Evolution of metazoan genome architecture

We study major transitions in metazoan evolution from the perspective of the underlying genomic changes. Over the past years, we have contributed to the broader sampling of metazoan genomes, revealing ancestral metazoan and bilaterian genomic architectures and their diversification patterns. While we can trace back many gene families to the ancient metazoan ancestor, we also find many of them linked at both micro- (local gene cluster) and macro-syntenic (chromosomal) levels. The functional significance of most of those linkages during development is unknown. Having a broad phylogenetic focus we aim to (1) characterize and expand our knowledge of conserved and novel gene linkages and their associated (non-coding) elements across metazoans, (2) study their evolutionary dynamics through comparative genomics and modeling approaches, and (3) establishing molecular tools for investigating their role during development and clade-specific innovation. Inspired by the analysis of the octopus genome, current research focuses on characterizing the genomes of other cephalopod species, in particular investigating the gene linkage and repetitive element dynamics and their role in the emergence of cephalopod novelties. We are also contributing to the functional study of gene linkages in an emerging cephalopod model system Euprymna scolopes (Hawaiian bobtail squid) and the cnidarian hydra (Hydra magnipapillata).

Oleg Simakov studied Biology and obtained the Diploma degree at the University of Heidelberg, conducting his Diploma research in the group of Daniel Rokhsar at the University of California, Berkeley.

In 2013 he obtained his PhD working in the group of Detlev Arendt at EMBL Heidelberg. The work was conducted as a part of the EMBL International PhD Programme and co-supervised by Axel Meyer at the University of Konstanz, Germany.

In 2013 he worked as a research assistant in the group of Thomas Holstein, University of Heidelberg, followed by a postdoctoral appointment at the Okinawa Institute of Science and Technology Molecular Genetics Unit (led by Sydney Brenner and Daniel Rokhsar).

Since 2017 he is a tenure-track group leader at the University of Vienna

Currently, we are looking for a PhD student and postdocs! Contact: oleg.simakov@univie.ac.at

Selected Publications

Simakov, O. and T. Kawashima. "Independent evolution of genomic characters during major metazoan transitions." Dev Biol, 2016


Simakov O*, Kawashima T*, Marletaz F, Jenkins J, Koyanagi R, Mitros T, Hisata K, et al. (2015). “Hemichordate genomes and deuterostome origins.” Nature 527(7579):459-65 [*, equal contributions]


Baumgarten S, Simakov O, Esherick LY, Liew YJ, Lehnert EM, Michell CT, Li Y, Hambleton EA, Guse A, Oates ME, Gough J, Weis VM, Aranda M, Pringle JR, Voolstra  CR. “The genome of Aiptasia, a sea anemone model for coral symbiosis.” Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11893-8.


Petersen HO, Höger SK, Looso M, Lengfeld T, Kuhn A, Warnken U, Nishimiya-Fujisawa C, Schnölzer M, Krüger M, Özbek S, Simakov O, Holstein TW. “A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration.” Mol Biol Evol. 2015 Aug;32(8):1928-47.


Albertin CB*, Simakov O*, Mitros T, Wang ZY, Pungor JR, Edsinger-Gonzales E, Brenner S, Ragsdale CW, Rokhsar DS. (2015) “The octopus genome and the evolution of cephalopod neural and morphological novelties.” Nature 524(7564):220-4. [*, equal contributions]


Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, et al. (2013). “Insights into bilaterian evolution from three spiralian genomes” Nature. 493(7433):526-31.


Chapman JA*, Kirkness EF*, Simakov O*, et al. (2010). “The dynamic genome of Hydra.” Nature 464(7288):592-6. [*, equal contributions]


Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, et al. (2010). “The Amphimedon queenslandica genome and the evolution of animal complexity.” Nature 466(7307):720-6