Chapter 40
Amplicon Pyrosequencing Analysis of Endosymbiont Population Structure
Frank J. Stewart,
Colleen M. Cavanaugh,
Frank J. Stewart
Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
Search for more papers by this authorColleen M. Cavanaugh
Harvard University, Cambridge, Massachusetts, USA
Search for more papers by this authorFrank J. Stewart,
Colleen M. Cavanaugh,
Frank J. Stewart
Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
Search for more papers by this authorColleen M. Cavanaugh
Harvard University, Cambridge, Massachusetts, USA
Search for more papers by this authorBook Editor(s):Frans J. de Bruijn,
Frans J. de Bruijn
Laboratory of Plant Micro-organism Interaction, CNRS-INRA, Castanet Tolosan, France
Search for more papers by this authorFirst published: 16 September 2011
Summary
This chapter contains sections titled:
-
Introduction
-
Methods
-
Results and Discussion
-
Programs and Internet Resources Used in this Study
-
References
PROGRAMS AND INTERNET RESOURCES USED IN THIS STUDY
- TCS (http://darwin.uvigo.es/software/tcs.html)
- BlastClust—distributed as part of standalone BLAST package (http://www.ncbi.nlm.nih.gov/guide/data-software/)
- ClustalX (http://www.clustal.org/)
- MacClade (http://macclade.org/macclade.html)
- GSAmplicon (http://www.roche-applied-science.com/)
- REFERENCES
- Binladen J, Gilbert MTP, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E. 2007. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE 2: e197.
- Bordenstein SR, Reznikoff WS. 2005. Mobile DNA in obligate intra-cellular bacteria. Nat. Rev. Microbiol. 3: 688–699.
- Cary SC, Giovannoni SJ. 1993. Transovarial inheritance of endosym-biotic bacteria in clams inhabiting deep-sea hydrothermal vents and cold seeps. Proc. Natl. Acad. Sci. USA 90: 5695–5699.
- Clement M, Posada D, Crandall KA. 2000. TCS: A computer program to estimate gene genealogies. Mol. Ecol. 9: 1657–1659.
- Droege M, Hill B. 2008. The Genome Sequencer FLX™ System—Longer reads, more applications, straight forward bioinformatics and more complete data sets. J. Biotechnol. 136: 3–10.
- Dubilier N, Bergin C, Lott C. 2008. Symbiotic diversity in marine animals: The art of harnessing chemosynthesis. Nat. Rev. Microbiol. 6: 725–740.
- Goffredi SK, Hurtado LA, Hallam S, Vrijenhoek RC. 2003. Evolutionary relationships of deep-sea vent and seep clams (Mollusca: Vesicomyidae) of the “pacifica/lepta” species complex. Mar. Biol. 142: 311–320.
- Huber JA, Mark Welch D, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin ML. 2007. Microbial population structures in the deep marine biosphere. Science 318: 97–100.
- Hurtado LA, Mateos M, Lutz RA, Vrijenhoek RC. 2003. Coupling of bacterial endosymbiont and host mitochondrial genomes in the hydrothermal vent clam Calyptogena magnifica. Appl. Environ. Microbiol. 69: 2058–2064.
- Huse SM, Huber JA, Morrison HG, Sogin ML, Mark Welch D. 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8: R143.
- Kunin V, Engelbrektson A, Ochman H, Hugenholtz P. 2009. Wrinkles in the rare biosphere: Pyrosequencing errors lead to artificial inflation of diversity estimates. Environ. Microbiol. 12: 118–123.
- Mira A, Moran NA. 2002. Estimating population size and transmission bottlenecks in maternally transmitted endosymbiotic bacteria. Microb. Ecol. 44: 137–143.
- Moran NA. 1996. Accelerated evolution and Muller's ratchet in endosymbiotic bacteria. Proc Natl. Acad. Sci. USA 93: 2873–2878.
- Moran NA, McCutcheon JP, Nakabachi A. 2008. Genomics and Evolution of heritable bacterial symbionts. Annu. Rev. Genet. 42: 165–190.
- Newton ILG, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, et al. 2007. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315: 998–1000.
- Peek AS, Feldman RA, Lutz RA, Vrijenhoek RC. 1998. Cospeciation of chemoautotrophic bacteria and deep-sea clams. Proc. Natl. Acad. Sci. USA 95: 9962–9966.
- Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, et al. 2006. Microbial diversity in the deep sea and the underexplored “rare biosphere.” Proc. Natl. Acad. Sci. USA 103: 12115–12120.
- Stewart FJ, Cavanaugh CM. 2009. Pyrosequencing analysis of endosymbiont population structure: Co-occurrence of divergent symbiont lineages in a single vesicomyid host clam. Environ. Microbiol. 11: 2136–2147.
- Stewart FJ, Newton ILG, Cavanaugh CM. 2005. Chemosynthetic endosymbioses: Adaptations to oxic–anoxic interfaces. Trends Micro-biol. 13: 439–448.
- Stewart FJ, Young CR, Cavanaugh CM. 2008. Lateral symbiont acquisition in a maternally transmitted chemosynthetic clam endosymbiosis. Mol. Biol. Evol. 25: 673–687.
- Stewart FJ, Young CR, Cavanaugh CM. 2009. Evidence for homologous recombination in intracellular chemosynthetic clam symbionts. Mol. Biol. Evol. 26: 1391–1404.
- Wernegreen JJ. 2005. For better or for worse: Genomic consequences of intracellular mutualism and parasitism. Curr. Opin. Genet. Dev. 15: 572–583.
