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Viral Metagenomics

Overview of attention for book
Cover of 'Viral Metagenomics'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 Host-Associated Bacteriophage Isolation and Preparation for Viral Metagenomics
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    Chapter 2 Small RNA Isolation from Tissues of Grapevine and Woody Plants
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    Chapter 3 Double-Stranded RNA-Enriched Preparations to Identify Viroids by Next-Generation Sequencing
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    Chapter 4 Viral Double-Stranded RNAs (dsRNAs) from Plants: Alternative Nucleic Acid Substrates for High-Throughput Sequencing
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    Chapter 5 Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes
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    Chapter 6 Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples
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    Chapter 7 Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities
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    Chapter 8 Different Approaches to Discover Mycovirus Associated to Marine Organisms
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    Chapter 9 Use of siRNAs for Diagnosis of Viruses Associated to Woody Plants in Nurseries and Stock Collections
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    Chapter 10 The Use of High-Throughput Sequencing for the Study and Diagnosis of Plant Viruses and Viroids in Pollen
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    Chapter 11 High-Resolution Screening of Viral Communities and Identification of New Pathogens in Fish Using Next-Generation Sequencing
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    Chapter 12 Metagenomic Analyses of the Viruses Detected in Mycorrhizal Fungi and Their Host Orchid
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    Chapter 13 DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method
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    Chapter 14 From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool
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    Chapter 15 Shannon Entropy to Evaluate Substitution Rate Variation Among Viral Nucleotide Positions in Datasets of Viral siRNAs
  17. Altmetric Badge
    Chapter 16 Insect Virus Discovery by Metagenomic and Cell Culture-Based Approaches
Attention for Chapter 12: Metagenomic Analyses of the Viruses Detected in Mycorrhizal Fungi and Their Host Orchid
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Chapter title
Metagenomic Analyses of the Viruses Detected in Mycorrhizal Fungi and Their Host Orchid
Chapter number 12
Book title
Viral Metagenomics
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7683-6_12
Pubmed ID
Book ISBNs
978-1-4939-7682-9, 978-1-4939-7683-6
Authors

Hanako Shimura, Chikara Masuta, Yasunori Koda, Shimura, Hanako, Masuta, Chikara, Koda, Yasunori

Abstract

In nature, mycorrhizal association with soilborne fungi is indispensable for orchid families. Fungal structures from compatible endo-mycorrhizal fungi in orchid cells are digested in cells to be supplied to orchids as nutrition. Because orchid seeds lack the reserves for germination, they keep receiving nutrition through mycorrhizal formation from seed germination until shoots develop (leaves) and become photoautotrophic. Seeds of all orchid species surely geminate with the help of their own fungal partners, and this specific partnership has been acquired for a long evolutional history between orchids and fungi.We have studied the interactions between orchids and mycorrhizal fungi and recently conducted transcriptome analyses (RNAseq) by a next-generation sequencing (NGS) approach. It is possible that orchid RNA isolated form naturally grown plants is contaminated with RNAs derived from mycorrhizal fungi in the orchid cells. To avoid such contamination, we here prepared aseptically germinated orchid plants (i.e., fungus-free plants) together with a pure-cultured fungal isolate and field-growing orchid samples. In the cDNA library prepared from orchid and fungal tissues, we found that partitivirus-like sequences were common in an orchid and its mycorrhizal fungus. These partitivirus-like sequences were closely related by a phylogenetic analysis, suggesting that transmission of an ancestor virus between the two organisms occurred through the specific relation of the orchid and its associated fungus.

Twitter Demographics

The data shown below were collected from the profiles of 2 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 16 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 16 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 3 19%
Student > Ph. D. Student 3 19%
Student > Bachelor 1 6%
Other 1 6%
Lecturer 1 6%
Other 1 6%
Unknown 6 38%
Readers by discipline Count As %
Agricultural and Biological Sciences 5 31%
Biochemistry, Genetics and Molecular Biology 3 19%
Environmental Science 1 6%
Medicine and Dentistry 1 6%
Unknown 6 38%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 06 February 2019.
All research outputs
#13,758,094
of 21,190,873 outputs
Outputs from Methods in molecular biology
#4,119
of 11,951 outputs
Outputs of similar age
#173,728
of 294,198 outputs
Outputs of similar age from Methods in molecular biology
#5
of 5 outputs
Altmetric has tracked 21,190,873 research outputs across all sources so far. This one is in the 33rd percentile – i.e., 33% of other outputs scored the same or lower than it.
So far Altmetric has tracked 11,951 research outputs from this source. They receive a mean Attention Score of 3.3. This one has gotten more attention than average, scoring higher than 61% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 294,198 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 37th percentile – i.e., 37% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 5 others from the same source and published within six weeks on either side of this one.