Metagenomic Next-Generation Sequencing Reveal Presence of a Novel Ungulate Bocaparvovirus in Alpacas

Viruses belonging to the genus Bocaparvovirus (BoV) are a genetically diverse group of DNA viruses known to cause respiratory, enteric, and neurological diseases in animals, including humans. An intestinal sample from an alpaca (Vicugna pacos) herd with reoccurring diarrhea and respiratory disease was submitted for next-generation sequencing, revealing the presence of a BoV strain. The alpaca BoV strain (AlBoV) had a 58.58% whole genome nucleotide percent identity to a camel BoV from Dubai, belonging to a tentative ungulate BoV 8 species (UBoV8). Recombination events were lacking with other UBoV strains. The AlBoV genome was comprised of the NS1, NP1, and VP1 proteins. The NS1 protein had the highest amino acid percent identity range (57.89–67.85%) to the members of UBoV8, which was below the 85% cut-off set by the International Committee on Taxonomy of Viruses. The low NS1 amino acid identity suggests that AlBoV is a tentative new species. The whole genome, NS1, NP1, and VP1 phylogenetic trees illustrated distinct branching of AlBoV, sharing a common ancestor with UBoV8. Walker loop and Phospholipase A2 (PLA2) motifs that are vital for virus infectivity were identified in NS1 and VP1 proteins, respectively. Our study reports a novel BoV strain in an alpaca intestinal sample and highlights the need for additional BoV research.

Download Full-text

Comparative whole genome analysis of nucleopolyhedroviruses infecting saturniid silkworms by next-generation sequencing

10.1603/ice.2016.114235 ◽

2016 ◽

Author(s):

Jun Kobayashi

Keyword(s):

Next Generation Sequencing ◽

Genome Analysis ◽

Whole Genome ◽

Next Generation ◽

Whole Genome Analysis ◽

Generation Sequencing

Download Full-text

Laboratory implementation of Next Generation Sequencing for medium and high throughput whole genome analysis of clinical M. tuberculosis complex strains

10.26226/morressier.5991c409d462b80292388d15 ◽

2017 ◽

Author(s):

Christian Utpatel

Keyword(s):

Next Generation Sequencing ◽

High Throughput ◽

Genome Analysis ◽

Whole Genome ◽

Next Generation ◽

Tuberculosis Complex ◽

Whole Genome Analysis ◽

Generation Sequencing

Download Full-text

Next generation sequencing for whole genome analysis and surveillance of influenza A viruses

Journal of Clinical Virology ◽

10.1016/j.jcv.2016.03.005 ◽

2016 ◽

Vol 79 ◽

pp. 44-50 ◽

Cited By ~ 35

Author(s):

Jana McGinnis ◽

Jennifer Laplante ◽

Matthew Shudt ◽

Kirsten St. George

Keyword(s):

Next Generation Sequencing ◽

Genome Analysis ◽

Influenza A ◽

Whole Genome ◽

Next Generation ◽

Influenza A Viruses ◽

Whole Genome Analysis ◽

Generation Sequencing

Download Full-text

Rapid whole-genome mutational profiling using next-generation sequencing technologies

Genome Research ◽

10.1101/gr.077776.108 ◽

2008 ◽

Vol 18 (10) ◽

pp. 1638-1642 ◽

Cited By ~ 176

Author(s):

D. R. Smith ◽

A. R. Quinlan ◽

H. E. Peckham ◽

K. Makowsky ◽

W. Tao ◽

...

Keyword(s):

Next Generation Sequencing ◽

Whole Genome ◽

Next Generation ◽

Sequencing Technologies ◽

Mutational Profiling ◽

Generation Sequencing

Download Full-text

High throughput crop genome genotyping by a combination of pool next generation sequencing and haplotype-based data processing

10.21203/rs.3.rs-415602/v1 ◽

2021 ◽

Author(s):

Michael Schneider ◽

Asis Shrestha ◽

Agim Ballvora ◽

Jens Leon

Keyword(s):

Next Generation Sequencing ◽

Allele Frequency ◽

Frequency Estimation ◽

Whole Genome ◽

Next Generation ◽

Conservation Genomics ◽

High Coverage ◽

Allele Frequency Estimation ◽

Low Coverage ◽

Generation Sequencing

Abstract BackgroundThe identification of environmentally specific alleles and the observation of evolutional processes is a goal of conservation genomics. By generational changes of allele frequencies in populations, questions regarding effective population size, gene flow, drift, and selection can be addressed. The observation of such effects often is a trade-off of costs and resolution, when a decent sample of genotypes should be genotyped for many loci. Pool genotyping approaches can derive a high resolution and precision in allele frequency estimation, when high coverage sequencing is utilized. Still, pool high coverage pool sequencing of big genomes comes along with high costs.ResultsHere we present a reliable method to estimate a barley population’s allele frequency at low coverage sequencing. Three hundred genotypes were sampled from a barley backcross population to estimate the entire population’s allele frequency. The allele frequency estimation accuracy and yield were compared for three next generation sequencing methods. To reveal accurate allele frequency estimates on a low coverage sequencing level, a haplotyping approach was performed. Low coverage allele frequency of positional connected single polymorphisms were aggregated to a single haplotype allele frequency, resulting in two to 271 times higher depth and increased precision. We compared different haplotyping tactics, showing that gene and chip marker-based haplotypes perform on par or better than simple contig haplotype windows. The comparison of multiple pool samples and the referencing against an individual sequencing approach revealed whole genome pool resequencing having the highest correlation to individual genotyping (up to 0.97), while transcriptomics and genotyping by sequencing indicated higher error rates and lower correlations.ConclusionUsing the proposed method allows to identify the allele frequency of populations with high accuracy at low cost. This is particularly interesting for conservation genomics in species with big genomes, like barley or wheat. Whole genome low coverage resequencing at 10x coverage can deliver a highly accurate estimation of the allele frequency, when a loci-based haplotyping approach is applied. Using annotated haplotypes allows to capitalize from biological background and statistical robustness.

Download Full-text

Erratum to: Whole Genome DNA Methylation Analysis of Brachypodium distachyon Using Next-Generation Sequencing (BS-seq)

Brachypodium Genomics - Methods in Molecular Biology ◽

10.1007/978-1-4939-7278-4_19 ◽

2018 ◽

pp. E1-E1

Author(s):

I-Hsuan Lin

Keyword(s):

Dna Methylation ◽

Next Generation Sequencing ◽

Brachypodium Distachyon ◽

Whole Genome ◽

Next Generation ◽

Methylation Analysis ◽

Dna Methylation Analysis ◽

Generation Sequencing

Download Full-text

Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

10.1101/2021.04.16.440153 ◽

2021 ◽

Author(s):

Marcia Gumiel ◽

Oscar M Rollano-Penaloza ◽

Carmelo Peralta-Rivero ◽

Leslie Tejeda ◽

Valeria D. Palma Encinas ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Next Generation Sequencing ◽

Theobroma Cacao ◽

Phylogenetic Trees ◽

Plastid Genome ◽

Next Generation ◽

Center Of Origin ◽

Chloroplast Genomes ◽

Geographical Locations ◽

Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

Download Full-text

Whole genome sequencing suggests transmission of Corynebacterium diphtheriae-caused cutaneous diphtheria in two siblings, Germany, 2018

Eurosurveillance ◽

10.2807/1560-7917.es.2019.24.2.1800683 ◽

2019 ◽

Vol 24 (2) ◽

Cited By ~ 3

Author(s):

Anja Berger ◽

Alexandra Dangel ◽

Tilmann Schober ◽

Birgit Schmidbauer ◽

Regina Konrad ◽

...

Keyword(s):

Next Generation Sequencing ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Corynebacterium Diphtheriae ◽

Whole Genome ◽

Next Generation ◽

Insect Bites ◽

Next Generation Sequencing Ngs ◽

Ngs Data ◽

Generation Sequencing

In September 2018, a child who had returned from Somalia to Germany presented with cutaneous diphtheria by toxigenic Corynebacterium diphtheriae biovar mitis. The child’s sibling had superinfected insect bites harbouring also toxigenic C. diphtheriae. Next generation sequencing (NGS) revealed the same strain in both patients suggesting very recent human-to-human transmission. Epidemiological and NGS data suggest that the two cutaneous diphtheria cases constitute the first outbreak by toxigenic C. diphtheriae in Germany since the 1980s.

Download Full-text