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An Ancient Repeat Sequence in the ATP Synthase β-Subunit Gene of Forcipulate Sea Stars

Journal of Molecular Evolution volume 65, pages 564–573 (2007)Cite this article

Abstract

A novel repeat sequence with a conserved secondary structure is described from two nonadjacent introns of the ATP synthase β-subunit gene in sea stars of the order Forcipulatida (Echinodermata: Asteroidea). The repeat is present in both introns of all forcipulate sea stars examined, which suggests that it is an ancient feature of this gene (with an approximate age of 200 Mya). Both stem and loop regions show high levels of sequence constraint when compared to flanking nonrepetitive intronic regions. The repeat was also detected in (1) the family Pterasteridae, order Velatida and (2) the family Korethrasteridae, order Velatida. The repeat was not detected in (1) the family Echinasteridae, order Spinulosida, (2) the family Astropectinidae, order Paxillosida, (3) the family Solasteridae, order Velatida, or (4) the family Goniasteridae, order Valvatida. The repeat lacks similarity to published sequences in unrestricted GenBank searches, and there are no significant open reading frames in the repeat or in the flanking intron sequences. Comparison via parametric bootstrapping to a published phylogeny based on 4.2 kb of nuclear and mitochondrial sequence for a subset of these species allowed the null hypothesis of a congruent phylogeny to be rejected for each repeat, when compared separately to the published phylogeny. In contrast, the flanking nonrepetitive sequences in each intron yielded separate phylogenies that were each congruent with the published phylogeny. In four species, the repeat in one or both introns has apparently experienced gene conversion. The two introns also show a correlated pattern of nucleotide substitutions, even after excluding the putative cases of gene conversion.

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Acknowledgments

Drs. Scott W. Herke, Jinchuan Xing, Miriam Konkel, and Mark A. Batzer provided technical advice concerning the polymerase chain reaction (PCR) and cloning reactions. Drs. Batzer, Fareed Abou-Ela, Jonathan M. Flowers, Mark S. Hafner, and Luciano Matzkin provided useful discussion and advice. Dr. Robert Van Syoc arranged the loan of tissue pieces from the California Academy of Sciences collection. Dr. Christopher L. Mah confirmed some taxonomic identifications. AnhThao Nguyen, Ivy Nguyen, Michael Heier, and Cassie James assisted in the laboratory.

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  1. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803-1715, USA

    David W. Foltz

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  1. David W. Foltz
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Correspondence to David W. Foltz.

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Foltz, D.W. An Ancient Repeat Sequence in the ATP Synthase β-Subunit Gene of Forcipulate Sea Stars. J Mol Evol 65, 564–573 (2007). https://doi.org/10.1007/s00239-007-9036-6

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  • DOI: https://doi.org/10.1007/s00239-007-9036-6

Keywords

  • ATP synthase
  • Secondary structure
  • DNA repeat
  • Introns
  • Gene conversion
  • Sea stars

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