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The Mitochondrial Genome of a Deep-Sea Bamboo Coral (Cnidaria, Anthozoa, Octocorallia, Isididae): Genome Structure and Putative Origins of Replication Are Not Conserved Among Octocorals

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Abstract

Octocoral mitochondrial (mt) DNA is subject to an exceptionally low rate of substitution, and it has been suggested that mt genome content and structure are conserved across the subclass, an observation that has been supported for most octocorallian families by phylogenetic analyses using PCR products spanning gene boundaries. However, failure to recover amplification products spanning the nad4L–msh1 gene junction in species from the family Isididae (bamboo corals) prompted us to sequence the complete mt genome of a deep-sea bamboo coral (undescribed species). Compared to the “typical” octocoral mt genome, which has 12 genes transcribed on one strand and 5 genes on the opposite (cox2, atp8, atp6, cox3, trnM), in the bamboo coral genome a contiguous string of 5 genes (msh1, rnl, nad2, nad5, nad4) has undergone an inversion, likely in a single event. Analyses of strand-specific compositional asymmetry suggest that (i) the light-strand origin of replication was also inverted and is adjacent to nad4, and (ii) the orientation of the heavy-strand origin of replication (OriH) has reversed relative to that of previously known octocoral mt genomes. Comparative analyses suggest that intramitochondrial recombination and errors in replication at OriH may be responsible for changes in gene order in octocorals and hexacorals, respectively. Using primers flanking the regions at either end of the inverted set of five genes, we examined closely related taxa and determined that the novel gene order is restricted to the deep-sea subfamily Keratoisidinae; however, we found no evidence for strand-specific mutational biases that may influence phylogenetic analyses that include this subfamily of bamboo corals.

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Acknowledgments

The authors thank Megan Barkes, Wally Renne, Steve Allen, Allison Manning, and Joris L. van der Ham for their assistance in the lab; Eric Pante for help with R; the crews of the R/V Ronald H. Brown and IFE ROVs, Argus and Hercules, and our colleagues on the NOAA-OE Deep Atlantic Stepping Stones 2005 cruise for their assistance at sea; and Cathy McFadden and Phil Alderslade for additional samples. We also gratefully acknowledge Les Watling for his ongoing morphology-based identification of the bamboo corals. The manuscript was greatly improved by comments from Joe Neigel, E. Pante, Patricia Rosel, Jana Thoma, J.L. van der Ham, and three anonymous reviewers. M.R.B. was supported by a State of Louisiana Board of Regents doctoral fellowship (LEQSF[2004-09]-GF-21). Partial support for this research was provided by funding from NOAA’s Office of Ocean Exploration (NA05OAR4601061), NOAA/NMFS Auke Bay Laboratory (NFFS7400-5-00022), and NSF’s Ocean Sciences Division–Biological Oceanography Program (OCE-0624601).

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  1. Department of Biology, University of Louisiana at Lafayette, P.O. Box 42451, Lafayette, LA, 70504, USA

    Mercer R. Brugler & Scott C. France

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Mercer R. Brugler and Scott C. France have contributed equally to this work and their names are listed alphabetically.

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Brugler, M.R., France, S.C. The Mitochondrial Genome of a Deep-Sea Bamboo Coral (Cnidaria, Anthozoa, Octocorallia, Isididae): Genome Structure and Putative Origins of Replication Are Not Conserved Among Octocorals. J Mol Evol 67, 125–136 (2008). https://doi.org/10.1007/s00239-008-9116-2

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