454-pyrosequencing: a molecular battiscope for freshwater viral ecology

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454-pyrosequencing : a molecular battiscope for freshwater viral ecology. / Rooks, David J; Smith, Darren L; McDonald, James E; Woodward, Martin J; McCarthy, Alan J; Allison, Heather E.

In: Genes, Vol. 1, No. 2, 21.07.2010, p. 210-26.

Research output: Contribution to journalArticle

HarvardHarvard

Rooks, DJ, Smith, DL, McDonald, JE, Woodward, MJ, McCarthy, AJ & Allison, HE 2010, '454-pyrosequencing: a molecular battiscope for freshwater viral ecology', Genes, vol. 1, no. 2, pp. 210-26. https://doi.org/10.3390/genes1020210

APA

Rooks, D. J., Smith, D. L., McDonald, J. E., Woodward, M. J., McCarthy, A. J., & Allison, H. E. (2010). 454-pyrosequencing: a molecular battiscope for freshwater viral ecology. Genes, 1(2), 210-26. https://doi.org/10.3390/genes1020210

CBE

Rooks DJ, Smith DL, McDonald JE, Woodward MJ, McCarthy AJ, Allison HE. 2010. 454-pyrosequencing: a molecular battiscope for freshwater viral ecology. Genes. 1(2):210-26. https://doi.org/10.3390/genes1020210

MLA

VancouverVancouver

Rooks DJ, Smith DL, McDonald JE, Woodward MJ, McCarthy AJ, Allison HE. 454-pyrosequencing: a molecular battiscope for freshwater viral ecology. Genes. 2010 Jul 21;1(2):210-26. https://doi.org/10.3390/genes1020210

Author

Rooks, David J ; Smith, Darren L ; McDonald, James E ; Woodward, Martin J ; McCarthy, Alan J ; Allison, Heather E. / 454-pyrosequencing : a molecular battiscope for freshwater viral ecology. In: Genes. 2010 ; Vol. 1, No. 2. pp. 210-26.

RIS

TY - JOUR

T1 - 454-pyrosequencing

T2 - Genes

AU - Rooks, David J

AU - Smith, Darren L

AU - McDonald, James E

AU - Woodward, Martin J

AU - McCarthy, Alan J

AU - Allison, Heather E

PY - 2010/7/21

Y1 - 2010/7/21

N2 - Viruses, the most abundant biological entities on the planet, are capable of infecting organisms from all three branches of life, although the majority infect bacteria where the greatest degree of cellular diversity lies. However, the characterization and assessment of viral diversity in natural environments is only beginning to become a possibility. Through the development of a novel technique for the harvest of viral DNA and the application of 454 pyrosequencing, a snapshot of the diversity of the DNA viruses harvested from a standing pond on a cattle farm has been obtained. A high abundance of viral genotypes (785) were present within the virome. The absolute numbers of lambdoid and Shiga toxin (Stx) encoding phages detected suggested that the depth of sequencing had enabled recovery of only ca. 8% of the total virus population, numbers that agreed within less than an order of magnitude with predictions made by rarefaction analysis. The most abundant viral genotypes in the pond were bacteriophages (93.7%). The predominant viral genotypes infecting higher life forms found in association with the farm were pathogens that cause disease in cattle and humans, e.g. members of the Herpesviridae. The techniques and analysis described here provide a fresh approach to the monitoring of viral populations in the aquatic environment, with the potential to become integral to the development of risk analysis tools for monitoring the dissemination of viral agents of animal, plant and human diseases.

AB - Viruses, the most abundant biological entities on the planet, are capable of infecting organisms from all three branches of life, although the majority infect bacteria where the greatest degree of cellular diversity lies. However, the characterization and assessment of viral diversity in natural environments is only beginning to become a possibility. Through the development of a novel technique for the harvest of viral DNA and the application of 454 pyrosequencing, a snapshot of the diversity of the DNA viruses harvested from a standing pond on a cattle farm has been obtained. A high abundance of viral genotypes (785) were present within the virome. The absolute numbers of lambdoid and Shiga toxin (Stx) encoding phages detected suggested that the depth of sequencing had enabled recovery of only ca. 8% of the total virus population, numbers that agreed within less than an order of magnitude with predictions made by rarefaction analysis. The most abundant viral genotypes in the pond were bacteriophages (93.7%). The predominant viral genotypes infecting higher life forms found in association with the farm were pathogens that cause disease in cattle and humans, e.g. members of the Herpesviridae. The techniques and analysis described here provide a fresh approach to the monitoring of viral populations in the aquatic environment, with the potential to become integral to the development of risk analysis tools for monitoring the dissemination of viral agents of animal, plant and human diseases.

KW - Journal Article

U2 - 10.3390/genes1020210

DO - 10.3390/genes1020210

M3 - Article

VL - 1

SP - 210

EP - 226

JO - Genes

JF - Genes

SN - 2073-4425

IS - 2

ER -