title: Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks.
abstract: BACKGROUND
  The evolutionary mechanisms involved in shaping complex gene regulatory networks (GRN) that encode for morphologically similar structures in distantly related animals remain elusive. In this context, echinoderm larval skeletons found in brittle stars and sea urchins provide an ideal system. Here, we characterize for the first time the development of the larval skeleton in the ophiuroid Amphiura filiformis and compare it systematically with its counterpart in sea urchin.
  
  
  RESULTS
  We show that ophiuroids and euechinoids, that split at least 480 Million years ago (Mya), have remarkable similarities in tempo and mode of skeletal development. Despite morphological and ontological similarities, our high-resolution study of the dynamics of genetic regulatory states in A. filiformis highlights numerous differences in the architecture of their underlying GRNs. Importantly, the A.filiformis pplx, the closest gene to the sea urchin double negative gate (DNG) repressor pmar1, fails to drive the skeletogenic program in sea urchin, showing important evolutionary differences in protein function. hesC, the second repressor of the DNG, is co-expressed with most of the genes that are repressed in sea urchin, indicating the absence of direct repression of tbr, ets1/2, and delta in A. filiformis. Furthermore, the absence of expression in later stages of brittle star skeleton development of key regulatory genes, such as foxb and dri, shows significantly different regulatory states.
  
  
  CONCLUSIONS
  Our data fill up an important gap in the picture of larval mesoderm in echinoderms and allows us to explore the evolutionary implications relative to the recently established phylogeny of echinoderm classes. In light of recent studies on other echinoderms, our data highlight a high evolutionary plasticity of the same nodes throughout evolution of echinoderm skeletogenesis. Finally, gene duplication, protein function diversification, and cis-regulatory element evolution all contributed to shape the regulatory program for larval skeletogenesis in different branches of echinoderms.
authors.affiliation: Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK ; CoMPLEX/SysBio, UCL, Gower Street, London, WC1E 6BT UK ; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
authors.forename: David Viktor
authors.initials: DV
authors.lastname: Dylus
authors.affiliation: Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK.
authors.forename: Anna
authors.initials: A
authors.lastname: Czarkwiani
authors.affiliation: Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK ; Research Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
authors.forename: Josefine
authors.initials: J
authors.lastname: Stångberg
authors.affiliation: Department of Biological and Environmental Sciences, Sven Lovén Centre for Marine Sciences, University of Gothenburg, Kristineberg 566, 451 78 Fiskebäckskil, Sweden.
authors.forename: Olga
authors.initials: O
authors.lastname: Ortega-Martinez
authors.affiliation: Department of Biological and Environmental Sciences, Sven Lovén Centre for Marine Sciences, University of Gothenburg, Kristineberg 566, 451 78 Fiskebäckskil, Sweden.
authors.forename: Sam
authors.initials: S
authors.lastname: Dupont
authors.affiliation: Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK.
authors.forename: Paola
authors.identifier: 0000-0002-3477-8529
authors.initials: P
authors.lastname: Oliveri
keywords: Amphiura filiformis; Brittle star; Echinoderms; Evolution; Gene regulatory network; Skeleton