scholarly journals Prevalence and Genomic Characterization of Brucella canis Strains Isolated from Kennels, Household, and Stray Dogs in Chile

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2073
Author(s):  
Nicolás Galarce ◽  
Beatriz Escobar ◽  
Eduard Martínez ◽  
Natalia Alvarado ◽  
Gabriela Peralta ◽  
...  
Keyword(s):  
Public Health ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Stray Dogs ◽  
Control Programs ◽  
Official Control ◽  
Brucella Canis ◽  
Genomic Characterization ◽  
Canine Brucellosis

Canine brucellosis caused by Brucella canis is a zoonotic disease that causes reproductive alterations in dogs, such as infertility, abortion, and epididymitis. This pathogen is especially prevalent in South America, and due to the lack of official control programs and the growing trend of adopting dogs it constitutes a public health risk that must be addressed. The aim of this study was to determine the prevalence of B. canis infection in kennel, shelter, and household dogs and to characterize the genomic properties of circulating strains, including ure and virB operons and omp25/31 genes. Samples from 771 dogs were obtained, and the infection was detected by blood culture and/or serology in 7.0% of the animals. The complete ure and virB operons and the omp25/31 genes were detected. Interestingly, we found different single-nucleotide polymorphisms (SNPs) in some of the analyzed genes, which could mean a change in the fitness or virulence of these strains. This study provides further evidence about dogs as a source of B. canis strains that can infect people. This also highlights the need to implement official control programs, including the mandatory testing of dogs, especially stray dogs, before adoption.

scholarly journals From raw reads to trees: Whole genome SNP phylogenetics across the tree of life

2015 ◽  
Author(s):  
Sanaa Afroz Ahmed ◽  
Chien-Chi Lo ◽  
Po-E Li ◽  
Karen W Davenport ◽  
Patrick S.G. Chain
Keyword(s):  
Ad Hoc ◽  
Phylogenetic Reconstruction ◽  
Clinical Samples ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complex Samples ◽  
Phylogenetic Characterization ◽  
Genome Wide ◽  
Genome Assemblies

Next-generation sequencing is increasingly being used to examine closely related organisms. However, while genome-wide single nucleotide polymorphisms (SNPs) provide an excellent resource for phylogenetic reconstruction, to date evolutionary analyses have been performed using different ad hoc methods that are not often widely applicable across different projects. To facilitate the construction of robust phylogenies, we have developed a method for genome-wide identification/characterization of SNPs from sequencing reads and genome assemblies. Our phylogenetic and molecular evolutionary (PhaME) analysis software is unique in its ability to take reads and draft/complete genome(s) as input, derive core genome alignments, identify SNPs, construct phylogenies and perform evolutionary analyses. Several examples using genomes and read datasets for bacterial, eukaryotic and viral linages demonstrate the broad and robust functionality of PhaME. Furthermore, the ability to incorporate raw metagenomic reads from clinical samples with suspected infectious agents shows promise for the rapid phylogenetic characterization of pathogens within complex samples.

scholarly journals Characterization of Single-Nucleotide Polymorphisms in the Tumor Necrosis Factor α Promoter Region and in Lymphotoxin α in Squamous Intraepithelial Lesions, Precursors of Cervical Cancer

2011 ◽  
Vol 4 (6) ◽  
pp. 336-344 ◽  
Author(s):  
Miriam Enriqueta Nieves-Ramirez ◽  
Oswaldo Partida-Rodriguez ◽  
Pedro Eduardo Alegre-Crespo ◽  
Maria del Carmen Tapia-Lugo ◽  
Martha Esthela Perez-Rodriguez
Keyword(s):  
Promoter Region ◽  
Tumor Necrosis ◽  
Tumor Necrosis Factor Α ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Factor Α ◽  
Lymphotoxin Α ◽  
Intraepithelial Lesions ◽  
Necrosis Factor

scholarly journals Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Weizhuo Zhu ◽  
Yiyi Guo ◽  
Yeke Chen ◽  
Dezhi Wu ◽  
Lixi Jiang
Keyword(s):  
Brassica Napus ◽  
Stress Condition ◽  
Expression Patterns ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Good Opportunity ◽  
Domain Structures ◽  
Genome Wide ◽  
A Genome

Abstract Background Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little information on the GATA genes in Brassica napus is available. The release of the reference genome of B. napus provides a good opportunity to perform a genome-wide characterization of GATA family genes in rapeseed. Results In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus, which were classified into four subfamilies based on phylogenetic analysis and their domain structures. The amino acids of BnGATAs were obvious divergence among four subfamilies in terms of their GATA domains, structures and motif compositions. Gene duplication and synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distributions of BnGATAs in a core collection germplasm are probably associated with functional disparity under environmental stress condition in different genotypes of B. napus. Conclusion The present study was investigated genomic structures, evolution features, expression patterns and SNP distributions of 96 BnGATAs. The results enrich our understanding of the GATA genes in rapeseed.

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