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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12-02

AUTHORS

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 B. Yin, Shi Huang, Nimaichand Salam, Jian-Yu Jiao, Zijun Wu, Zhenjiang Z. Xu, Kalen Cantrell, Yimeng Yang, Erfan Sayyari, Maryam Rabiee, James T. Morton, Sheila Podell, Dan Knights, Wen-Jun Li, Curtis Huttenhower, Nicola Segata, Larry Smarr, Siavash Mirarab, Rob Knight

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. More... »

PAGES

5477

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  • Journal

    TITLE

    Nature Communications

    ISSUE

    1

    VOLUME

    10

    Author Affiliations

  • Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
  • Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
  • San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA
  • Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Giessen, Germany
  • Department CIBIO, University of Trento, Trento, Italy
  • Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
  • Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
  • Department of Mathematics, University of California San Diego, La Jolla, CA, USA
  • Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
  • State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
  • Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
  • Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
  • Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
  • The Broad Institute of MIT and Harvard, Cambridge, MA, USA
  • California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA
  • Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41467-019-13443-4

    DOI

    http://dx.doi.org/10.1038/s41467-019-13443-4

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1123048808

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/31792218


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