scholarly journals Complete Genome Sequence of Peste des Petits Ruminants Virus from Georgia, 2016

2017 ◽  
Vol 5 (41) ◽  
Author(s):  
Paulina Z. Rajko-Nenow ◽  
Tabitha G. Cunliffe ◽  
John T. Flannery ◽  
Honorata M. Ropiak ◽  
Lasha Avaliani ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sanger Sequencing ◽  
Peste Des Petits Ruminants ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Lineage Iv ◽  
Generation Sequencing

ABSTRACT We report here the complete genome sequence of a peste des petits ruminants virus (PPRV) from the first outbreak of the disease in Georgia in January 2016. Genome sequencing was performed using Illumina next-generation sequencing technology in conjunction with Sanger sequencing. This PPRV/Georgia/Tbilisi/2016 genome sequence clustered within lineage IV PPRV viruses.

scholarly journals Complete Genome Sequence of Bovine Adenovirus Type 7 Strain Fukuroi, Isolated from a Cow with Respiratory Disease

2021 ◽  
Vol 10 (10) ◽  
Author(s):  
Asuka Kumagai ◽  
Sayo Kajikawa ◽  
Ayako Miyazaki ◽  
Shinichi Hatama
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Viral Genome ◽  
Complete Genome ◽  
Adenovirus Type ◽  
Prototype Strain ◽  
Sequencing Technology ◽  
Bovine Adenovirus ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

ABSTRACT We determined the complete genome sequence of the bovine adenovirus type 7 prototype strain Fukuroi using next-generation sequencing technology. We found that the viral genome is 30,034 bp long and has the shortest inverted terminal repeats among known adenoviruses.

scholarly journals Complete Genome Sequence of Ornithogalum Mosaic Virus Infecting Gladiolus spp. in South Korea

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Sang-Yun Cho ◽  
Seungmo Lim ◽  
Hongsup Kim ◽  
Seung-In Yi ◽  
Jae Sun Moon
Keyword(s):  
Next Generation Sequencing ◽  
South Korea ◽  
Mosaic Virus ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sanger Sequencing ◽  
Sequence Information ◽  
Next Generation ◽  
Generation Sequencing

We report here the first complete genome sequence of Ornithogalum mosaic virus (OrMV) isolated from Taean, South Korea, in 2011, which was obtained by next-generation sequencing and Sanger sequencing. The sequence information provided here may serve as a potential reference for other OrMV isolates.

scholarly journals De Novo Genome Assembly of a Foxtail Millet Cultivar Huagu11 Uncovered the Genetic Difference to the Cultivar Yugu1, and the Genetic Mechanism of Imazethapyr Tolerance

2021 ◽  
Author(s):  
Jie Wang ◽  
Shiming Li ◽  
Lei Lan ◽  
Mushan Xie ◽  
Shu Cheng ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Reference Genome ◽  
Foxtail Millet ◽  
Setaria Italica ◽  
Genome Comparison ◽  
Sequencing Technology ◽  
High Quality ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

Abstract Background: Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. Results: Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97% and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. Conclusions: A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was found that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.

scholarly journals Complete Genome Sequence of Matlo Bat Lyssavirus

2021 ◽  
Vol 10 (20) ◽  
Author(s):  
Colyn S. Grobler ◽  
Jessica Coertse ◽  
Wanda Markotter
Keyword(s):  
South Africa ◽  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Novel Species ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequencing Technologies ◽  
Generation Sequencing

ABSTRACT The genus Lyssavirus includes rabies virus as well as multiple diverse and recently described novel species. Using next-generation sequencing technologies, we have obtained the whole-genome sequence of Matlo bat lyssavirus, which was isolated from a Natal long-fingered bat (Miniopterus natalensis) in South Africa.

scholarly journals Complete Genome Sequences of Lineage IV Peste des Petits Ruminants Viruses from the Indian Subcontinent

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Aliyu Abdullahi Masdooq ◽  
Rahul Mohanchandra Pawar ◽  
Aravindh Babu R. Parthiban ◽  
K. Ragavendhar ◽  
G. Sundarapandian ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Indian Subcontinent ◽  
Peste Des Petits Ruminants ◽  
Genome Sequences ◽  
First Report ◽  
Lineage Iv

The complete genome sequences of two virulent lineage IV peste des petits ruminants viruses (PPRVs) isolated from clinically infected goats in the Indian subcontinent are reported here. This is the first report of a complete genome sequence of a virulent PPRV isolate from India in recent decades.

scholarly journals Complete Genome Sequence of a Novel Human Gammapapillomavirus Isolated from Skin

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Rosario N. Brancaccio ◽  
Alexis Robitaille ◽  
Sankhadeep Dutta ◽  
Dana E. Rollison ◽  
Nicole Fischer ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frame ◽  
Next Generation ◽  
Degenerate Pcr ◽  
Reading Frame ◽  
Generation Sequencing

ABSTRACT A novel human papillomavirus (HPV ICB1) was fully characterized from a skin swab by using a sensitive degenerate PCR protocol combined with next-generation sequencing. The L1 open reading frame of HPV ICB1 shares 70.54% nucleotide homology with its closest relative, HPV164, and thus constitutes a novel human gammapapillomavirus.

scholarly journals Complete Genome Characterization of the Porcine Deltacoronavirus HKD/JPN/2016, Isolated in Japan, 2016

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Tohru Suzuki ◽  
Jun Hayakawa ◽  
Seiichi Ohashi
Keyword(s):  
Next Generation Sequencing ◽  
High Mortality ◽  
Complete Genome ◽  
Swine Farm ◽  
Sequencing Technology ◽  
Genome Characterization ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing Technology ◽  
Generation Sequencing

ABSTRACT In 2016, an outbreak of diarrhea with high mortality in piglets occurred on a swine farm in Hokkaido prefecture, Japan. The causative porcine deltacoronavirus HDK/JPN/2016 was isolated from intestinal samples of the dead piglets on LLC-PK1 cells. The complete genome of HKD/JPN/2016 was sequenced and analyzed by next-generation sequencing technology.

scholarly journals Complete Genome Sequence of an Emergent Recombinant GII.P16-GII.2 Norovirus Strain Associated with an Epidemic Spread in the Winter of 2016-2017 in Hong Kong, China

2017 ◽  
Vol 5 (20) ◽  
Author(s):  
Martin C. W. Chan ◽  
Kirsty Kwok ◽  
Tin-Nok Hung ◽  
Lok-Yi Chan ◽  
Paul K. S. Chan
Keyword(s):  
Hong Kong ◽  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Nucleotide Identity ◽  
Epidemic Spread ◽  
Next Generation ◽  
Generation Sequencing

ABSTRACT A new recombinant norovirus, GII.P16-GII.2, emerged in the winter of 2016-2017. Here, we report the complete genome of this strain (Hu/GII/HK/2016/GII.P16-GII.2/CUHK-NS-1082), which was collected from a patient hospitalized with gastroenteritis in September 2016 in Hong Kong, China, and sequenced using next-generation sequencing. This genome had a 95.2% nucleotide identity to the closest sequence in GenBank.

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