From comparative to functional genomics of social amoeba

• Applicants: Professor Dr. Gernot Glöckner (†); Professorin Dr. Angelika A. Noegel
• Subject Area: General Genetics and Functional Genome Biology
• Term: from 2006 to 2009
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 17424032

• Final Report Year: 2011

Final Report Abstract

We sequenced and analysed two genomes within the social amoebae, a major branch of eukaryote evolution. Next generation sequencing methods allowed us to finish the genomes to a very high standard. Comparing these two genomes to the previously published genome of the model organism D. discoideum revealed several exciting facts about social amoebae evolution. Genome size, chromosome numbers, and gene content remained stable over a long time period, whereas constituents of chromosome structures underwent major changes. This emphasizes that chromosome structures are not bound to specific sequence motifs. Instead, different modules of a genome can be recruited to fulfill their functions. We did not find evidence for a whole genome duplication event in this lineage. Rather, expansions of specific gene families seem to be the major drivers of diversification in social amoebae. We found exciting evidence that mainly genes involved in predation, defense, and signal perception underwent major species specific gene family expansions. We hypothesize that the early invention of a sophisticated, hard-wired developmental cycle constrained diversifying evolution. Synteny analysis and phylogenetic reconstruction suggest that social amoebae evolution predates the Cambrian explosion. Thus, social amoebae survived several catastrophes in earth history without major changes in their genomes.

Publications

• (2007). A GPCR involved in post aggregation events in Dictyostelium discoideum. Dev. Biol. 312, 29-34
  Prabhu, Y, Mondal, S., Eichinger, L., Noegel, A.A.
  
• (2008). Mitochondrial Genome Evolution in the Social Amoebae. Mol. Blol. Evol. 25(7):1440-50
  Heidel A.J., G. Glöckner
  
• (2008). The actinome of Dictyostelium discoideum in comparison to actins and actin-related proteins from other organisms. PloS ONE 3(7): e2654
  Joseph, J. M., Fey. P, Ramalingam, N., Liu, X. I., Rohlfs, M., Noegel, A. A., Müller-Taubenberger, A., Glöckner, G., Schleicher, M.
  
• (2009). Centromere sequence and dynamics in Dictyostelium discoideum. Nucl. Adds Res. 37, 1809-1816
  Glöckner, G., A.J. Heidel
  
• (2010). Acytohesin homolog in Dictyostelium amoebae. PloS ONE 5, e9378
  Shina, M. C , Müller, R., Blau-Wasser, R., Glöckner, G., Schleicher, M., Eichinger, L., Noegel, A. A., Kolanus, W.
  
• (2010). Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum. BMC Genomics, 11:115
  Barrantes, I., G. Glöckner, S. Meyer, W. Marwan
  
• (2011). Redundant and unique roles of coronin proteins in Dictyostelium. Cell Mol Life Sci. 68, 303-313
  Shina, M. C. Müller-Taubenberger, A., Ünal, C., Schleicher, M., Steinert, M., Eichinger, L., Müller, R., Blau-Wasser, R., Glöckner, G., Noegel, A. A.