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Sequencing and analysis of the complete organellar genomes of Parmales, a closely related group to Bacillariophyta (diatoms)

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Abstract

We sequenced the complete plastid and mitochondrial genomes of the unicellular marine phytoplankton Triparma laevis, belonging to the order Parmales (Heterokonta). The cells of Parmales are surrounded by silicified cell walls, similar to Bacillariophyta (diatoms). T. laevis was recognized as a sister group of Bacillariophyta using a molecular phylogenetic analysis based on SSU rDNA and rbcL sequences. Bacillariophyta are the most successful group of phytoplankton in the modern ocean, but the origin and early evolution of them have not been clearly established. Detailed molecular analyses of T. laevis may increase our understanding of the evolutionary relationships among Parmales and Bacillariophyta. The gene contents of the plastid and mitochondrial genomes are similar between T. laevis and Bacillariophyta. The gene order of the plastid genome is also similar to Bacillariophyta, whereas the gene order of the mitochondrial genome is not conserved in Bacillariophyta, but the structure is more compact than Bacillariophyta. Phylogenetic analyses, using plastid-encoded concatenated amino acid datasets and mitochondria-encoded concatenated amino acid datasets suggest that T. laevis is a sister group of Bacillariophyta. These results suggest that the characteristics of the organellar genomes of T. laevis are similar and conserve ancestral characteristics more than Bacillariophyta.

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Acknowledgments

This work was supported in part by a Grant-in-Aid for the Global COE Program, “From the Earth to Earths” and Scientific Research (No. 26291085) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan and the Canon Foundation (A. K. and N. S.).

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Authors and Affiliations

  1. Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo, 153-8902, Japan

    Naoyuki Tajima & Naoki Sato

  2. National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan

    Kenji Saitoh

  3. Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan

    Shusei Sato

  4. Graduate School of Medicine and Faculty of Medicine Kyoto University, Section of Microbiology, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan

    Fumito Maruyama

  5. Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Tsukide 3-1-100, Higashi, Kumamoto, 862-8502, Japan

    Mutsuo Ichinomiya

  6. Faculty of Marine Bioscience, Fukui Prefectural University, 1-1 Gakuen-cho, Obama, Fukui, 917-0003, Japan

    Shinya Yoshikawa

  7. Department of Biological Information, Tokyo Institute of Technology, 4259-B65, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan

    Ken Kurokawa

  8. Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B65, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan

    Hiroyuki Ohta

  9. Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, 292-0818, Japan

    Satoshi Tabata

  10. Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Shinhamacho 3-27-5, Shiogama, Miyagi, 985-0001, Japan

    Akira Kuwata

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  1. Naoyuki Tajima
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  2. Kenji Saitoh
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  6. Shinya Yoshikawa
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  8. Hiroyuki Ohta
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  9. Satoshi Tabata
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  10. Akira Kuwata
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  11. Naoki Sato
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Correspondence to Naoyuki Tajima.

Additional information

Communicated by M. Kupiec.

This work is part of a dissertation submitted to the University of Tokyo in partial fulfillment of the requirements for the PhD degree.

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Tajima, N., Saitoh, K., Sato, S. et al. Sequencing and analysis of the complete organellar genomes of Parmales, a closely related group to Bacillariophyta (diatoms). Curr Genet 62, 887–896 (2016). https://doi.org/10.1007/s00294-016-0598-y

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