scholarly journals Whole-Genome Sequencing of Tibetan Macaque (Macaca thibetana) Provides New Insight into the Macaque Evolutionary History

2014 ◽  
Vol 31 (6) ◽  
pp. 1475-1489 ◽  
Author(s):  
Zhenxin Fan ◽  
Guang Zhao ◽  
Peng Li ◽  
Naoki Osada ◽  
Jinchuan Xing ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Evolutionary History ◽  
Whole Genome ◽  
Macaca Thibetana ◽  
Tibetan Macaque ◽  
Insight Into

scholarly journals Evolutionary history of Tibetans inferred from whole-genome sequencing

PLoS Genetics ◽  
2017 ◽  
Vol 13 (4) ◽  
pp. e1006675 ◽  
Author(s):  
Hao Hu ◽  
Nayia Petousi ◽  
Gustavo Glusman ◽  
Yao Yu ◽  
Ryan Bohlender ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Evolutionary History ◽  
Whole Genome ◽  
History Of

scholarly journals Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1803
Author(s):  
Jitendra Singh ◽  
Anvita Gupta Malhotra ◽  
Debasis Biswas ◽  
Prem Shankar ◽  
Leena Lokhande ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Spike Protein ◽  
Whole Genome ◽  
The Novel ◽  
Genome Sequences ◽  
Second Wave ◽  
Insight Into

India experienced a tragic second wave after the end of March 2021, which was far more massive than the first wave and was driven by the emergence of the novel delta variant (B.1.617.2) of the SARS-CoV-2 virus. In this study, we explored the local and national landscape of the viral variants in the period immediately preceding the second wave to gain insight into the mechanism of emergence of the delta variant and thus improve our understanding of the causation of the second wave. We randomly selected 20 SARS-CoV-2 positive samples diagnosed in our lab between 3 February and 8 March 2021 and subjected them to whole genome sequencing. Nine of the 20 sequenced genomes were classified as kappa variant (B.1.617.1). The phylogenetic analysis of pan-India SARS-CoV-2 genome sequences also suggested the gradual replacement of the α variant with the kappa variant during this period. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. This study demonstrates the predominance of the kappa variant in the period immediately prior to the second wave and underscores its role as the “bridging variant” between the α and delta variants that drove the first and second waves of COVID-19 in India, respectively.

scholarly journals Insight Into Whole Genome of Aeromonas veronii Isolated From Freshwater Fish by Resistome Analysis Reveal Extensively Antibiotic Resistant Traits

2021 ◽  
Vol 12 ◽  
Author(s):  
Rungnapa Sakulworakan ◽  
Putita Chokmangmeepisarn ◽  
Nguyen Dinh-Hung ◽  
Elayaraja Sivaramasamy ◽  
Ikuo Hirono ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Whole Genome Sequencing ◽  
Freshwater Fish ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Antibiotic Resistant ◽  
Aeromonas Veronii ◽  
Insight Into

Aeromonas veronii outbreaks in tilapia farming caused relatively high mortalities, and the bacteria was resistant to many kinds of antimicrobials used in Thailand aquaculture. According to the CLSI standard, the determination of antimicrobials efficacy has been limited to phenotypic analyses, and a genomics study is required. This research aimed to analyze the resistome of A. veronii isolated from diseased tilapia in Chainat, Nong Khai, and Uttaradit provinces in Thailand. A total of 12 isolates of A. veronii were identified based on the gyrB sequencing and then, the MIC values to eight antimicrobials (AMP, AML, GEN, ENR, OXO, OTC, SXT, and FFC) were determined. According to the MIC patterns, whole genome sequencing (WGS) of five representatives and resistome analysis were performed, including 15 genomes of A. veronii isolated from freshwater fish available in the NCBI. All tilapia isolates were susceptible to FFC but resistant to AML and AMP while OTC resistance was the most dominant. In addition to the WGS analysis, 4.5 Mbp of A. veronii was characterized. A total of 20 ARGs were detected by resistome analysis and 16 genes were shared among the A. veronii population. In conclusion, A. veronii strains isolated from tilapia exhibited a resistance to several antimicrobials and multidrug resistance (MDR) which was related to the presence of multiple ARGs. Aeromonas veronii shared the ARGs in their population worldwide with a possibility of a plasmid-mediated acquisition due to the presence of resistance islands.

scholarly journals Whole Genome Sequencing in Psychiatric Disorders: the WGSPD Consortium

2017 ◽  
Author(s):  
Stephan J. Sanders ◽  
Benjamin M. Neale ◽  
Hailiang Huang ◽  
Donna M. Werling ◽  
Joon-Yong An ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Psychiatric Disorders ◽  
Genome Sequencing ◽  
Rare Variants ◽  
Autism Spectrum ◽  
Whole Genome ◽  
Complex Disorders ◽  
Computationally Intensive ◽  
Insight Into

AbstractAs technology advances, whole genome sequencing (WGS) is likely to supersede other genotyping technologies. The rate of this change depends on its relative cost and utility. Variants identified uniquely through WGS may reveal novel biological pathways underlying complex disorders and provide high-resolution insight into when, where, and in which cell type these pathways are affected. Alternatively, cheaper and less computationally intensive approaches may yield equivalent insights. Understanding the role of rare variants in the noncoding gene-regulating genome, through pilot WGS projects, will be critical to determine which of these two extremes best represents reality. With large cohorts, well-defined risk loci, and a compelling need to understand the underlying biology, psychiatric disorders have a role to play in this preliminary WGS assessment. The WGSPD consortium will integrate data for 18,000 individuals with psychiatric disorders, beginning with autism spectrum disorder, schizophrenia, bipolar disorder, and major depressive disorder, along with over 150,000 controls.

scholarly journals Genomic and phylogenetic analysis ofSalmonellaTyphimurium and its monophasic variants responsible for invasive endemic infections in Colombia

2019 ◽  
Author(s):  
Yan Li ◽  
Caisey V. Pulford ◽  
Paula Díaz ◽  
Blanca M. Perez-Sepulveda ◽  
Carolina Duarte ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Nalidixic Acid ◽  
Genome Sequencing ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Large Scale ◽  
Multidrug Resistant ◽  
Human Infection ◽  
Sequence Type ◽  
Whole Genome

AbstractSalmonellosis is an endemic human infection, associated with both sporadic cases and outbreaks throughout Colombia. Typhimurium is the most common Colombian serovar ofSalmonella enterica, responsible for 32.5% of theSalmonellainfections. Whole genome sequencing (WGS) is being used increasingly in Europe and the USA to study the epidemiology ofSalmonella, but there has not yet been a WGS-based analysis ofSalmonellaassociated with bloodstream infection in Colombia. Here, we analysed 209 genome sequences of ColombianS. Typhimurium and monophasicS. 4,[5],12:i:-isolates from Colombia from 1999 to 2017. We used a core genome-based maximum likelihood tree to define seven distinct clusters which were predominantly Sequence Type (ST) 19 isolates. We also identified the first ST313 and monophasic ST34 isolates to be reported in Colombia. The history of each cluster was reconstructed with a Bayesian tree to reveal a timeline of evolution. Cluster 7 was closely related to European multidrug-resistant (MDR) DT104. Cluster 4 became the dominant variant ofSalmonellain 2016, and resistance to nalidixic acid was associated with a plasmid-encodedqnrB19gene. Our findings suggest multiple transfers ofS. Typhimurium between Europe and Colombia.Author summaryThe large-scale genome sequencing ofSalmonellaTyphimurium and monophasicSalmonella4,[5],12:i:-involved bloodstream isolates from Colombia. The two serovars were responsible for about 1/3 ofSalmonellainfections in Colombia in the past 20 years. To identify the population structure we used Whole Genome Sequencing, performedin silicosequence typing, obtained phylogenetic trees, inferred the evolutionary history, detected the plasmids and prophages, and associated the antibiotic resistance (AMR) genotype with phenotype. Different clusters showed temporal replacement. The Colombian sequence type 313 was distinct from African lineages due to the absence of a key virulence-related gene,bstA. One of the Colombian clusters is likely to belong to the global epidemic of DT104, according to the evolutionary history and the AMR profile. The most common cluster in recent years was resistant to nalidixic acid and carried a plasmid-mediated antibiotic resistant geneqnrB19. Our findings will inform the ongoing efforts to combat Salmonellosis by Colombian public health departments.

Sign in / Sign up

Export Citation Format

Share Document