scholarly journals Comparison of the Virome of Quarantined Sugarcane Varieties and the Virome of Grasses Growing near the Quarantine Station

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 922
Author(s):  
Jean H. Daugrois ◽  
Denis Filloux ◽  
Charlotte Julian ◽  
Lisa Claude ◽  
Romain Ferdinand ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Illumina Sequencing ◽  
Virus Movement ◽  
Virus Species ◽  
Library Preparation ◽  
The South ◽  
Sugarcane Varieties ◽  
Barrier Failure ◽  
Quarantine Station ◽  
Safe Control

Visacane is a sugarcane quarantine station located in the South of France, far away from sugarcane growing areas. Visacane imports up to 100 sugarcane varieties per year, using safe control and confinement measures of plants and their wastes to prevent any risk of pathogen spread outside of the facilities. Viruses hosted by the imported material are either known or unknown to cause disease in cultivated sugarcane. Poaceae viruses occurring in plants surrounding the quarantine glasshouse are currently unknown. These viruses could be considered as a source of new sugarcane infections and potentially cause new sugarcane diseases in cases of confinement barrier failure. The aim of this study was to compare the plant virome inside and outside of the quarantine station to identify potential confinement failures and risks of cross infections. Leaves from quarantined sugarcane varieties and from wild Poaceae growing near the quarantine were collected and processed by a metagenomics approach based on virion-associated nucleic acids extraction and library preparation for Illumina sequencing. While viruses belonging to the same virus genus or family were identified in the sugarcane quarantine and its surroundings, no virus species was detected in both environments. Based on the data obtained in this study, no virus movement between quarantined sugarcane and nearby grassland has occurred so far, and the confinement procedures of Visacane appear to be properly implemented.

scholarly journals Current Perspectives on High-Throughput Sequencing (HTS) for Adventitious Virus Detection: Upstream Sample Processing and Library Preparation

Viruses ◽  
2018 ◽  
Vol 10 (10) ◽  
pp. 566 ◽  
Author(s):  
Siemon Ng ◽  
Cassandra Braxton ◽  
Marc Eloit ◽  
Szi Feng ◽  
Romain Fragnoud ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Nucleic Acids ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Virus Detection ◽  
Extraction Methods ◽  
Control Measures ◽  
Acid Extraction ◽  
Library Preparation ◽  
Sample Processing

A key step for broad viral detection using high-throughput sequencing (HTS) is optimizing the sample preparation strategy for extracting viral-specific nucleic acids since viral genomes are diverse: They can be single-stranded or double-stranded RNA or DNA, and can vary from a few thousand bases to over millions of bases, which might introduce biases during nucleic acid extraction. In addition, viral particles can be enveloped or non-enveloped with variable resistance to pre-treatment, which may influence their susceptibility to extraction procedures. Since the identity of the potential adventitious agents is unknown prior to their detection, efficient sample preparation should be unbiased toward all different viral types in order to maximize the probability of detecting any potential adventitious viruses using HTS. Furthermore, the quality assessment of each step for sample processing is also a critical but challenging aspect. This paper presents our current perspectives for optimizing upstream sample processing and library preparation as part of the discussion in the Advanced Virus Detection Technologies Interest group (AVDTIG). The topics include: Use of nuclease treatment to enrich for encapsidated nucleic acids, techniques for amplifying low amounts of virus nucleic acids, selection of different extraction methods, relevant controls, the use of spike recovery experiments, and quality control measures during library preparation.

scholarly journals Method for improved Illumina sequencing library preparation using NuGEN Ovation RNA-Seq System

BioTechniques ◽  
2011 ◽  
Vol 50 (3) ◽  
pp. 177-181 ◽  
Author(s):  
Steven R. Head ◽  
H.Kiyomi Komori ◽  
G.Traver Hart ◽  
John Shimashita ◽  
Lana Schaffer ◽  
...  
Keyword(s):  
Illumina Sequencing ◽  
Library Preparation ◽  
Rna Seq ◽  
Sequencing Library ◽  
Sequencing Library Preparation

scholarly journals Visualization and characterization of tobacco mosaic virus movement protein binding to single-stranded nucleic acids.

1992 ◽  
Vol 4 (4) ◽  
pp. 397-411 ◽  
Author(s):  
V Citovsky ◽  
M L Wong ◽  
A L Shaw ◽  
B V Prasad ◽  
P Zambryski
Keyword(s):  
Nucleic Acids ◽  
Protein Binding ◽  
Tobacco Mosaic Virus ◽  
Mosaic Virus ◽  
Movement Protein ◽  
Virus Movement

scholarly journals Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems

2017 ◽  
Author(s):  
A.M. Quattrini ◽  
B.C. Faircloth ◽  
L.F. Dueñas ◽  
T.C.L. Bridge ◽  
M. Brugler ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Illumina Sequencing ◽  
Phylogenetic Relationships ◽  
Evolutionary Relationships ◽  
Diverse Group ◽  
Target Enrichment ◽  
Library Preparation ◽  
Deep Waters ◽  
The Mean ◽  
Multiple Species

AbstractAnthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ∼7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,308 RNA baits to capture 720 Ultraconserved Element loci and 1,071 exon loci. Library preparation and target enrichment was performed on 33 taxa from all orders within the class Anthozoa. Following Illumina sequencing and Trinity assembly, we recovered 1,774 of 1,791 targeted loci. The mean number of loci recovered from each species was 638 ± 222, with more loci recovered from octocorals (783 ± 138 loci) than hexacorals (475 ±187 loci). Phylogenetically informative sites ranged from 26-49% for alignments at differing hierarchical taxonomic levels (e.g., Anthozoa, Octocorallia, Hexacorallia). The percent of variable sites within each of three genera (Acropora, Alcyonium, andSinularia) for which multiple species were sequenced ranged from 4.7-30%. Maximum likelihood analyses recovered highly resolved trees with topologies matching those supported by other studies, including the monophyly of the order Scleractinia. Our results demonstrate the utility of this target-enrichment approach to resolve phylogenetic relationships from relatively old to recent divergences. Re-designing the baits with improved affinities to capture loci within each sub-class will provide a valuable toolset to address systematic questions and further our understanding of the timing of diversifications in the class Anthozoa.

scholarly journals RB965902 and RB965917 Early/medium maturing sugarcane varieties

2011 ◽  
Vol 11 (3) ◽  
pp. 280-285 ◽  
Author(s):  
Monalisa Sampaio Carneiro ◽  
João Ricardo Bachega Feijó Rosa ◽  
Fernanda Zatti Barreto ◽  
Thiago Willian Almeida Balsalobre ◽  
Roberto Giacomini Chapola ◽  
...  
Keyword(s):  
Central Region ◽  
The South ◽  
Sugarcane Varieties ◽  
South Central ◽  
Extraction Period

The varieties RB965902 and RB965917 were developed for harvesting at the beginning to the middle of the sucrose extraction period (early/medium maturity) and released for the South-Central region of Brazil. In specific environments, the tons of Pol per area (sucrose yield) of these varieties is higher than of the commercial standard RB855453 and they are resistant to the main diseases of the crop.

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