Comparing the hyper-variable V4 and V9 regions of the small subunit rDNA for assessment of ciliate environmental diversity

Journal of Eukaryotic Microbiology

Volumn 59, Issue 2, 2012, Pages 185-187

  Dunthorn, Micah ^a   Klier, Julia ^a,c   Bunge, John ^b   Stoeck, Thorsten ^a  

^a Rheinland Pfälzische Technische Universität Kaiserslautern Landau   (Germany)

^b Department of Obstetrics Gynecology   (United States)

^c LEIBNIZ INSTITUTE FOR BALTIC SEA RESEARCH   (Germany)

Author keywords

454 Pyrosequencing; Ciliophora; environmental sequencing; Illumina Solexa

Indexed keywords

PROTOZOAL DNA; RIBOSOME DNA;

CILIATE; COMPARATIVE STUDY; GENETIC VARIATION;

ARTICLE; BIODIVERSITY; CHEMISTRY; CILIATE; CLASSIFICATION; COMPARATIVE STUDY; CONFORMATION; GENETICS; SEQUENCE HOMOLOGY;

BIODIVERSITY; CILIOPHORA; DNA, PROTOZOAN; DNA, RIBOSOMAL; NUCLEIC ACID CONFORMATION; SEQUENCE HOMOLOGY, NUCLEIC ACID;

CILIOPHORA; EUKARYOTA;

EID: 84858702221     PISSN: 10665234     EISSN: 15507408     Source Type: Journal    
DOI: 10.1111/j.1550-7408.2011.00602.x     Document Type: Article

References (14)

1. Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W., &, Huse, S. M., 2009. A method for studying protistian diversity using massively parallel sequencing of V9 hypervariable region of small-subunit ribosomal RNA genes. PLoS ONE, 4: 7.
2. Bráte, J., Logares, R., Berney, C., Ree, D. K., Klaveness, D., Jakobsen, K. S., &, Shalchian-Tabrizi, K., 2010. Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA. ISME J., 4: 1144-1153.
3. Caron, D. A., Countway, P. D., Savai, P., Gast, R. J., Schnetzer, A., Moorthi, S. D., Dennett, M. R., Moran, D. M., &, Jones, A. C., 2009. Defining DNA-based operational taxonomic units for microbial-eukaryote ecology. Appl. Environ. Microbiol., 75: 5797-5808.
4. Cheung, M. K., Au, C. H., Chu, K. H., Kwan, H. S., &, Wong, C. K., 2010. Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing. ISME J., 4: 1053-1059.
5. Edgcomb, V., Orsi, W., Bunge, J., Jeon, S., Christen, R., Leslin, C., Holder, M., Taylor, G. T., Suarez, P., Varela, R., &, Epstein, S., 2011. Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequncing vs. Sanger insights into species richness. ISEM J., 5: 1357-1373.
6. Huber, J. A., Morrison, H. G., Huse, S. M., Neal, P. R., Sogin, M. L., &, Mark Welch, D. B., 2009. Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environ. Microbiol., 11: 1292-1302.
7. Lecroq, B., Lejzerowicz, F., Bachar, D., Christen, R., Esling, P., Baerlocher, L., Ásterás, M., Farinelli, L., &, Pawlowski, J., 2011. Ultra-deep sequencing of foraminiferal microbarcodes unveils hiddern richness of early monothalamous lineages in deep-sea sediments. Proc. Natl Acad. Sci. USA, 108: 13177-13182.
8. Medinger, R., Nolte, V., Pandey, R. V., Jost, S., Otenwälder, B., Schlötterer, C., &, Boenigk, J., 2010. Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys or moleclar diversity of eukaryotic microorganisms. Mol. Ecol., 19: 32-40.
9. Nebel, M., Pfabel, C., Stock, A., Dunthorn, M., &, Stoeck, T., 2011. Delimiting operational taxonomic units for assessing ciliate environmental diversity of small subunit rRNA gene sequences. Environ. Microbiol. Rep., 3: 154-158.
10. Nolte, V., Pandey, R. V., Jost, S., Medinger, R., Ottenwälder, B., Boenigk, J., &, Schlötterer, C., 2010. Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Mol. Ecol., 19: 2908-2915.
11. Pruesse, E., Quast, C., Knittel, K., Fuchs, B., Ludwig, W., Peplies, J., &, Glöckner, F. O., 2007. SILVA: a comprehensive online source for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res., 35: 7188-7196.
12. Stoeck, T., Bass, D., Nebel, M., Christen, R., Jones, M. D. M., Breiner, H. W., &, Richards, T. A., 2010. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol. Ecol., 19: 21-31.
13. Stoeck, T., Anke, B., Christen, R., Amaral-Zettler, L., Rodriguez-Mora, M. J., Chistoserdov, A., Orsi, W., &, Edgcomb, V. P., 2009. Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biol., 7: 72.
14. Thompson, J. D., Higgins, D. G., &, Gibson, T. J., 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22: 4673-4680. (Pubitemid 24354800)