title: Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals.
abstract: Cell-type specification through differential genome regulation is a hallmark of complex multicellularity. However, it remains unclear how this process evolved during the transition from unicellular to multicellular organisms. To address this question, we investigated transcriptional dynamics in the ichthyosporean Creolimax fragrantissima, a relative of animals that undergoes coenocytic development. We find that Creolimax utilizes dynamic regulation of alternative splicing, long inter-genic non-coding RNAs and co-regulated gene modules associated with animal multicellularity in a cell-type specific manner. Moreover, our study suggests that the different cell types of the three closest animal relatives (ichthyosporeans, filastereans and choanoflagellates) are the product of lineage-specific innovations. Additionally, a proteomic survey of the secretome reveals adaptations to a fungal-like lifestyle. In summary, the diversity of cell types among protistan relatives of animals and their complex genome regulation demonstrates that the last unicellular ancestor of animals was already capable of elaborate specification of cell types.
authors.affiliation: Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Alex
authors.identifier: http://orcid.org/0000-0002-6441-6529
authors.initials: A
authors.lastname: de Mendoza
authors.affiliation: Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain.|Prefectural University of Hiroshima, Shobara, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Suga
authors.affiliation: EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation, Barcelona, Spain.|Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Jon
authors.initials: J
authors.lastname: Permanyer
authors.affiliation: EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation, Barcelona, Spain.|Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Irimia
authors.affiliation: Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain.|Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
authors.forename: Iñaki
authors.initials: I
authors.lastname: Ruiz-Trillo
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D005786:Gene Expression Regulation; D050298:Mesomycetozoea / Q000235:genetics* / Q000254:growth & development / Q000502:physiology*; D020543:Proteome / Q000032:analysis
chemical_list: D020543:Proteome
keywords: alternative splicing; comparative genomics; developmental biology; evolutionary biology; genomics; lateral gene transfer; lincRNA; multicellularity; secretome; stem cells