The landscape of coadaptation in Vibrio parahaemolyticus

  1. Yujun Cui  Is a corresponding author
  2. Chao Yang
  3. Hongling Qiu
  4. Hui Wang
  5. Ruifu Yang
  6. Daniel Falush  Is a corresponding author
  1. Beijing Institute of Microbiology and Epidemiology, China
  2. Institute for Nutritional Sciences, Chinese Academy of Sciences, China
  3. Institute Pasteur of Shanghai, Chinese Academy of Sciences, China

Abstract

Investigating fitness interactions in natural populations remains a considerable challenge. We take advantage of the unique population structure of Vibrio parahaemolyticus, a bacterial pathogen of humans and shrimp, to perform a genome-wide screen for coadapted genetic elements. We identified 90 interaction groups (IGs) involving 1,560 coding genes. 82 IGs are between accessory genes, many of which have functions related to carbohydrate transport and metabolism. Only 8 involve both core and accessory genomes. The largest includes 1,540 SNPs in 82 genes and 338 accessory genome elements, many involved in lateral flagella and cell wall biogenesis. The interactions have a complex hierarchical structure encoding at least four distinct ecological strategies. One strategy involves a divergent profile in multiple genome regions, while the others involve fewer genes and are more plastic. Our results imply that most genetic alliances are ephemeral but that increasingly complex strategies can evolve and eventually cause speciation.

Data availability

All data are publicly available.

The following previously published data sets were used

Article and author information

Author details

  1. Yujun Cui

    State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
    For correspondence
    cuiyujun.new@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
  2. Chao Yang

    State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0626-0586
  3. Hongling Qiu

    Institute for Nutritional Sciences, Chinese Academy of Sciences, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Hui Wang

    Institute for Nutritional Sciences, Chinese Academy of Sciences, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.
  5. Ruifu Yang

    State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Daniel Falush

    Center for Microbes, Development and Health, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
    For correspondence
    danielfalush@googlemail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2956-0795

Funding

National Key Research & Development Program of China (No. 2017YFC1601503 and 2018YFC1603902)

  • Yujun Cui

National Key Program for Infectious Diseases of China (No. 2018ZX10101003 and 2018ZX10714-002)

  • Yujun Cui

Sanming Project of Medicine in Shenzhen (No. SZSM201811071)

  • Yujun Cui

National Natural Science Foundation of China (No. ZDRW-ZS-2017-1)

  • Yujun Cui

Medical Research Council (MR/M501608/1)

  • Daniel Falush

Shanghai Municipal Science and Technology Major Project (2019SHZDZX02)

  • Daniel Falush

Chinese Academy of Sciences 100 talents program

  • Daniel Falush

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Paul B Rainey, Max Planck Institute for Evolutionary Biology, Germany

Publication history

  1. Received: December 3, 2019
  2. Accepted: March 19, 2020
  3. Accepted Manuscript published: March 20, 2020 (version 1)
  4. Version of Record published: March 27, 2020 (version 2)

Copyright

© 2020, Cui et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Yujun Cui
  2. Chao Yang
  3. Hongling Qiu
  4. Hui Wang
  5. Ruifu Yang
  6. Daniel Falush
(2020)
The landscape of coadaptation in Vibrio parahaemolyticus
eLife 9:e54136.
https://doi.org/10.7554/eLife.54136

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