title: Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle.
abstract: Despite half a century of research, the biology of dinoflagellates remains enigmatic: they defy many functional and genetic traits attributed to typical eukaryotic cells. Genomic approaches to study dinoflagellates are often stymied due to their large, multi-gigabase genomes. Members of the genus Symbiodinium are photosynthetic endosymbionts of stony corals that provide the foundation of coral reef ecosystems. Their smaller genome sizes provide an opportunity to interrogate evolution and functionality of dinoflagellate genomes and endosymbiosis. We sequenced the genome of the ancestral Symbiodinium microadriaticum and compared it to the genomes of the more derived Symbiodinium minutum and Symbiodinium kawagutii and eukaryote model systems as well as transcriptomes from other dinoflagellates. Comparative analyses of genome and transcriptome protein sets show that all dinoflagellates, not only Symbiodinium, possess significantly more transmembrane transporters involved in the exchange of amino acids, lipids, and glycerol than other eukaryotes. Importantly, we find that only Symbiodinium harbor an extensive transporter repertoire associated with the provisioning of carbon and nitrogen. Analyses of these transporters show species-specific expansions, which provides a genomic basis to explain differential compatibilities to an array of hosts and environments, and highlights the putative importance of gene duplications as an evolutionary mechanism in dinoflagellates and Symbiodinium.
authors.affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: M
authors.initials: M
authors.lastname: Aranda
authors.affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Y
authors.initials: Y
authors.lastname: Li
authors.affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Y J
authors.initials: YJ
authors.lastname: Liew
authors.affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: S
authors.initials: S
authors.lastname: Baumgarten
authors.affiliation: Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany.
authors.forename: O
authors.initials: O
authors.lastname: Simakov
authors.affiliation: Institute of Microbiology, Eidgenössische Technische Hochschule Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
authors.forename: M C
authors.initials: MC
authors.lastname: Wilson
authors.affiliation: Institute of Microbiology, Eidgenössische Technische Hochschule Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
authors.forename: J
authors.initials: J
authors.lastname: Piel
authors.affiliation: Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: H
authors.initials: H
authors.lastname: Ashoor
authors.affiliation: Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: S
authors.initials: S
authors.lastname: Bougouffa
authors.affiliation: Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: V B
authors.initials: VB
authors.lastname: Bajic
authors.affiliation: KAUST Environmental Epigenetics Program (KEEP), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: T
authors.initials: T
authors.lastname: Ryu
authors.affiliation: KAUST Environmental Epigenetics Program (KEEP), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: T
authors.initials: T
authors.lastname: Ravasi
authors.affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.|GEOMAR Department: Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
authors.forename: T
authors.initials: T
authors.lastname: Bayer
authors.affiliation: Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
authors.forename: G
authors.initials: G
authors.lastname: Micklem
authors.affiliation: Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea.
authors.forename: H
authors.initials: H
authors.lastname: Kim
authors.affiliation: Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea.
authors.forename: J
authors.initials: J
authors.lastname: Bhak
authors.affiliation: Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: T C
authors.initials: TC
authors.lastname: LaJeunesse
authors.affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: C R
authors.initials: CR
authors.lastname: Voolstra
mesh_terms: D000220:Adaptation, Biological / Q000502:physiology*; D000818:Animals; D037421:Anthozoa / Q000502:physiology*; D004141:Dinoflagellida / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D016678:Genome; D013559:Symbiosis / Q000502:physiology*