The ancestral animal genetic toolkit revealed by diverse choanoflagellate transcriptomes

Daniel Richter, Parinaz Fozouni, Michael Eisen, Nicole King

Preprint posted on December 26, 2017

Which set of genes distinguishes animals from other organisms? Work from the King lab suggests we need to rewrite textbooks.

Selected by Rafael Galupa


As humans, we are morphologically very different from butterflies or jellyfish, yet we belong together in the phylogenetic branch of Animalia/Metazoa, separate from other multicellular eukaryotes such as plants or fungi. So what makes up an animal? Comparing animal genomes to those of other organisms, especially their closest living relatives, choanoflagellates, can tell us which genes have specifically appeared or disappeared during animal evolution. However, only two genomes of choanoflagellate species have been sequenced to date, limiting the power of such comparisons to identify genes that are truly animal innovations.

Key findings

The authors sequenced the transcriptome of 19 choanoflagellate species, substantially increasing the available genomic information on these organisms and allowing a more refined comparison to animal genomes. This revealed:

(1) More than a thousand animal-specific gene families (including well-known developmental players such as TGF-β, Hedgehog, Pax and Sox), most of which were lost in one or more extant lineages. Only 36 gene families were found conserved across all animal genomes available, including components of the Wnt pathway and cell-cell adhesion molecules

(2) More than a thousand gene families present in the common ancestor but specifically lost in animals, reflecting changes in ecology and metabolism (e.g. pathways necessary for the biosynthesis of essential amino acids)

(3) Many gene families believed to be animal-specific are actually present in choanoflagellates, indicating that they evolved before the emergence of the animal lineages. These include Notch receptors and ligands, critical innate immunity receptors (TLRs) and enzymes involved in extracellular matrix remodelling.

What I like about this preprint

Not only the fact that the authors are asking a BIG fundamental biological question – where we came from, as animals, and what happened along the way, from a genomic perspective – but also that their study ends up challenging the current view of which genes constitute an “animal signature”, probably leading to changes in our textbooks. And who would have guessed how much we could learn from studying… choanoflagellates?! A reminder of how important it is to explore even the more unlikely organisms.

Open questions

It will be exciting to explore whether gene families common between animals and choanoflagellates serve similar biological functions in the two lineages, or whether they might have been exploited differently. For example, what could be the significance of the Notch pathway in single-cell choanoflagellates?

Curiosity corner

The authors had to optimise specific growth conditions and RNA extraction protocols for each of the 19 species of choanoflagellates they sequenced!

Tags: animal evolution, choanoflagellates, comparative genomics, metazoa

Read preprint (2 votes)

  • Have your say

    Your email address will not be published. Required fields are marked *

    Sign up to customise the site to your preferences and to receive alerts

    Register here

    Also in the evolutionary biology category:

    A SoxB gene acts as an anterior gap gene and regulates posterior segment addition in the spider Parasteatoda tepidariorum

    Christian L. B. Paese, Anna Schoenauer, Daniel J. Leite, et al.

    Selected by Erik Clark


    Germ layer specific regulation of cell polarity and adhesion gives insight into the evolution of mesoderm.

    Miguel Salinas-Saavedra, Amber Q. Rock, Mark Q. Martindale

    Selected by ClaireS & SophieM


    Wnt/β-catenin regulates an ancient signaling network during zebrafish scale development

    Andrew J Aman, Alexis N Fulbright, David M Parichy

    Selected by Andreas van Impel

    Bacteriophage cooperation suppresses CRISPR-Cas3 and Cas9 immunity

    Adair L Borges, Jenny Y Zhang, MaryClare Rollins, et al.


    Anti-CRISPR phages cooperate to overcome CRISPR-Cas immunity

    Mariann Landsberger, Sylvain Gandon, Sean Meaden, et al.

    Selected by Fillip Port

    Dynamic Kinetochore Size Regulation Promotes Microtubule Capture And Chromosome Biorientation In Mitosis

    Carlos Sacristan, Misbha Ahmad, Jenny Keller, et al.


    Self-assembly of the RZZ complex into filaments drives kinetochore expansion in the absence of microtubule attachment

    Cláudia Pereira, Rita M Reis, José B Gama, et al.

    Selected by Gautam Dey

    Individual- and population-level drivers of consistent foraging success across environments

    Lysanne Snijders, Ralf HJM Kurvers, Stefan Krause, et al.

    Selected by Rasmus Ern

    Genome-wide selection scans integrated with association mapping reveal mechanisms of physiological adaptation across a salinity gradient in killifish

    Reid S. Brennan, Timothy M. Healy, Heather J. Bryant, et al.

    Selected by Andy Turko

    From Armament to Ornament: Performance Trade-Offs in the Sexual Weaponry of Neotropical Electric Fishes

    Kory M. Evans, Maxwell J. Bernt, Matthew A. Kolmann, et al.

    Selected by Cassandra Donatelli

    Insect wings and body wall evolved from ancient leg segments

    Heather S Bruce, Nipam H Patel


    Two sets of wing homologs in the crustacean, Parhyale hawaiensis

    Courtney M Clark-Hachtel, Yoshinori Tomoyasu

    Selected by Erik Clark


    Also in the genomics category:


    We want to make our website, and the services we provide, useful and reliable. This sometimes involves placing small amounts of information called cookies on the device you used to access the internet. If you continue to use this website we will assume you are happy to accept our cookies.