Exploration of the virome of the European brown shrimp (Crangon crangon)

Crangon crangon is economically a very important species. Recently, promising culture attempts have been made, but a major problem is the uncontrollable mortality during the grow-out phase. As of yet, the life cycle of C. crangon is not closed in captivity so wild-caught individuals are used for further rearing. Therefore, it is important to investigate the virome of C. crangon both in wild-caught animals as in cultured animals. In recent years, next-generation-sequencing (NGS) technologies have been very important in the unravelling of the virome of a wide range of environments and matrices, such as soil, sea, potable water, but also of a wide range of animal species. This will be the first report of a virome study in C. crangon using NGS in combination with the NetoVIR protocol. The near complete genomes of 16 novel viruses were described, most of which were rather distantly related to unclassified viruses or viruses belonging to the Picornavirales, Bunyavirales Nudiviridae, Parvoviridae, Flaviviridae, Hepeviridae, Tombusviridae, Narnaviridae, Nodaviridae, Sobemovirus. A difference in virome composition was observed between muscle and hepatopancreatic tissue, suggesting a distinct tissue tropism of several of these viruses. Some differences in the viral composition were noted between the cultured and wild shrimp, which could indicate that in sub-optimal aquaculture conditions some viruses become more abundant. This research showed that a plethora of unknown viruses is present in C. crangon and that more research is needed to determine which virus is potentially dangerous for the culture of C. crangon.

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Next-generation sequencing in neuropathological diagnosis of infections of the nervous system

10.1101/039222 ◽

2016 ◽

Author(s):

Steven L. Salzberg ◽

Florian Breitwieser ◽

Anupama Kumar ◽

Haiping Hao ◽

Peter Burger ◽

...

Keyword(s):

Spinal Cord ◽

Nervous System ◽

Next Generation Sequencing ◽

Large Scale ◽

Infectious Agent ◽

Next Generation ◽

Dna And Rna ◽

Wide Range ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Objective: To determine the feasibility of next-generation sequencing (NGS) microbiome approaches in the diagnosis of infectious disorders in brain or spinal cord biopsies in patients with suspected central nervous system (CNS) infections. Methods: In a prospective-pilot study, we applied NGS in combination with a new computational analysis pipeline to detect the presence of pathogenic microbes in brain or spinal cord biopsies from ten patients with neurological problems indicating possible infection but for whom conventional clinical and microbiology studies yielded negative or inconclusive results. Results: Direct DNA and RNA sequencing of brain tissue biopsies generated 8.3 million to 29.1 million sequence reads per sample, which successfully identified with high confidence the infectious agent in three patients, identified possible pathogens in two more, and helped to understand neuropathological processes in three others, demonstrating the power of large-scale unbiased sequencing as a novel diagnostic tool. Validation techniques confirmed the pathogens identified by NGS in each of the three positive cases. Clinical outcomes were consistent with the findings yielded by NGS on the presence or absence of an infectious pathogenic process in eight of ten cases, and were non-contributory in the remaining two. Conclusions: NGS-guided metagenomic studies of brain, spinal cord or meningeal biopsies offer the possibility for dramatic improvements in our ability to detect (or rule out) a wide range of CNS pathogens, with potential benefits in speed, sensitivity, and cost. NGS-based microbiome approaches present a major new opportunity to investigate the potential role of infectious pathogens in the pathogenesis of neuroinflammatory disorders.

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Characterization and Diversity of 243 Complete Human Papillomavirus Genomes in Cervical Swabs Using Next Generation Sequencing

Viruses ◽

10.3390/v12121437 ◽

2020 ◽

Vol 12 (12) ◽

pp. 1437

Author(s):

Ardashel Latsuzbaia ◽

Anke Wienecke-Baldacchino ◽

Jessica Tapp ◽

Marc Arbyn ◽

Irma Karabegović ◽

...

Keyword(s):

Human Papillomavirus ◽

Next Generation Sequencing ◽

High Risk ◽

Pairwise Distance ◽

Next Generation ◽

Hpv Genotypes ◽

Complete Genomes ◽

Hpv Types ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

In recent years, next generation sequencing (NGS) technology has been widely used for the discovery of novel human papillomavirus (HPV) genotypes, variant characterization and genotyping. Here, we compared the analytical performance of NGS with a commercial PCR-based assay (Anyplex II HPV28) in cervical samples of 744 women. Overall, HPV positivity was 50.2% by the Anyplex and 45.5% by the NGS. With the NGS, we detected 25 genotypes covered by Anyplex and 41 additional genotypes. Agreement between the two methods for HPV positivity was 80.8% (kappa = 0.616) and 84.8% (kappa = 0.652) for 28 HPV genotypes and 14 high-risk genotypes, respectively. We recovered and characterized 243 complete HPV genomes from 153 samples spanning 40 different genotypes. According to phylogenetic analysis and pairwise distance, we identified novel lineages and sublineages of four high-risk and 16 low-risk genotypes. In total, 17 novel lineages and 14 novel sublineages were proposed, including novel lineages of HPV45, HPV52, HPV66 and a novel sublineage of HPV59. Our study provides important genomic insights on HPV types and lineages, where few complete genomes were publicly available.

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DNA metabarcoding allows non-invasive identification of arthropod prey provisioned to nestling Rufous hummingbirds (Selasphorus rufus)

PeerJ ◽

10.7717/peerj.6596 ◽

2019 ◽

Vol 7 ◽

pp. e6596 ◽

Cited By ~ 7

Author(s):

Alison J. Moran ◽

Sean W.J. Prosser ◽

Jonathan A. Moran

Keyword(s):

Alimentary Tract ◽

Selasphorus Rufus ◽

Non Invasive ◽

Single Pellet ◽

Wide Range ◽

Dna Metabarcoding ◽

Rufous Hummingbird ◽

Almost All ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Hummingbirds consume sugars from nectar, sap and honeydew, and obtain protein, fat and minerals from arthropods. To date, the identity of arthropod taxa in hummingbird diets has been investigated by observation of foraging or examination of alimentary tract contents. Direct examination of nestling provisioning adds the extra complication of disturbance to the young and mother. Here, we show that arthropod food items provisioned to Rufous hummingbird (Selasphorus rufus) nestlings can be identified by a safe and non-invasive protocol using next-generation sequencing (NGS) of DNA from nestling fecal pellets collected post-fledging. We found that females on southern Vancouver Island (British Columbia, Canada) provisioned nestlings with a wide range of arthropod taxa. The samples examined contained three Classes, eight Orders, 48 Families, and 87 Genera, with from one to 15 Families being identified in a single pellet. Soft-bodied Dipterans were found most frequently and had the highest relative abundance; hard-bodied prey items were absent from almost all samples. Substantial differences in taxa were found within season and between years, indicating the importance of multi-year sampling when defining a prey spectrum.

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Genomic Tools for the Enhancement of Vegetable Crops: A Case in Eggplant

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha46110936 ◽

2018 ◽

Vol 46 (1) ◽

pp. 1-13 ◽

Cited By ~ 13

Author(s):

Pietro GRAMAZIO ◽

Jaime PROHENS ◽

Mariola PLAZAS ◽

Giulio MANGINO ◽

Francisco J. HERRAIZ ◽

...

Keyword(s):

Solanum Melongena ◽

Relevant Information ◽

Wild Relatives ◽

Biological Processes ◽

Vegetable Crops ◽

Genomic Tools ◽

Wide Range ◽

Different Types ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Dramatic advances in genomics during the last decades have led to a revolution in the field of vegetable crops breeding. Some vegetables, like tomato, have served as model crops in the application of genomic tools to plant breeding but other important crops, like eggplant (Solanum melongena), lagged behind. The advent of next generation sequencing (NGS) technologies and the continuous decrease of the sequencing costs have allowed to develop genomic tools with a greatly benefit for no-model plants such as eggplant. In this review we present the currently available genomic resources in eggplant and discuss their interest for breeding. The first draft of eggplant genome sequence and the new upcoming improved assembly, as well as, the transcriptomes and RNA-based studies represent important genomic tools. The transcriptomes of cultivated eggplant and several wild relatives of eggplant are also available and have provided relevant information for the development of markers and understanding biological processes in eggplant. In addition, a historical overview of the eggplant genetic mapping studies, performed with different types of markers and experimental populations, provides a picture of the increase over time of the precision and resolution in the identification of candidate genes and QTLs for a wide range of stresses, and morpho-agronomic and domestication traits. Finally, we discuss how the development of new genetic and genomic tools in eggplant can pave the way for increasing the efficiency of eggplant breeding for developing improved varieties able to cope with the old and new challenges in horticultural production.

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Genotyping of 25 Leukemia-Associated Genes in a Single Work Flow by Next-Generation Sequencing Technology with Low Amounts of Input Template DNA

Clinical Chemistry ◽

10.1373/clinchem.2013.204099 ◽

2013 ◽

Vol 59 (8) ◽

pp. 1238-1250 ◽

Cited By ~ 14

Author(s):

Jenny Rinke ◽

Vivien Schäfer ◽

Mathias Schmidt ◽

Janine Ziermann ◽

Alexander Kohlmann ◽

...

Keyword(s):

Next Generation Sequencing ◽

Target Genes ◽

Work Flow ◽

Next Generation ◽

Next Generation Sequencing Technology ◽

Wide Range ◽

Next Generation Sequencing Ngs ◽

Template Dna ◽

Ngs Data ◽

Generation Sequencing

BACKGROUND We sought to establish a convenient, sensitive next-generation sequencing (NGS) method for genotyping the 26 most commonly mutated leukemia-associated genes in a single work flow and to optimize this method for low amounts of input template DNA. METHODS We designed 184 PCR amplicons that cover all of the candidate genes. NGS was performed with genomic DNA (gDNA) from a cohort of 10 individuals with chronic myelomonocytic leukemia. The results were compared with NGS data obtained from sequencing of DNA generated by whole-genome amplification (WGA) of 20 ng template gDNA. Differences between gDNA and WGA samples in variant frequencies were determined for 2 different WGA kits. RESULTS For gDNA samples, 25 of 26 genes were successfully sequenced with a sensitivity of 5%, which was achieved by a median coverage of 492 reads (range, 308–636 reads) per amplicon. We identified 24 distinct mutations in 11 genes. With WGA samples, we reliably detected all mutations above 5% sensitivity with a median coverage of 506 reads (range, 256–653 reads) per amplicon. With all variants included in the analysis, WGA amplification by the 2 kits tested yielded differences in variant frequencies that ranged from −28.19% to +9.94% [mean (SD) difference, −0.2% (4.08%)] and from −35.03% to +18.67% [mean difference, −0.75% (5.12%)]. CONCLUSIONS Our method permits simultaneous analysis of a wide range of leukemia-associated target genes in a single sequencing run. NGS can be performed after WGA of template DNA for reliable detection of variants without introducing appreciable bias.

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Registration of animal rabies in Krasnodar region

Veterinaria Kubani ◽

10.33861/2071-8020-2020-4-3-4 ◽

2020 ◽

pp. 3-4

Author(s):

Oleg Yu. Chernykh ◽

◽

Vadim A. Bobrov ◽

Sergey N. Zabashta ◽

Roman A. Krivonos ◽

...

Keyword(s):

Urban Form ◽

Animal Species ◽

Farm Animals ◽

Natural Focus ◽

Dead End ◽

Wide Range ◽

Epizootic Process ◽

Krasnodar Region ◽

Spread Of Infection ◽

Reporting Data

Rabies remains a constant threat to humanity in many parts of the world. At the same time, scientifically grounded antiepizootic measures should be based on the peculiarities of the regional epizootology of this zooanthroponosis. The authors studied the epizootological and statistical reporting data of the Kropotkin Regional Veterinary Laboratory, presented an analysis of the registration of rabies in animals in Krasnodar region. From the obtained data, it should be noted that despite the wide range of animals involved in the epizootic process of rabies infection in Krasnodar region, dogs, cats and foxes play a major role in the reservation and spread of infection, which account for 78.6. Of the total number of registered cases, 15.5% falls on foxes, that indicates the natural focus of the disease, along with the manifestation of the disease in an urban form. At the same time, stray and neglected dogs and cats, which occupy a significant place among the total number of sick animals, are also sources and spread of the infection. Thus farm animals (8.3% of the total number of infected animals) are a biological dead end for the infection. Isolated cases of the disease were noted in muskrat, donkey, raccoon, raccoon dog, marten, ferret and jackal. The authors also established the specific morbidity of various animal species with rabies infection, that is an important aspect in the development and implementation of antiepizootic measures complex

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