Ecogenomics: Using massively parallel pyrosequencing to understand virus ecology

Marilyn J. Roossinck, Prasenjit Saha, Graham B. Wiley, Jiaxi Quan, James D. White, Hongshing Lai, Felipe Chavarría, Guoan Shen, Bruce A. Roe

Research output: Contribution to journalArticle

139 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)81-88
Number of pages8
JournalMolecular ecology
Volume19
Issue numberSUPPL. 1
DOIs
StatePublished - Mar 1 2010

Fingerprint

Ecology
Plant Viruses
virus
ecology
Viruses
viruses
RNA Virus Infections
High-Throughput Nucleotide Sequencing
Metagenomics
Double-Stranded RNA
Biodiversity
plant viruses
RNA
sampling
Nucleotides
Complementary DNA
Technology
double-stranded RNA
host plant
biodiversity

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Roossinck, Marilyn J. ; Saha, Prasenjit ; Wiley, Graham B. ; Quan, Jiaxi ; White, James D. ; Lai, Hongshing ; Chavarría, Felipe ; Shen, Guoan ; Roe, Bruce A. / Ecogenomics : Using massively parallel pyrosequencing to understand virus ecology. In: Molecular ecology. 2010 ; Vol. 19, No. SUPPL. 1. pp. 81-88.
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Roossinck, MJ, Saha, P, Wiley, GB, Quan, J, White, JD, Lai, H, Chavarría, F, Shen, G & Roe, BA 2010, 'Ecogenomics: Using massively parallel pyrosequencing to understand virus ecology', Molecular ecology, vol. 19, no. SUPPL. 1, pp. 81-88. https://doi.org/10.1111/j.1365-294X.2009.04470.x

Ecogenomics : Using massively parallel pyrosequencing to understand virus ecology. / Roossinck, Marilyn J.; Saha, Prasenjit; Wiley, Graham B.; Quan, Jiaxi; White, James D.; Lai, Hongshing; Chavarría, Felipe; Shen, Guoan; Roe, Bruce A.

In: Molecular ecology, Vol. 19, No. SUPPL. 1, 01.03.2010, p. 81-88.

Research output: Contribution to journalArticle

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