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Complete mitogenome of the edible sea urchin Loxechinus albus: genetic structure and comparative genomics within Echinozoa

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Abstract

The edible Chilean red sea urchin, Loxechinus albus, is the only species of its genus and endemic to the Southeastern Pacific. In this study, we reconstructed the mitochondrial genome of L. albus by combining Sanger and pyrosequencing technologies. The mtDNA genome had a length of 15,737 bp and encoded the same 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes as other animal mtDNAs. The size of this mitogenome was similar to those of other Echinodermata species. Structural comparisons showed a highly conserved structure, composition, and gene order within Echinoidea and Holothuroidea, and nearly identical gene organization to that found in Asteroidea and Crinoidea, with the majority of differences explained by the inversions of some tRNA genes. Phylogenetic reconstruction supported the monophyly of Echinozoa and recovered the monophyletic relationship of Holothuroidea and Echinoidea. Within Holothuroidea, Bayesian and maximum likelihood analyses recovered a sister-group relationship between Dendrochirotacea and Aspidochirotida. Similarly within Echinoidea, these analyses revealed that L. albus was closely related to Paracentrotus lividus, both being part of a sister group to Strongylocentrotidae and Echinometridae. In addition, two major clades were found within Strongylocentrotidae. One of these clades comprised all of the representative species Strongylocentrotus and Hemicentrotus, whereas the other included species of Mesocentrotus and Pseudocentrotus.

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Acknowledgments

The authors express their thanks to the editor and the anonymous referees for their constructive suggestions, which considerably improved the quality of the paper. This study was financial supported by Fondo de Fomento al Desarrollo Cientifico y Tecnológico FONDEF D09I1065.  Finally, the Millennium Nucleus Center for the Study of Multiple-drivers on Marine Socio-Ecological Systems (MUSELS) by MINECON Project NC120086 also supported this work during the final stage. J.D.G.E. was supported by FONDECYT-Postdoctoral grant no. 3130381.

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  1. Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile

    Graciela Cea, Juan Diego Gaitán-Espitia & Leyla Cárdenas

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  1. Graciela Cea
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  2. Juan Diego Gaitán-Espitia
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  3. Leyla Cárdenas
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Correspondence to Leyla Cárdenas.

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Figure S1. Putative secondary structures of 22 tRNAs encoded by the mitochondrial genome of Loxechinus albus. (PDF 468 kb)

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Cea, G., Gaitán-Espitia, J.D. & Cárdenas, L. Complete mitogenome of the edible sea urchin Loxechinus albus: genetic structure and comparative genomics within Echinozoa. Mol Biol Rep 42, 1081–1089 (2015). https://doi.org/10.1007/s11033-014-3847-5

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