Mol Ecol. 2010 Mar;19 Suppl 1:81-8.

Ecogenomics: using massively parallel pyrosequencing to understand virus ecology.

Roossinck MJ, Saha P, Wiley GB, Quan J, White JD, Lai H, Chavarría F, Shen G, Roe BA.

Source

The Samuel Roberts Noble Foundation, Ardmore, OK 73402, USA. mroossinck@noble.org

Abstract

Environmental samples have been analysed for viruses in metagenomic studies, but these studies have not linked individual viruses to their hosts. We designed a strategy to isolate double-stranded RNA, a hallmark of RNA virus infection, from individual plants and convert this to cDNA with a unique four nucleotide Tag at each end. Using 96 different Tags allowed us to pool samples and still retain the link to the original sample. We then analysed the sequence of pooled samples using massively parallel sequencing with Roche 454 pyrosequencing such that 384 samples could be assessed per picotiter plate. Using this method we have been able to analyse thousands of plants, and we have discovered several thousand new plant viruses, all linked to their specific plant hosts. Here we describe the method in detail, including the results and analysis for eight pools of samples. This technology will be extremely useful in understanding the full scope of plant virus biodiversity.

PMID:: 20331772; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances

Publication Types

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Related citations

Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard. [Virology. 2010]
Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard.
Coetzee B, Freeborough MJ, Maree HJ, Celton JM, Rees DJ, Burger JT. Virology. 2010 May 10; 400(2):157-63. Epub 2010 Feb 20.
Complete nucleotide sequences and genome characterization of a novel double-stranded RNA virus infecting Rosa multiflora. [Arch Virol. 2008]
Complete nucleotide sequences and genome characterization of a novel double-stranded RNA virus infecting Rosa multiflora.
Salem NM, Golino DA, Falk BW, Rowhani A. Arch Virol. 2008; 153(3):455-62. Epub 2008 Jan 3.
A strategy for rapid cDNA cloning from double-stranded RNA templates isolated from plants infected with RNA viruses by using Taq DNA polymerase. [J Virol Methods. 2000]
A strategy for rapid cDNA cloning from double-stranded RNA templates isolated from plants infected with RNA viruses by using Taq DNA polymerase.
Zhang YP, Rowhani A. J Virol Methods. 2000 Jan; 84(1):59-63.
Review Microarrays for rapid identification of plant viruses. [Annu Rev Phytopathol. 2007]
Review Microarrays for rapid identification of plant viruses.
Boonham N, Tomlinson J, Mumford R. Annu Rev Phytopathol. 2007; 45:307-28.
Review Genomic organization of T and W, a new family of double-stranded RNAs from Saccharomyces cerevisiae. [Prog Nucleic Acid Res Mol Biol. 1993]
Review Genomic organization of T and W, a new family of double-stranded RNAs from Saccharomyces cerevisiae.
Esteban R, Rodríguez-Cousiño N, Esteban LM. Prog Nucleic Acid Res Mol Biol. 1993; 46:155-82.

See reviews... See all...

Cited by 4 PubMed Central articles

Viral ancestors of antiviral systems. [Viruses. 2011]
Viral ancestors of antiviral systems.
Villarreal LP. Viruses. 2011 Oct; 3(10):1933-58. Epub 2011 Oct 20.
Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies. [PLoS One. 2011]
Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies.
Ng TF, Duffy S, Polston JE, Bixby E, Vallad GE, Breitbart M. PLoS One. 2011 Apr 22; 6(4):e19050. Epub 2011 Apr 22.
Metagenomic analysis of the viromes of three North American bat species: viral diversity among different bat species that share a common habitat. [J Virol. 2010]
Metagenomic analysis of the viromes of three North American bat species: viral diversity among different bat species that share a common habitat.
Donaldson EF, Haskew AN, Gates JE, Huynh J, Moore CJ, Frieman MB. J Virol. 2010 Dec; 84(24):13004-18. Epub 2010 Oct 6.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Ecogenomics: using massively parallel pyrosequencing to understand virus ecology...
Ecogenomics: using massively parallel pyrosequencing to understand virus ecology.
Mol Ecol. 2010 Mar ;19 Suppl 1:81-8.

PubMed
Effect of Epimedium brevicornum Maxim extract on elicitation of penile erection ...
Effect of Epimedium brevicornum Maxim extract on elicitation of penile erection in the rat.
Urology. 2006 Mar ;67(3):631-5.

PubMed
Juvenile onset systemic sclerosis: a single center experience of 23 cases from A...
Juvenile onset systemic sclerosis: a single center experience of 23 cases from Asia.
Clin Rheumatol. 2007 Aug ;26(8):1259-62. Epub 2006 Dec 19 .

PubMed
Tamoxifen for early breast cancer: an overview of the randomised trials. Early B...
Tamoxifen for early breast cancer: an overview of the randomised trials. Early Breast Cancer Trialists' Collaborative Group.
Lancet. 1998 May 16 ;351(9114):1451-67.

PubMed
Lichen sclerosus and eosinophilic fasciitis as manifestations of chronic graft-v...
Lichen sclerosus and eosinophilic fasciitis as manifestations of chronic graft-versus-host disease: expanding the sclerodermoid spectrum.
J Am Acad Dermatol. 2005 Oct ;53(4):591-601.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: