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A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes
Open accessAbstract
BACKGROUND: Massively parallel pyrosequencing of amplicons from the V6 hypervariable regions of small-subunit (SSU) ribosomal RNA (rRNA) genes is commonly used to assess diversity and richness in bacterial and archaeal populations. Recent advances in pyrosequencing technology provide read lengths of up to 240 nucleotides. Amplicon pyrosequencing can now be applied to longer variable regions of the SSU rRNA gene including the V9 region in eukaryotes. METHODOLOGY/PRINCIPAL FINDINGS: We present a protocol for the amplicon pyrosequencing of V9 regions for eukaryotic environmental samples for biodiversity inventories and species richness estimation. The International Census of Marine Microbes (ICoMM) and the Microbial Inventory Research Across Diverse Aquatic Long Term Ecological Research Sites (MIRADA-LTERs) projects are already employing this protocol for tag sequencing of eukaryotic samples in a wide diversity of both marine and freshwater environments. CONCLUSIONS/SIGNIFICANCE: Massively parallel pyrosequencing of eukaryotic V9 hypervariable regions of SSU rRNA genes provides a means of estimating species richness from deeply-sampled populations and for discovering novel species from the environment.
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Cited by
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Self-citationChen, W., Ren, K., Isabwe, A., Chen, H., Liu, M., & Yang, J. (2019) · Microbiome · doi:10.1186/s40168-019-0749-8 · Cited by 804
Insights into global diatom distribution and diversity in the world’s ocean
Malviya, S., Scalco, E., Audic, S., Vincent, F., Veluchamy, A., Poulain, J., Wincker, P., Iudicone, D., de Vargas, C., Bittner, L., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1509523113 · Cited by 773
The role of ciliate protozoa in the rumen
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Ramirez, K. S., Leff, J. W., Barberán, A., Bates, S. T., Betley, J., Crowther, T. W., Kelly, E. F., Oldfield, E. E., Shaw, E. A., Steenbock, C., et al. (2014) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2014.1988 · Cited by 423
Metadata
- Authors
- Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W., & Huse, S. M.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2009-07-27
- Volume
- 4
- Issue
- 7
- Pages
- e6372
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W1998599366
- Cited by
- 1,076
- References
- 0
- FWCI
- 7.44
- Type
- journal article
- Language
- en
- Open access
- gold
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- Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W., & Huse, S. M. (2009). A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes. PLoS ONE. https://doi.org/10.1371/journal.pone.0006372
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