Comparative Genomics and Transcriptomics in Placozoa

We have been sequencing and are currently analyzing several genomes and transcriptomes of placozoan species. We expect valuable insights into the phylogeny, genetic diversity and mechanisms of selection of an entire phylum. Placozoa have become an emerging model system for evo-devo research because of their simple bauplan and a basal position in the tree of life. We propose that placozoans are also well suited to become a model phylum in marine comparative genomics and ocean climate studies because: 1. they are abundant throughout the oceans in benthic communities 2. different lineages differ in their geographical distribution and associated tolerance for environmental factors 3. their compact genome is comparatively time and cost efficiently to sequence 4. assumed passive dispersal along oceanic currents allows to study effects of migration and local adaptation.

The Enigmatic Phylum Placozoa

The first placozoan species, Trichoplax adhaerens, was discovered by F.E. Schulze in 1883 [1]⁠ in aquarium samples. More members (species, yet undescribed) of this phylum have been found in shallow tropical, sub-tropical and temperate waters [2,3]⁠. They are irregular disc-shaped benthic animals of only a few millimeters which crawl over hard substrates. Placozoans exhibit the simplest morphology of all living metazoans, harboring only six somatic cell types [4,5]⁠ that are arranged in an upper epithelium, a lower epithelium and an intermediate layer (for review see [6]⁠). This simple bauplan and a supposed basal position of placozoans in the tree of life has led to many speculations regarding the origin of Metazoa [7]⁠. Consequently the Trichoplax mitochondrial [8]⁠ and nuclear [9]⁠ genomes have been among the first sequenced non-bilaterian genomes and support the phylum's basal position [10]⁠.

A Case to Sequence the Phylum Placozoa

The fact that T. adhaerens has remained the only described species can mainly be attributed to the uniform morphology of the phylum and to the difficulty of observing placozoans in the field. This view changed when genetic studies by Voigt et al. and Eitel et al. [3,11,12]⁠ revealed substantial diversity within the phylum. Moreover, different lineages show remarkable differences in their geographical range and tolerance for environmental factors. For example, the cosmopolitan haplotype H2 has been found in tropical to temperate waters in all oceans, while the haplotype H3 seems to be restricted to the Caribbean. Currently the Placozoa consists of around 25 lineages, presently defined by their 16S haplotypes [3,12]⁠. While their genetic distances as well as physiological differences leave no doubt that they represent valid species, attempts for species descriptions have only been partially successful, again, mainly due to the simple morphology of placozoans [13]⁠.
To resolve the tabula rasa Placozoa and to assess the phylum’s genetic diversity, the genomes and transcriptomes of the major lineages are currently sequenced, a process which is greatly facilitated by the small (100Mb) genome size of placozoans. In the future we plan to establish a genotyping-by-sequencing approach [14] to study global population dynamics of placozoans.

References

[1] Schulze FE. Trichoplax adhaerens, nov. gen., nov. spec. Zool Anz 1883;6:92–7.
[2] Pearse VB, Voigt O. Field biology of placozoans (Trichoplax): distribution, diversity, biotic interactions. Integr Comp Biol 2007;47:677–92. doi:10.1093/icb/icm015.
[3] Eitel M, Osigus H-J, DeSalle R, Schierwater B. Global Diversity of the Placozoa. PLoS One 2013;8:e57131. doi:10.1371/journal.pone.0057131.
[4] Jakob W, Sagasser S, Dellaporta S, Holland P, Kuhn K, Schierwater B. The Trox-2 Hox/ParaHox gene of Trichoplax (Placozoa) marks an epithelial boundary. Dev Genes Evol 2004;214:170–5. doi:10.1007/s00427-004-0390-8.
[5] Smith CL, Varoqueaux F, Kittelmann M, Azzam RN, Cooper B, Winters CA, et al. Novel cell types, neurosecretory cells, and body plan of the early-diverging metazoan Trichoplax adhaerens. Curr Biol 2014;24:1565–72. doi:10.1016/j.cub.2014.05.046.
[6] Schierwater B. My favorite animal,Trichoplax adhaerens. BioEssays 2005;27:1294–302. doi:10.1002/bies.20320.
[7] DeSalle R, Schierwater B. Key transitions in animal evolution. Integr Comp Biol 2007;47:667–9. doi:10.1093/icb/icm042.
[8] Dellaporta SL, Xu A, Sagasser S, Jakob W, Moreno M a, Buss LW, et al. Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum. Proc Natl Acad Sci U S A 2006;103:8751–6. doi:10.1073/pnas.0602076103.
[9] Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, et al. The Trichoplax genome and the nature of placozoans. Nature 2008;454:955–60. doi:10.1038/nature07191.
[10] Schierwater B, Eitel M, Jakob W, Osigus H-J, Hadrys H, Dellaporta SL, et al. Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis. PLoS Biol 2009;7:e1000020. doi:10.1371/journal.pbio.1000020.
[11] Voigt O, Collins AG, Pearse VB, Pearse JS, Ender A, Hadrys H, et al. Placozoa -- no longer a phylum of one. Curr Biol 2004;14:R944-5. doi:10.1016/j.cub.2004.10.036.
[12] Eitel M, Schierwater B. The phylogeography of the Placozoa suggests a taxon-rich phylum in tropical and subtropical waters. Mol Ecol 2010;19:2315–27. doi:10.1111/j.1365-294X.2010.04617.x.
[13] Guidi L, Eitel M, Cesarini E, Schierwater B, Balsamo M. Ultrastructural analyses support different morphological lineages in the phylum placozoa Grell, 1971. J Morphol 2011;272:371–8. doi:10.1002/jmor.10922.
[14] Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, et al. A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. PLoS One 2011;6:e19379. doi:10.1371/journal.pone.0019379.

 

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