Comparative genomics and the nature of placozoan species

PLoS Biol. 2018 Jul 31;16(7):e2005359. doi: 10.1371/journal.pbio.2005359. eCollection 2018 Jul.

Abstract

Placozoans are a phylum of nonbilaterian marine animals currently represented by a single described species, Trichoplax adhaerens, Schulze 1883. Placozoans arguably show the simplest animal morphology, which is identical among isolates collected worldwide, despite an apparently sizeable genetic diversity within the phylum. Here, we use a comparative genomics approach for a deeper appreciation of the structure and causes of the deeply diverging lineages in the Placozoa. We generated a high-quality draft genome of the genetic lineage H13 isolated from Hong Kong and compared it to the distantly related T. adhaerens. We uncovered substantial structural differences between the two genomes that point to a deep genomic separation and provide support that adaptation by gene duplication is likely a crucial mechanism in placozoan speciation. We further provide genetic evidence for reproductively isolated species and suggest a genus-level difference of H13 to T. adhaerens, justifying the designation of H13 as a new species, Hoilungia hongkongensis nov. gen., nov. spec., now the second described placozoan species and the first in a new genus. Our multilevel comparative genomics approach is, therefore, likely to prove valuable for species distinctions in other cryptic microscopic animal groups that lack diagnostic morphological characters, such as some nematodes, copepods, rotifers, or mites.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Animals
  • Base Sequence
  • DNA, Ribosomal / genetics
  • Gene Duplication
  • Gene Rearrangement / genetics
  • Genetic Speciation
  • Genetic Variation
  • Genome
  • Genomics*
  • Molecular Sequence Annotation
  • Phylogeny
  • Placozoa / genetics*
  • Placozoa / ultrastructure
  • Reproductive Isolation

Substances

  • DNA, Ribosomal

Grants and funding

LMUexcellent https://www.en.uni-muenchen.de/about_lmu/research/excellence_initiative/index.html. Funding through the LMU Munich’s Institutional Strategy LMUexcellent within the framework of the German Excellence Initiative to GW and HB. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Deutsche Forschungsgemeinschaft (DFG) www.dfg.de (grant number SCHI 277/26-1, SCHI 277/29-1). Funding to BS. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The University of Hongkong. Funding through a Small Project Fund of The University of Hong Kong to GAW and ME (grant number 201109176175). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Studienstiftung des deutschen Volkes. Doctoral fellowship to HJO. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Deutscher Akademischer Austauschdienst (DAAD) www.daad.de. A postdoctoral research fellowship to M.E. that supported specimen collection and establishment of cultures. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. European Union’s Horizon 2020, Marie Skłodowska-Curie Innovative Training Networks https://ec.europa.eu/research/mariecurieactions/actions/get-funding/innovative-training-networks_en (grant number 764840 [ITN IGNITE]). Funding to GW. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Deutsche Forschungsgemeinschaft (DFG) www.dfg.de (grant number Wo896/19-1). Funding to GW within the DFG Priority Program SPP 1991 “TaxonOMICs”. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.