scholarly journals Phylogenetic relationships investigation of Mycobacterium caprae strains from sympatric wild boar and goats based on whole genome sequencing

2020 ◽  
Author(s):  
Giovanna Ciaravino ◽  
Enric Vidal ◽  
Martí Cortey ◽  
Maite Martín ◽  
Albert Sanz ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Wild Boar ◽  
Genome Sequencing ◽  
Phylogenetic Relationships ◽  
Whole Genome ◽  
Mycobacterium Caprae

scholarly journals Whole Genome Sequencing Refines Knowledge on the Population Structure of Mycobacterium bovis from a Multi-Host Tuberculosis System

2021 ◽  
Vol 9 (8) ◽  
pp. 1585
Author(s):  
Ana C. Reis ◽  
Liliana C. M. Salvador ◽  
Suelee Robbe-Austerman ◽  
Rogério Tenreiro ◽  
Ana Botelho ◽  
...  
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Wild Boar ◽  
Genome Sequencing ◽  
Mycobacterium Bovis ◽  
Red Deer ◽  
Variable Number Tandem Repeat ◽  
Variant Calling ◽  
Whole Genome ◽  
Network Analyses

Classical molecular analyses of Mycobacterium bovis based on spoligotyping and Variable Number Tandem Repeat (MIRU-VNTR) brought the first insights into the epidemiology of animal tuberculosis (TB) in Portugal, showing high genotypic diversity of circulating strains that mostly cluster within the European 2 clonal complex. Previous surveillance provided valuable information on the prevalence and spatial occurrence of TB and highlighted prevalent genotypes in areas where livestock and wild ungulates are sympatric. However, links at the wildlife–livestock interfaces were established mainly via classical genotype associations. Here, we apply whole genome sequencing (WGS) to cattle, red deer and wild boar isolates to reconstruct the M. bovis population structure in a multi-host, multi-region disease system and to explore links at a fine genomic scale between M. bovis from wildlife hosts and cattle. Whole genome sequences of 44 representative M. bovis isolates, obtained between 2003 and 2015 from three TB hotspots, were compared through single nucleotide polymorphism (SNP) variant calling analyses. Consistent with previous results combining classical genotyping with Bayesian population admixture modelling, SNP-based phylogenies support the branching of this M. bovis population into five genetic clades, three with apparent geographic specificities, as well as the establishment of an SNP catalogue specific to each clade, which may be explored in the future as phylogenetic markers. The core genome alignment of SNPs was integrated within a spatiotemporal metadata framework to further structure this M. bovis population by host species and TB hotspots, providing a baseline for network analyses in different epidemiological and disease control contexts. WGS of M. bovis isolates from Portugal is reported for the first time in this pilot study, refining the spatiotemporal context of TB at the wildlife–livestock interface and providing further support to the key role of red deer and wild boar on disease maintenance. The SNP diversity observed within this dataset supports the natural circulation of M. bovis for a long time period, as well as multiple introduction events of the pathogen in this Iberian multi-host system.

scholarly journals Whole Genome Sequencing Characterization of HEV3-e and HEV3-f Subtypes among the Wild Boar Population in the Abruzzo Region, Italy: First Report

2020 ◽  
Vol 8 (9) ◽  
pp. 1393
Author(s):  
Giuseppe Aprea ◽  
Silvia Scattolini ◽  
Daniela D’Angelantonio ◽  
Alexandra Chiaverini ◽  
Valeria Di Lollo ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Wild Boar ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Wild Animals ◽  
Wild Boar Population ◽  
Wild Boars ◽  
First Report ◽  
Depth Analysis ◽  
Human Infections

Hepatitis E virus (HEV) is an emergent zoonotic pathogen, causing worldwide acute and chronic hepatitis in humans. HEV comprises eight genotypes and several subtypes. HEV genotypes 3 and 4 (HEV3 and HEV4) are zoonotic. In Italy, the most part of HEV infections (80%) is due to autochthonous HEV3 circulation of the virus, and the key role played by wild animals is generally accepted. Abruzzo is an Italian region officially considered an HEV “hot spot”, with subtype HEV3-c being up to now the only one reported among wild boars. During the year 2018–2019, a group of wild boars in Abruzzo were screened for HEV; positive RNA liver samples were subjected to HEV characterization by using the whole genome sequencing (WGS) approach methodology. This represents the first report about the detection of HEV-3 subtypes e and f in the wild boar population in this area. Since in Italy human infections from HEV 3-e and f have been associated with pork meat consumption, our findings deserve more in-depth analysis with the aim of evaluating any potential correlation between wild animals, the pork chain production and HEV human infections.

scholarly journals An Approximate Bayesian Computation Approach to Examining the Phylogenetic Relationships among the Four Gibbon Genera using Whole Genome Sequence Data

2014 ◽  
Author(s):  
Krishna Veeramah ◽  
August E Woerner ◽  
Laurel Johnstone ◽  
Ivo Gut ◽  
Marta Gut ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Phylogenetic Relationships ◽  
Approximate Bayesian Computation ◽  
Whole Genome Sequence ◽  
Sequencing Error ◽  
Computation Method ◽  
Bayesian Computation ◽  
Whole Genome ◽  
Approximate Bayesian

Gibbons are believed to have diverged from the larger great apes ~16.8 Mya and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the familyHylobatidaeis divided into four genera,Nomascus,Symphalangus,HoolockandHylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mtDNA, the Y chromosome, and short autosomal sequences have been inconclusive. To examine the relationships among gibbon genera in more depth, we performed 2nd generation whole genome sequencing to a mean of ~15X coverage in two individuals from each genus. We developed a coalescent-based Approximate Bayesian Computation method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. AlthoughHoolockandSymphalangusare likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Our combined results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1x10-9/site/year this speciation process occurred ~5 Mya during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera.

Extracting phylogenetic information from whole-genome sequencing projects: the lactic acid bacteria as a test case

Microbiology ◽  
2003 ◽  
Vol 149 (12) ◽  
pp. 3507-3517 ◽  
Author(s):  
Tom Coenye ◽  
Peter Vandamme
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Test Case ◽  
Whole Genome

The availability of an ever increasing number of complete genome sequences of diverse prokaryotic taxa has led to the introduction of novel approaches to infer phylogenetic relationships among bacteria. In the present study the sequences of the 16S rRNA gene and nine housekeeping genes were compared with the fraction of shared putative orthologous protein-encoding genes, conservation of gene order, dinucleotide relative abundance and codon usage among 11 genomes of species belonging to the lactic acid bacteria. In general there is a good correlation between the results obtained with various approaches, although it is clear that there is a stronger phylogenetic signal in some datasets than in others, and that different parameters have different taxonomic resolutions. It appears that trees based on different kinds of information derived from whole-genome sequencing projects do not provide much additional information about the phylogenetic relationships among bacterial taxa compared to more traditional alignment-based methods. Nevertheless, it is expected that the study of these novel forms of information will have its value in taxonomy, to determine which genes are shared, when genes or sets of genes were lost in evolutionary history, to detect the presence of horizontally transferred genes and/or confirm or enhance the phylogenetic signal derived from traditional methods. Although these conclusions are based on a relatively small dataset, they are largely in agreement with other studies and it is anticipated that similar trends will be observed when comparing other genomes.

Utility of Whole Genome Sequencing in diagnosing complex disorders: lesson from renal tubular disorders

2018 ◽  
Author(s):  
Mark Stevenson ◽  
Alistair T Pagnamenta ◽  
Heather G Mack ◽  
Judith A Savige ◽  
Kate E Lines ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Complex Disorders ◽  
Tubular Disorders ◽  
Renal Tubular Disorders ◽  
Renal Tubular

0306 Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 146-146
Author(s):  
D. M. Bickhart ◽  
L. Xu ◽  
J. L. Hutchison ◽  
J. B. Cole ◽  
D. J. Null ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Copy Number ◽  
Large Scale ◽  
Copy Number Variants ◽  
Whole Genome
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