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Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

Author

Listed:
  • Qiyun Zhu

    (University of California San Diego)

  • Uyen Mai

    (University of California San Diego)

  • Wayne Pfeiffer

    (University of California San Diego)

  • Stefan Janssen

    (University of California San Diego
    Justus Liebig University Gießen)

  • Francesco Asnicar

    (University of Trento)

  • Jon G. Sanders

    (University of California San Diego)

  • Pedro Belda-Ferre

    (University of California San Diego)

  • Gabriel A. Al-Ghalith

    (University of Minnesota)

  • Evguenia Kopylova

    (University of California San Diego)

  • Daniel McDonald

    (University of California San Diego)

  • Tomasz Kosciolek

    (University of California San Diego
    Jagiellonian University)

  • John B. Yin

    (University of California San Diego
    University of California San Diego)

  • Shi Huang

    (University of California San Diego
    Chinese Academy of Sciences)

  • Nimaichand Salam

    (Sun Yat-sen University)

  • Jian-Yu Jiao

    (Sun Yat-sen University)

  • Zijun Wu

    (University of California San Diego
    University of California San Diego)

  • Zhenjiang Z. Xu

    (University of California San Diego)

  • Kalen Cantrell

    (University of Minnesota)

  • Yimeng Yang

    (University of Minnesota)

  • Erfan Sayyari

    (University of California San Diego)

  • Maryam Rabiee

    (University of California San Diego)

  • James T. Morton

    (University of California San Diego
    University of California San Diego)

  • Sheila Podell

    (University of California San Diego)

  • Dan Knights

    (University of Minnesota)

  • Wen-Jun Li

    (Sun Yat-sen University)

  • Curtis Huttenhower

    (Harvard T. H. Chan School of Public Health
    The Broad Institute of MIT and Harvard)

  • Nicola Segata

    (University of Trento)

  • Larry Smarr

    (University of California San Diego
    University of California San Diego
    University of California San Diego)

  • Siavash Mirarab

    (Jagiellonian University)

  • Rob Knight

    (University of California San Diego
    University of California San Diego
    University of California San Diego
    University of California San Diego)

Abstract

Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer “core” genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.

Suggested Citation

  • Qiyun Zhu & Uyen Mai & Wayne Pfeiffer & Stefan Janssen & Francesco Asnicar & Jon G. Sanders & Pedro Belda-Ferre & Gabriel A. Al-Ghalith & Evguenia Kopylova & Daniel McDonald & Tomasz Kosciolek & John , 2019. "Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-13443-4
    DOI: 10.1038/s41467-019-13443-4
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    Cited by:

    1. Tara A. Mahendrarajah & Edmund R. R. Moody & Dominik Schrempf & Lénárd L. Szánthó & Nina Dombrowski & Adrián A. Davín & Davide Pisani & Philip C. J. Donoghue & Gergely J. Szöllősi & Tom A. Williams & , 2023. "ATP synthase evolution on a cross-braced dated tree of life," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    2. Nils Giordano & Marinna Gaudin & Camille Trottier & Erwan Delage & Charlotte Nef & Chris Bowler & Samuel Chaffron, 2024. "Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Hao Leng & Yinzhao Wang & Weishu Zhao & Stefan M. Sievert & Xiang Xiao, 2023. "Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Meng-Shu Hao & Scott Mazurkewich & He Li & Alma Kvammen & Srijani Saha & Salla Koskela & Annie R. Inman & Masahiro Nakajima & Nobukiyo Tanaka & Hiroyuki Nakai & Gisela Brändén & Vincent Bulone & Johan, 2024. "Structural and biochemical analysis of family 92 carbohydrate-binding modules uncovers multivalent binding to β-glucans," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    5. Tatsuya Dokoshi & Yang Chen & Kellen J. Cavagnero & Gibraan Rahman & Daniel Hakim & Samantha Brinton & Hana Schwarz & Elizabeth A. Brown & Alan O’Neill & Yoshiyuki Nakamura & Fengwu Li & Nita H. Salzm, 2024. "Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    6. Joanne S. Boden & Juntao Zhong & Rika E. Anderson & Eva E. Stüeken, 2024. "Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    7. Jojo A. Prentice & Robert Weerd & Andrew A. Bridges, 2024. "Cell-lysis sensing drives biofilm formation in Vibrio cholerae," Nature Communications, Nature, vol. 15(1), pages 1-10, December.

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