1. Evolutionary Biology
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Gene family innovation, conservation and loss on the animal stem lineage

  1. Daniel J Richter
  2. Parinaz Fozouni
  3. Michael Eisen
  4. Nicole King  Is a corresponding author
  1. Howard Hughes Medical Institute, University of California, Berkeley, United States
Research Article
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Cite this article as: eLife 2018;7:e34226 doi: 10.7554/eLife.34226

Abstract

Choanoflagellates, the closest living relatives of animals, can provide unique insights into the changes in gene content that preceded the origin of animals. However, only two choanoflagellate genomes are currently available, providing poor coverage of their diversity. We sequenced transcriptomes of 19 additional choanoflagellate species to produce a comprehensive reconstruction of the gains and losses that shaped the ancestral animal gene repertoire. We identified ~1,944 gene families that originated on the animal stem lineage, of which only 39 are conserved across all animals in our study. In addition, ~372 gene families previously thought to be animal-specific, including Notch, Delta, and homologs of the animal Toll-like receptor genes, instead evolved prior to the animal-choanoflagellate divergence. Our findings contribute to an increasingly detailed portrait of the gene families that defined the biology of the Urmetazoan and that may underpin core features of extant animals.

Article and author information

Author details

  1. Daniel J Richter

    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9238-5571
  2. Parinaz Fozouni

    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Michael Eisen

    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7528-738X
  4. Nicole King

    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
    For correspondence
    nking@berkeley.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6409-1111

Funding

Howard Hughes Medical Institute

  • Michael Eisen
  • Nicole King

National Institutes of Health

  • Nicole King

U.S. Department of Defense (National Defense Science and Engineering Graduate Fellowship)

  • Daniel J Richter

National Science Foundation (Central Europe Summer Research Institute Fellowship)

  • Daniel J Richter

Chang-Lin Tien Fellowship in Environmental Sciences and Biodiversity

  • Daniel J Richter

Conseil Régional de Bretagne (Postdoctoral Fellowship)

  • Daniel J Richter

Investissements d'Avenir (ANR-11-BTBR-0008)

  • Daniel J Richter

National Science Foundation (955517)

  • Parinaz Fozouni

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

Reviewing Editor

  1. Maximilian J Telford, University College London, United Kingdom

Publication history

  1. Received: December 10, 2017
  2. Accepted: May 26, 2018
  3. Accepted Manuscript published: May 31, 2018 (version 1)
  4. Accepted Manuscript updated: June 15, 2018 (version 2)
  5. Version of Record published: July 3, 2018 (version 3)

Copyright

© 2018, Richter 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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