scholarly journals Population genomics of bank vole populations reveals associations between immune related genes and the epidemiology of Puumala hantavirus in Sweden

2017 ◽  
Author(s):  
Audrey Rohfritsch ◽  
Maxime Galan ◽  
Mathieu Gautier ◽  
Karim Gharbi ◽  
Gert Olsson ◽  
...  
Keyword(s):  
High Throughput ◽  
Bank Vole ◽  
High Throughput Sequencing ◽  
Population Genomics ◽  
Reservoir Host ◽  
Model Organisms ◽  
Myodes Glareolus ◽  
A Genome ◽  
Outlier Loci ◽  
Immune Related Genes

AbstractInfectious pathogens are major selective forces acting on individuals. The recent advent of high-throughput sequencing technologies now enables to investigate the genetic bases of resistance/susceptibility to infections in non-model organisms. From an evolutionary perspective, the analysis of the genetic diversity observed at these genes in natural populations provides insight into the mechanisms maintaining polymorphism and their epidemiological consequences. We explored these questions in the context of the interactions between Puumala hantavirus (PUUV) and its reservoir host, the bank vole Myodes glareolus. Despite the continuous spatial distribution of M. glareolus in Europe, PUUV distribution is strongly heterogeneous. Different defence strategies might have evolved in bank voles as a result of co-adaptation with PUUV, which may in turn reinforce spatial heterogeneity in PUUV distribution. We performed a genome scan study of six bank vole populations sampled along a North/South transect in Sweden, including PUUV endemic and non-endemic areas. We combined candidate gene analyses (Tlr4, Tlr7, Mx2 genes) and high throughput sequencing of RAD (Restriction-site Associated DNA) markers. We found evidence for outlier loci showing high levels of genetic differentiation. Ten outliers among the 52 that matched to mouse protein-coding genes corresponded to immune related genes and were detected using ecological associations with variations in PUUV prevalence. One third of the enriched pathways concerned immune processes, including platelet activation and TLR pathway. In the future, functional experimentations should enable to confirm the role of these these immune related genes with regard to the interactions between M. glareolus and PUUV.

scholarly journals Comprehensive profiling of TCRβ repertoire in a non-model species (the bank vole) using high-throughput sequencing

2017 ◽  
Author(s):  
Magdalena Migalska ◽  
Alvaro Sebastian ◽  
Jacek Radwan
Keyword(s):  
High Throughput ◽  
Bank Vole ◽  
High Throughput Sequencing ◽  
Length Distribution ◽  
Amino Acid Sequences ◽  
Myodes Glareolus ◽  
Model Species ◽  
Immune Repertoire ◽  
Important Species ◽  
Repertoire Sequencing

AbstractIn recent years, immune repertoire profiling with high-throughput sequencing (HTS) has advanced our understanding of adaptive immunity. However, fast progress in the field applied mostly to human and mouse research, with only few studies devoted to other model vertebrates. We present the first in-depth characterization of the TCRβ repertoire in a non-model mammal with limited genomic resources available – the bank vole (Myodes glareolus). We used 5′RACE and Illumina HTS to describe V and J segments and to qualitatively characterize preferential V–J segment usage and CDR3 length distribution. Finally, a molecular protocol integrating unique molecular identifiers was used for quantitative analysis of CDR3 repertoire with stringent error correction. We found 37 V and 11 J genes that were orthologous to mice genes. A conservative, lower bound estimation of the TCRβ repertoire was 1.7–2.3×105 clonotypes, and the degree of sharing of the observed repertoire between any two individuals was 3.6% of nucleotide sequences and 14.3% of amino acid sequences. Our work adds a crucial element to the immunogenetic resources available for the bank vole, an important species in ecological and evolutionary research. The workflow that we developed can be applied for immune repertoire sequencing of non-model species, including endangered vertebrates.

scholarly journals In Vivo Characterization of a Bank Vole-Derived Cowpox Virus Isolate in Natural Hosts and the Rat Model

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 237
Author(s):  
Saskia Weber ◽  
Kathrin Jeske ◽  
Rainer G. Ulrich ◽  
Christian Imholt ◽  
Jens Jacob ◽  
...  
Keyword(s):  
Bank Vole ◽  
Wistar Rats ◽  
Reservoir Host ◽  
Myodes Glareolus ◽  
Replication Capacity ◽  
Cowpox Virus ◽  
Saguinus Oedipus ◽  
Bank Voles ◽  
Common Voles

Cowpox virus (CPXV) belongs to the genus Orthopoxvirus in the Poxviridae family and is endemic in western Eurasia. Based on seroprevalence studies in different voles from continental Europe and UK, voles are suspected to be the major reservoir host. Recently, a CPXV was isolated from a bank vole (Myodes glareolus) in Germany that showed a high genetic similarity to another isolate originating from a Cotton-top tamarin (Saguinus oedipus). Here we characterize this first bank vole-derived CPXV isolate in comparison to the related tamarin-derived isolate. Both isolates grouped genetically within the provisionally called CPXV-like 3 clade. Previous phylogenetic analysis indicated that CPXV is polyphyletic and CPXV-like 3 clade represents probably a different species if categorized by the rules used for other orthopoxviruses. Experimental infection studies with bank voles, common voles (Microtus arvalis) and Wistar rats showed very clear differences. The bank vole isolate was avirulent in both common voles and Wistar rats with seroconversion seen only in the rats. In contrast, inoculated bank voles exhibited viral shedding and seroconversion for both tested CPXV isolates. In addition, bank voles infected with the tamarin-derived isolate experienced a marked weight loss. Our findings allow for the conclusion that CPXV isolates might differ in their replication capacity in different vole species and rats depending on their original host. Moreover, the results indicate host-specific differences concerning CPXV-specific virulence. Further experiments are needed to identify individual virulence and host factors involved in the susceptibility and outcome of CPXV-infections in the different reservoir hosts.

scholarly journals A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 144 ◽  
Author(s):  
Laís Coelho ◽  
Lukas Musher ◽  
Joel Cracraft
Keyword(s):  
Genome Assembly ◽  
High Throughput Sequencing ◽  
Population Genomics ◽  
De Novo ◽  
Structural Difference ◽  
Whole Genome ◽  
Sequencing Technology ◽  
A Genome ◽  
Avian Genomes ◽  
Chromosome Level

Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.

scholarly journals jackalope: a swift, versatile phylogenomic and high-throughput sequencing simulator

2019 ◽  
Author(s):  
Lucas A. Nell
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Population Genomics ◽  
R Package ◽  
Gene Trees ◽  
Sequencing Platform ◽  
Genomic Variants ◽  
Pacific Biosciences ◽  
Wide Range ◽  
Reference Genomes

AbstractHigh-throughput sequencing (HTS) is central to the study of population genomics and has an increasingly important role in constructing phylogenies. Choices in research design for sequencing projects can include a wide range of factors, such as sequencing platform, depth of coverage, and bioinformatic tools. Simulating HTS data better informs these decisions. However, current standalone HTS simulators cannot generate genomic variants under even somewhat complex evolutionary scenarios, which greatly reduces their usefulness for fields such as population genomics and phylogenomics. Here I present the R package jackalope that simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. Genomic variants can be simulated using phylogenies, gene trees, coalescent-simulation output, population-genomic summary statistics, and Variant Call Format (VCF) files. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences. These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. It can read reference genomes from FASTA files and can simulate new ones, and all outputs can be written to standard file formats. jackalope is available for Mac, Windows, and Linux systems.

Whole human exome capture for high-throughput sequencing

Genome ◽  
2010 ◽  
Vol 53 (7) ◽  
pp. 568-574 ◽  
Author(s):  
Dae-Won Kim ◽  
Seong-Hyeuk Nam ◽  
Ryong Nam Kim ◽  
Sang-Haeng Choi ◽  
Hong-Seog Park
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Exome Capture ◽  
Microarray Design ◽  
Genome Wide ◽  
Human Genes ◽  
Practical Usefulness ◽  
A Genome ◽  
Wide Scale ◽  
Total Base

We captured the whole human exome by hybridization using synthesized oligonucleotides, based on a high-density microarray design, and we sequenced those captured human exons using high-throughput sequencing on a Genome Sequencer FLX instrument. Of the uniquely mapped reads, 71% fell within target regions, and these corresponded to coverage of 94% of human genes, 87% of exons, and 70% of the total base-pair length of the CCDS set. Our study provides strong evidence for the practical usefulness of this method on a genome-wide scale, showing the resequenced whole human exome database with 501 microRNAs and 307 novel SNPs.

Environmental and ecological potential for enzootic cycles of Puumala hantavirus in Great Britain

2009 ◽  
Vol 138 (1) ◽  
pp. 91-98 ◽  
Author(s):  
E. BENNETT ◽  
J. CLEMENT ◽  
P. SANSOM ◽  
I. HALL ◽  
S. LEACH ◽  
...  
Keyword(s):  
Great Britain ◽  
Environmental Factors ◽  
Bank Vole ◽  
Regression Models ◽  
Reservoir Host ◽  
Myodes Glareolus ◽  
Puumala Virus ◽  
Climate Data ◽  
Northwest Europe ◽  
Climatic Constraints

SUMMARYPuumala virus (PUUV) is a zoonotic rodent-borne hantavirus in continental Europe. Its reservoir host, the bank vole (Myodes glareolus), is ubiquitous in Great Britain (GB); however, there has been no reported incidence of virus in either animals or humans. In northwest Europe, increases in bank vole numbers, stimulated by increases in production of beech/oak crops (mast), are associated with outbreaks of nephropathia epidemica (NE) in humans. These so-called ‘mast years’ are determined by sequential climatic events. This paper investigates the contribution of a number of ecological and environmental factors driving outbreaks of PUUV in northwest Europe and assesses whether such factors might also permit enzootic PUUV circulation in GB. Analysis of GB climate data, using regression models, confirms that mast years in GB are stimulated, and can be predicted, by the same climatic events as mast years in PUUV-endemic regions of northwest Europe. A number of other possible non-climatic constraints on enzootic cycles are discussed.

scholarly journals Identification and characterization of salt-tolerance relative miRNAs in Procambarus clarkii by high-throughput sequencing

ExRNA ◽  
2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Fangfang Jin ◽  
Yuling Sun
Keyword(s):  
Salt Tolerance ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Procambarus Clarkii ◽  
Economic Losses ◽  
Srna Library ◽  
Genome Wide ◽  
A Genome

Abstract Procambarus clarkii is one of the important economic species in China and has been served as tasty food in recent years after being introduced to Nanjing. Significant problems of environment factors, such as salinity, pH and temperature, especially salinity, has the potential to result in significant economic losses in many crayfish-producing farms in China. miRNAs are a kind of ~ 22 nucleotide small non coding RNAs which were encoded by plants, animals and some viruses with functions in RNA silencing or post-transcription regulation. We constructed four sRNA library of P. clarkia from different tissues and treatments by using high-throughput sequencing technology. A total of 101 conserved miRNAs and two novel pre-miRNAs were identified and RT-qPCR were further performed to confirm existence of part of identified miRNAs. A genome wide expression profile of salt-tolerance miRNAs was proved and three miRNAs were further validated by RT-qPCR with dynamic response to different salinity stages. The study of miRNAs in P. clarkia can help us better understanding the role of miRNAs in salt-tolerance in P. clarkia.

scholarly journals Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data

2016 ◽  
Author(s):  
Guillaume Devailly ◽  
Anna Mantsoki ◽  
Anagha Joshi
Keyword(s):  
High Throughput ◽  
Web Application ◽  
High Throughput Sequencing ◽  
Single Gene ◽  
Public Domain ◽  
Web Tool ◽  
The Public ◽  
Link Type ◽  
A Genome ◽  
Public Data

SummaryBetter protocols and decreasing costs have made high-throughput sequencing experiments now accessible even to small experimental laboratories. However, comparing one or few experiments generated by an individual lab to the vast amount of relevant data freely available in the public domain might be limited due to lack of bioinformatics expertise. Though several tools, including genome browsers, allow such comparison at a single gene level, they do not provide a genome-wide view. We developed Heat*seq, a web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain. Heat*seq currently contains over 12,000 experiments across diverse tissue and cell types in human, mouse and drosophila. Heat*seq displays interactive correlation heatmaps, with an ability to dynamically subset datasets to contextualise user experiments. High quality figures and tables are produced and can be downloaded in multiple formats.AvailabilityWeb application:www.heatstarseq.roslin.ed.ac.uk/. Source code:https://github.com/[email protected];[email protected]

scholarly journals Rapid isolation and characterization of microsatellites in the critically endangered Mountain Bongo (Tragelaphus eurycerus isaaci)

2019 ◽  
Author(s):  
Fraser John Combe ◽  
Evelyn Taylor cox ◽  
Graeme fox ◽  
Tommy Sandri ◽  
Bradley Cain ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Population Analysis ◽  
Illumina Miseq ◽  
Model Organisms ◽  
Conservation Genomics ◽  
Adaptive Genetic Variation ◽  
Genetics Research ◽  
Isolation And Characterization ◽  
Neutral Markers

High-throughput sequencing tools promise to revolutionize many aspects of genetics research, e.g. by allowing the identification of functional adaptive genetic variation. However, the expense and expertise required to apply these tools to basic conservation questions is a challenge for applications outside academia, resulting in a so-called “conservation genomics gap” (Shafer et al. 2015). The conservation genetics paradigm is that basic information about inbreeding and gene flow are often critical to inform conservation management of small populations (Ouborg et al. 2010). This information is often needed quickly and ideally should be accessible to workers without special expertise in genomics (DeSalle & Amato 2004). While the inferential power of high-throughput sequencing to interrogate the genome is profound, the cost for population analysis is higher (though decreasing) than for traditional neutral markers. Thus, the use of neutral markers is still relevant in conservation applications. However, this assumes that neutral markers have been discovered and characterized for a given species of conservation concern, which is often untrue for non-model organisms. Here, we use a fast, cost-efficient, high-throughput sequencing method (Illumina MiSeq) to rapidly identify and characterize microsatellites in the mountain bongo (Tragelaphus eurycerus isaaci, hereafter bongo), which has a clear and timely conservation imperative but lacks any described neutral markers.

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