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Complete genome and bimodal genomic structure of the amoebal symbiont Neochlamydia strain S13 revealed by ultra-long reads obtained from MinION

Journal of Human Genetics volume 65, pages 41–48 (2020)Cite this article

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Abstract

Neochlamydia strain S13 is an amoebal symbiont of an Acanthamoeba sp. The symbiont confers resistance to Legionella pneumophila on its host; however, the molecular mechanism underlying this resistance is not completely understood. Genome analyses have been crucial for understanding the complicated host–symbiont relationship but segregating the host’s genome DNA from the symbiont’s DNA is often challenging. In this study, we successfully identified a bimodal genomic structure in Neochlamydia strain S13 using PacBio RS II supported by ultra-long reads derived from MinION. One mode consisted of circular sequences of 2,586,667 and 231,307 bp; the other was an integrated sequence of the two via long homologous regions. They encoded 2175 protein-coding regions, some of which were implied to be acquired via horizontal gene transfer. They were specifically conserved in the genus Neochlamydia and formed a cluster in the genome, presumably by multiplication through genome replication. Moreover, it was notable that the sequenced DNA was obtained without segregating the symbiont DNA from the host. This is an easy and versatile technique that facilitates the characterization of diverse hosts and symbionts in nature.

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Acknowledgements

We thank Aiko Ohnuma and Naoko Kawai for conducting sequencing. This study was supported by grants-in-aid for Japan Society for the Promotion Science (JSPS) KAKENHI, grant numbers 16K15270, 26670206, 24659194, and 24117501 “Innovation Areas (Matryoshka-type evolution).”

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Authors and Affiliations

  1. Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan

    Junya Yamagishi, Kyoko Hayashida & Chihiro Sugimoto

  2. Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, Sapporo, Hokkaido, Japan

    Junya Yamagishi & Chihiro Sugimoto

  3. School of Medical Technology, Health Sciences University of Hokkaido, Sapporo, Hokkaido, Japan

    Junji Matsuo

  4. Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan

    Torahiko Okubo & Hiroyuki Yamaguchi

  5. Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan

    Makoto Kuroda & Tsuyoshi Sekizuka

  6. Research Institute for Microbial Diseases, Osaka University, Osaka, Japan

    Hiroki Nagai

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  1. Junya Yamagishi
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Correspondence to Junya Yamagishi.

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Yamagishi, J., Hayashida, K., Matsuo, J. et al. Complete genome and bimodal genomic structure of the amoebal symbiont Neochlamydia strain S13 revealed by ultra-long reads obtained from MinION. J Hum Genet 65, 41–48 (2020). https://doi.org/10.1038/s10038-019-0684-3

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