Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing

@article{Akinyemi2016EcogenomicSO,
  title={Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing},
  author={Ibukun A. Akinyemi and Fang Wang and Benguo Zhou and Shuishui Qi and Qingfa Wu},
  journal={Virology Journal},
  year={2016},
  volume={13}
}
BackgroundThe invasion of plant by viruses cause major damage to plants and reduces crop yield and integrity. Devastating plant virus infection has been experienced at different times all over the world, which are attributed to different events of mutation, re-assortment and recombination occurring in the viruses. Strategies for proper virus management has been mostly limited to eradicating the vectors that spreads the plant viruses. However, development of prompt and effective diagnostic… 

Figures and Tables from this paper

Identification of Plant Viruses Infecting Pear Using RNA Sequencing
TLDR
The virome of a major pear cultivar in Korea is described, and the diversity of viral communities in this cultivar is looked into, to provide valuable information on the complexity of genetic variability of viruses infecting pear trees.
Next-generation sequencing identification and multiplex RT-PCR detection for viruses infecting cigar and flue-cured tobacco.
TLDR
A fast and sensitive multiplex reverse transcription polymerase chain reaction assay was developed for the simultaneous detection of the most frequent RNA viruses infecting cigar and flue-cured tobacco in Sichuan.
Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution
TLDR
The techniques used for plant virus diagnosis and disease control are reviewed, including characteristics such as accuracy, detection level, multiplexing, quantification, portability, and designability.
Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review
TLDR
This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases.
Identification of Viruses Infecting Oats in Korea by Metatranscriptomics
Controlling infectious plant viruses presents a constant challenge in agriculture. As a source of valuable nutrients for human health, the cultivation of oats (Avena sativa L.) has recently been
Integrating CRISPR-Cas and Next Generation Sequencing in Plant Virology
TLDR
This review provides a snapshot vision of emerging developments in NGS technologies for the characterization of plant viruses and their potential utilities, advantages, and limitations in plant viral diagnostics.
Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales
TLDR
This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.
Simultaneous detection of virus infecting tobacco plant using multiplex-PCR in Klaten, Indonesia
TLDR
This study determined the viruses that attack tobacco plants in Klaten, Indonesia through simultaneous detection using multiplex-PCR and found that the tobacco isolate was positively infected by the Tomato yellow leaf curl Kanchanaburi virus, Cucumber mosaic virus (CMV) and Potato virus (PVY).
Metagenomic Analysis of Plant Viruses Associated With Papaya Ringspot Disease in Carica papaya L. in Kenya
TLDR
The nature of viruses responsible for PRSD was elucidated in papaya leaves collected from 22 counties through Illumina MiSeq next-generation sequencing (NGS) and validated by RT-PCR and Sanger sequencing, and surprisingly, PRSV was not detected.
Full genome sequence analysis and putative host-shifting of Milk vetch dwarf virus infecting tobacco (Nicotiana tabacum) in China
TLDR
This is the first full genome annotation of a Nanovirus, infecting tobacco in natural field conditions, also the first extended analysis on host-shifting behavior of MDV.
...
1
2
3
...

References

SHOWING 1-10 OF 59 REFERENCES
Advances in plant virus evolution: translating evolutionary insights into better disease management.
TLDR
The analyzed data indicate that systematic disruption of some specific parameters of evolving virus populations could lead to more efficient ways of disease prevention, eradication, or tolerable virus-plant coexistence.
Plant Virology and Next Generation Sequencing: Experiences with a Potyvirus
TLDR
The current system of nomenclature based on biological properties be replaced by numbered groups (I–IX) because use of whole genomes revealed that the previous phylogenetic grouping system based on partial sequences of virus genomes and original isolation hosts was unsustainable.
Crop immunity against viruses: outcomes and future challenges
TLDR
This review aims at describing some of the most devastating diseases caused by viruses on crops and summarizes current knowledge about plant–virus interactions, focusing on resistance mechanisms that prevent or limit viral infection in plants.
Genetic Structure and Molecular Variability of Cucumber mosaic virus Isolates in the United States
TLDR
Sequence and phylogenetic analyses revealed that CMV subgroup I is predominant in the US and further showed that the CMV population is a mixture of subgroups IA and IB, which suggest that different regions of theCMV genome are under different evolutionary constraints.
A Case Study on Discovery of Novel Citrus Leprosis Virus Cytoplasmic Type 2 Utilizing Small RNA Libraries by Next Generation Sequencing and Bioinformatic Analyses
TLDR
The utilization of the Illumina GA IIX platform combined with the application of molecular biology and bioinformatic tools for the discovery of a novel cytoplasmic Citrus leprosis virus (CiLV), which was not detected with either serological or PCR-based assays for the previously described virus.
Phylogeography and Molecular Evolution of Potato virus
TLDR
The results show that both geographic and hostdriven adaptations explain PVY diversification, and purifying selection is the main force driving PVY evolution, although some indications of positive selection accounted for the diversification of the different strains.
Genetic diversity of Potato virus Y infecting tobacco crops in China.
TLDR
When PVY isolate from potato were included, no host-specific clustering of the PVY isolates was observed in phylogenetic and nucleotide diversity analyses, suggesting frequent spread of PVYisolates between potato and tobacco crops in the field.
Phylogeography and Molecular Evolution of Potato virus Y
TLDR
Interestingly, the analysis of P3N-PIPO, a recently described gene in potyviruses, seems to show a variable length among the isolates analyzed, and this variability is explained, in part, by host-driven adaptation.
Discussion paper: The naming of Potato virus Y strains infecting potato
TLDR
This discussion paper proposes that any newly found isolates of PVY should be described within the context of the original strain groups based on the original methods of distinguishing strains, and sequence characterization of the complete genomes of isolates is highly recommended.
...
1
2
3
4
5
...