scholarly journals Comprehensive characterization of horse genome variation by whole-genome sequencing of 88 horses

2018 ◽  
Vol 50 (1) ◽  
pp. 74-77 ◽  
Author(s):  
V. Jagannathan ◽  
V. Gerber ◽  
S. Rieder ◽  
J. Tetens ◽  
G. Thaller ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Genome Variation ◽  
Horse Genome ◽  
Comprehensive Characterization

scholarly journals Comprehensive Characterization of Human Genome Variation by High Coverage Whole-Genome Sequencing of Forty Four Caucasians

PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e59494 ◽  
Author(s):  
Hui Shen ◽  
Jian Li ◽  
Jigang Zhang ◽  
Chao Xu ◽  
Yan Jiang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Human Genome ◽  
Genome Sequencing ◽  
Whole Genome ◽  
High Coverage ◽  
Genome Variation ◽  
Comprehensive Characterization

scholarly journals Comprehensive Characterization of Transgene Integration in a Similar Intragenesis Rice Event Using Paired-end Whole-genome Sequencing Approach

2021 ◽  
Author(s):  
Wenting Xu ◽  
Hanwen Zhang ◽  
Yuchen Zhang ◽  
Rong Li ◽  
Litao Yang
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Rice Chromosome ◽  
Whole Genome ◽  
Transgene Integration ◽  
Gm Rice ◽  
Genome Level ◽  
Comprehensive Characterization

Abstract Efficient, accurate molecular characterization of genetically modified (GM) organisms is challenging, especially for novel transgenic products of cisgenesis/intragenesis transferred with genes/elements of recipient species. Herein, GM rice event G281, involving transfer with native promoters and an RNA interference (RNAi) expression cassette in a process similar to intragenesis, was subjected to molecular characterization using paired-end whole genome sequencing (PE-WGS). The results showed that transgenes integrated at rice chromosome 3 locus 16,439,674 included a 36 bp deletion of rice genomic DNA, and the whole integration contained two copies of the complete transfer DNA (T-DNA) in a head-to-head arrangement. No unintended insertion or backbone sequence of the transformed plasmid were observed at the whole genome level. Molecular characterization of the G281 event will assist risk assessment and application for a commercial license. Additionally, the findings demonstrate the applicability of PE-WGS for molecular characterization of cisgenesis/intragenesis crops.

scholarly journals SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Weili Cai ◽  
Schyler Nunziata ◽  
John Rascoe ◽  
Michael J. Stulberg
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Coverage ◽  
Metagenomic Sample ◽  
Liberibacter Asiaticus

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

First isolation and characterization of Brucella suis from yak

Genome ◽  
2020 ◽  
Vol 63 (8) ◽  
pp. 397-405
Author(s):  
Xiaowen Yang ◽  
Ning Wang ◽  
Xiaofang Cao ◽  
Pengfei Bie ◽  
Zhifeng Xing ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Health And Safety ◽  
Host Cells ◽  
Whole Genome ◽  
Genetic Characteristics ◽  
Qinghai Province ◽  
Isolation And Characterization ◽  
Smooth Strain

Brucella spp., facultative intracellular pathogens that can persistently colonize animal host cells and cause zoonosis, affect public health and safety. A Brucella strain was isolated from yak in Qinghai Province. To detect whether this isolate could cause an outbreak of brucellosis and to reveal its genetic characteristics, several typing and whole-genome sequencing methods were applied to identify its species and genetic characteristics. Phylogenetic analysis based on MLVA and whole-genome sequencing revealed the genetic characteristics of the isolated strain. The results showed that the isolated strain is a B. suis biovar 1 smooth strain, and this isolate was named B. suis QH05. The results of comparative genomics and MLVA showed that B. suis QH05 is not a vaccine strain. Comparison with other B. suis strains isolated from humans and animals indicated that B. suis QH05 may be linked to specific animal and human sources. In conclusion, B. suis QH05 does not belong to the Brucella epidemic species in China, and as the first isolation of B. suis from yak, this strain expands the host range of B. suis.

Characterization of Salmonella enterica Isolates from Selected U.S. Swine Feed Mills by Whole-Genome Sequencing

2020 ◽  
Vol 17 (2) ◽  
pp. 126-136 ◽  
Author(s):  
Valentina Trinetta ◽  
Gabriela Magossi ◽  
Marc W. Allard ◽  
Sandra M. Tallent ◽  
Eric W. Brown ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Whole Genome ◽  
Swine Feed

Whole genome sequencing and characterization of a virulent Newcastle disease virus isolated from an outbreak in Sweden

Virus Genes ◽  
2011 ◽  
Vol 43 (2) ◽  
pp. 261-271 ◽  
Author(s):  
Muhammad Munir ◽  
Anna-Malin Linde ◽  
Siamak Zohari ◽  
Karl Ståhl ◽  
Claudia Baule ◽  
...  
Keyword(s):  
Newcastle Disease Virus ◽  
Whole Genome Sequencing ◽  
Disease Virus ◽  
Genome Sequencing ◽  
Newcastle Disease ◽  
Whole Genome ◽  
Virulent Newcastle Disease Virus

scholarly journals Whole-genome sequencing and characterization of an antibiotic resistant Neisseria meningitidis B isolate from a military unit in Vietnam

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Thach Xuan Tran ◽  
Trang Thu Le ◽  
Long Phi Trieu ◽  
Christopher M. Austin ◽  
Dong Van Quyen ◽  
...  
Keyword(s):  
Neisseria Meningitidis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Antibiotic Resistant ◽  
Military Unit

scholarly journals Characterization of SXT/R391 Integrative and Conjugative Elements in Proteus mirabilis Isolates from Food-Producing Animals in China

2016 ◽  
Vol 60 (3) ◽  
pp. 1935-1938 ◽  
Author(s):  
Chang-Wei Lei ◽  
An-Yun Zhang ◽  
Hong-Ning Wang ◽  
Bi-Hui Liu ◽  
Li-Qin Yang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Proteus Mirabilis ◽  
Whole Genome ◽  
Content Type ◽  
Integrative And Conjugative Elements ◽  
Animal Farms

SXT/R391 integrative and conjugative elements (ICEs) were detected in 8 out of 125Proteus mirabilisisolates from food-producing animals in China. Whole-genome sequencing revealed that seven ICEs were identical to ICEPmiJpn1, carrying the cephalosporinase geneblaCMY-2. Another one, designated ICEPmiChn1, carried five resistance genes. All eight ICEs could be transferred toEscherichia colivia conjugation. The results highlight the idea that animal farms are important reservoir of the SXT/R391 ICE-containingP. mirabilis.

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