kb in length and placing 106 previously unlocalized scaffolds. We also discovered additional sites of retrotransposon integration previously unreported in GRCz11 and observed their expression in adult zebrafish under physiologic conditions, implying they have active mobility in the zebrafish genome and contribute to the ever-changing genomic landscape.

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