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MBE Advance Access published online on March 16, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp049
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Evidence for homologous recombination in intracellular chemosynthetic clam symbionts

Frank J. Stewart1, Curtis R. Young2 and Colleen M. Cavanaugh2,*

1 Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
2 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138

* Mailing address: Department of Organismic and Evolutionary Biology, Harvard University, The Biological Laboratories, 16 Divinity Avenue, Cambridge, MA 02138. Phone: (617) 495-2177. Fax: (617) 496-6933. Email: cavanaug{at}fas.harvard.edu

Received for publication January 17, 2009. Revision received March 4, 2009. Accepted for publication March 9, 2009.

Homologous recombination is a fundamental mechanism for the genetic diversification of free-living bacteria. However, recombination may be limited in endosymbiotic bacteria, as these taxa are locked into an intracellular niche and may rarely encounter sources of foreign DNA. This study tested the hypothesis that vertically transmitted endosymbionts of deep-sea clams (Bivalvia:Vesicomyidae) show little or no evidence of recombination. Phylogenetic analysis of 13 loci distributed across the genomes of 14 vesicomyid symbionts revealed multiple, well-supported inconsistencies among gene tree topologies, and maximum likelihood-based tests rejected a hypothesis of shared evolutionary history (linkage) among loci. Further, multiple statistical methods confirmed the presence of recombination by detecting intragenic breakpoints in two symbiont loci. Recombination may be confined to a subset of vesicomyid symbionts, as some clades showed high levels of genomic stability, while others showed clear patterns of homologous exchange. Notably, a mosaic genome is present in symB, a symbiont lineage shown to have been acquired laterally (i.e., non-vertically) by Vesicomya sp. JdF clams. The majority of loci analyzed here supported a tight sister clustering of symB with the symbiont of a host species from the Mid-Atlantic Ridge, while others placed symB in a clade with symA, the dominant phylotype of V. sp. JdF clams. This result raises the hypothesis that lateral symbiont transfer between hosts may facilitate recombination by bringing divergent symbiont lineages into contact. Together, the data show that homologous recombination contributes to the diversification of vesicomyid clam symbionts, despite the intracellular lifestyle of these bacteria.

Key Words: genome evolution • recombination • lateral transmission • chemosynthesis • Calyptogena • hydrothermal vent


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F. J. Stewart, A. H. Y. Baik, and C. M. Cavanaugh
Genetic Subdivision of Chemosynthetic Endosymbionts of Solemya velum along the Southern New England Coast
Appl. Envir. Microbiol., September 15, 2009; 75(18): 6005 - 6007.
[Abstract] [Full Text] [PDF]


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