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Massively parallel sequencing (MPS) assays for sequencing mitochondrial genomes: the phylogenomic implications for Acropora staghorn corals (Scleractinia; Acroporidae)

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Abstract

Based on only a handful of mitochondrial and nuclear loci, the phylogenetic relationships within the genus Acropora have been unclear. However, with the new sequencing technology of massively parallel sequencing (MPS), the inter-specific relationships within Acropora may be resolved. We performed multiplex sequencing of the mitochondrial genome of eleven Acropora species representing different groups using the Illumina Solexa platform. Mitochondrial genomes were sequenced from long PCR-amplified templates ligated with different index sequences (~9 kbp) and analyzed using the mitochondrial genome of Acropora tenuis as a reference. A total of 75 million read outputs in one Illumina lane were obtained, with mapping results having coverage up to 44,000-fold. Assembly results of multiplex samples confirmed with Sanger sequencing produced <0.03 % error. Aligning the eleven mitochondrial genomes with the reference sequence revealed only 110 phylogenetically informative sites over the mitochondrial genome. The largest pairwise genetic distance observed was in the putative control region (0.022). A comparison of two phylogenetic trees based on the whole mitochondrial genome and control region showed that the former tree produces a higher resolution of phylogenetic relationships. In this study, we demonstrated the first case of sequencing cnidarian mitochondrial genomes by using multiplex MPS and applying it in a phylogenomic analyses.

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Acknowledgments

This project was funded by the National Science Council (2010–2012), Academia Sinica Thematic Grant (2006–2010), and the Biodiversity Research Centre, Academia Sinica (BRCAS) to CAC. We would like to thank the staffs of Penghu Marine Biological Research Centre (PMBRC)-BRCAS joint Marine Laboratory, BRCAS Green Island Reef Laboratory (GIRL) Green Island Marine Station, and Kenting National Park for assistance with fieldwork. Special thanks go to CREEG members and the David Miller Group for intellectual inputs to this paper, and to Tyler McCraney and Buford Pruitt, Jr. for English language editing. We also greatly thank three anonymous reviewers and the communicating editor for useful comments and suggestions to improve the manuscript.

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Authors and Affiliations

  1. Biodiversity Research Centre, Academia Sinica, Nangang, Taipei, 115, Taiwan

    Shang-Yin Vanson Liu, Chia-Ling Carynn Chan, Silvia Fontana & Chaolun Allen Chen

  2. Penghu Marine Biological Research Center, Taiwan Fishery Research Institute, Makong City, Penghu, 880, Taiwan

    Hernyi Justin Hsieh

  3. Department of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan

    Silvia Fontana

  4. Taiwan International Graduate Program-Biodiversity, Academia Sinica, Nangang, Taipei, 115, Taiwan

    Silvia Fontana & Chaolun Allen Chen

  5. Museum of Tropical Queensland, Townsville, QLD, 4810, Australia

    Carden C. Wallace

  6. Institute of Oceanography, National Taiwan University, Taipei, 106, Taiwan

    Chaolun Allen Chen

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  1. Shang-Yin Vanson Liu
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Correspondence to Chaolun Allen Chen.

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Communicated by C. Riginos.

Shang-Yin Vanson Liu and Chia-Ling Carynn Chan are co-first authors.

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Liu, SY.V., Chan, CL.C., Hsieh, H.J. et al. Massively parallel sequencing (MPS) assays for sequencing mitochondrial genomes: the phylogenomic implications for Acropora staghorn corals (Scleractinia; Acroporidae). Mar Biol 162, 1383–1392 (2015). https://doi.org/10.1007/s00227-015-2657-1

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