scholarly journals Complete Genome Sequence of African Swine Fever Virus Isolated from a Domestic Pig in Timor-Leste, 2019

2021 ◽  
Vol 10 (26) ◽  
Author(s):  
Patrick Mileto ◽  
Felisiano da Conceição ◽  
Vittoria Stevens ◽  
David Cummins ◽  
Andrea Certoma ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Domestic Pig ◽  
Oxford Nanopore ◽  
Timor Leste ◽  
Long Read

Here, we report the complete genome sequence of the African swine fever virus (ASFV) isolate ASFV/Timor-Leste/2019/1, isolated from a domestic pig during the first outbreak of ASF in Timor-Leste in 2019. Using target enrichment short-read Illumina data combined with long-read Oxford Nanopore data, we assembled a full-length genome sequence of 192,237 bp.

scholarly journals Complete Genome Sequence of a Virulent African Swine Fever Virus from a Domestic Pig in Ukraine

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Ganna Kovalenko ◽  
Anne-Lise Ducluzeau ◽  
Liudmyla Ishchenko ◽  
Mykola Sushko ◽  
Maryna Sapachova ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Base Pairs ◽  
Domestic Pig ◽  
Long Read ◽  
Full Length Genome

Here, we report the complete genome sequence of an African swine fever (ASF) virus (ASFV/Kyiv/2016/131) isolated from the spleen of a domestic pig in Ukraine with a lethal case of African swine fever. Using only long-read Nanopore sequences, we assembled a full-length genome of 191,911 base pairs in a single contig.

scholarly journals Complete genome sequence of an African swine fever virus (ASFV POL/2015/Podlaskie) determined directly from pig erythrocyte-associated nucleic acid

2018 ◽  
Vol 261 ◽  
pp. 14-16 ◽  
Author(s):  
Ann Sofie Olesen ◽  
Louise Lohse ◽  
Marlene Danner Dalgaard ◽  
Grzegorz Woźniakowski ◽  
Graham J. Belsham ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus

scholarly journals Complete Genome Sequence of an African Swine Fever Virus Isolate from Sardinia, Italy

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Fredrik Granberg ◽  
Claudia Torresi ◽  
Annalisa Oggiano ◽  
Maja Malmberg ◽  
Carmen Iscaro ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Virus Isolate ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Genomic Regions ◽  
Virus Isolates

Previous genetic characterization of African swine fever virus isolates from the Italian island of Sardinia, where the virus has been present since 1978, has largely been limited to a few selected genomic regions. Here, we report the complete genome sequence of the isolate 47/Ss/08 collected during an outbreak in 2008.

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 Combined short and long-read sequencing reveals a complex transcriptomic architecture of African swine fever virus

2020 ◽  
Author(s):  
Gábor Torma ◽  
Dóra Tombácz ◽  
Zsolt Csabai ◽  
Norbert Moldován ◽  
István Mészáros ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
African Swine Fever Virus ◽  
Genetic Regulation ◽  
African Swine Fever ◽  
Fever Virus ◽  
Current View ◽  
Preparation Methods ◽  
Rna Molecules ◽  
Oxford Nanopore ◽  
Long Read

ABSTRACTAfrican swine fever virus (ASFV) is a large DNA virus belonging to the Asfarviridae family. Despite its agricultural importance, little is known about the fundamental molecular mechanisms of this pathogen. Understanding of genetic regulation provides new insights into the virus pathogenicity, which can help prevent epidemics. Short-read sequencing (SRS) is able to produce a huge amount of high-precision sequencing reads for transcriptomic profiling, but it is inefficient for the comprehensive annotation of transcriptomes. Long-read sequencing (LRS) is able to overcome some of the limitations of SRS, but they also have drawbacks, such as low-coverage and high error rate. The limitations of the two approaches can be surmounted by the combined use of these techniques. In this study, we used Illumina SRS and Oxford Nanopore Technologies LRS platforms with multiple library preparation methods (amplified and direct cDNA sequencings and native RNA sequencing) for constructing the transcriptomic atlas of ASFV. This work identified a large number of novel genes, transcripts and RNA isoforms, and annotated the precise termini of previously described RNA molecules. In contrast to the current view that the ASFV transcripts are monocistronic, we detected a significant extent of polycistronism. A multifaceted meshwork of transcriptional overlaps is also discovered.

scholarly journals Short and Long-read Sequencing Survey of the Dynamic Transcriptomes of African Swine Fever Virus and its Host

2020 ◽  
Author(s):  
Ferenc Olasz ◽  
Dóra Tombácz ◽  
Gábor Torma ◽  
Zsolt Csabai ◽  
Norbert Moldován ◽  
...  
Keyword(s):  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Economic Losses ◽  
Swine Industry ◽  
Rna Molecules ◽  
Oxford Nanopore ◽  
Combined Use ◽  
Long Read ◽  
Low Coverage

AbstractAfrican swine fever virus (ASFV) is an important animal pathogen causing substantial economic losses in the swine industry globally. At present, little is known about the molecular biology of ASFV, including its transcriptome organization. In this study, we applied cutting-edge sequencing approaches, namely the Illumina short-read sequencing (SRS) and the Oxford Nanopore Technologies long-read sequencing (LRS) techniques, together with several library preparation chemistries to analyze the ASFV dynamic transcriptome. SRS can generate a large amount of high-precision sequencing reads, but it is inefficient for identifying long RNA molecules, transcript isoforms and overlapping transcripts. LRS can overcome these limitations, but this approach also has shortcomings, such as its high error rate and the low coverage. Amplification-based LRS techniques produce relatively high read counts but also high levels of spurious transcripts, whereas the non-amplified cDNA and direct RNA sequencing techniques are more precise but achieve lower throughput. The drawbacks of the various technologies can be circumvented by the combined use of these approaches.

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 Coding-Complete Genome Sequence of an African Swine Fever Virus Strain Liv13/33 Isolate from Experimental Transmission between Pigs and Ornithodoros moubata Ticks

2020 ◽  
Vol 9 (17) ◽  
Author(s):  
Amélie Chastagner ◽  
Rémi Pereira de Oliveira ◽  
Evelyne Hutet ◽  
Mireille Le Dimna ◽  
Frédéric Paboeuf ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Virus Strain ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Genotype I ◽  
Experimental Transmission ◽  
Content Type ◽  
Ornithodoros Moubata

Here, we report the coding-complete genome sequence of African swine fever (ASF) virus strain Liv13/33, isolated from experimentally infected pigs and Ornithodoros moubata ticks. The 11 sequences that we obtained harbored no notable differences to each other, and all of them were closely related to the genome sequence of the Mkuzi 1979 strain of genotype I.

scholarly journals Genome Sequences of Five African Swine Fever Virus Genotype IX Isolates from Domestic Pigs in Uganda

2018 ◽  
Vol 7 (13) ◽  
Author(s):  
Charles Masembe ◽  
Vattipally B. Sreenu ◽  
Ana Da Silva Filipe ◽  
Gavin S. Wilkie ◽  
Peter Ogweng ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Genome Sequences ◽  
Virus Genotype ◽  
Domestic Pigs ◽  
Genotype Ix ◽  
Virus Isolates

Complete genome sequences of five African swine fever virus isolates were determined directly from clinical material obtained from domestic pigs in Uganda. Four sequences were essentially identical to each other, and all were closely related to the only known genome sequence of p72 genotype IX.

scholarly journals Complete Genome Sequence of Staphylococcus arlettae Strain P2, Isolated from a Laboratory Environment

2019 ◽  
Vol 8 (45) ◽  
Author(s):  
Hiroki Yu ◽  
Makoto Taniguchi ◽  
Kazuma Uesaka ◽  
Apirak Wiseschart ◽  
Kusol Pootanakit ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Hybrid Approach ◽  
Illumina Miseq ◽  
Sequencing Data ◽  
Content Type ◽  
Short Read Sequencing ◽  
Oxford Nanopore ◽  
Long Read

Staphylococcus arlettae is one coagulase-negative species in the bacterial genus Staphylococcus. Here, we describe the closed complete genome sequence of S. arlettae strain P2, which was obtained using a hybrid approach combining Oxford Nanopore long-read and Illumina MiSeq short-read sequencing data.

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