title: Hemichordate genomes and deuterostome origins.
abstract: Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.
authors.affiliation: Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.|Department of Molecular Evolution, Centre for Organismal Studies, University of Heidelberg, 69115 Heidelberg, Germany.
authors.forename: Oleg
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authors.lastname: Simakov
authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Takeshi
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authors.lastname: Kawashima
authors.affiliation: Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
authors.forename: Ferdinand
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authors.lastname: Marlétaz
authors.affiliation: HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA.
authors.forename: Jerry
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authors.lastname: Jenkins
authors.affiliation: DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Ryo
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authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA.
authors.forename: Therese
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authors.lastname: Mitros
authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Kanako
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authors.lastname: Hisata
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA.
authors.forename: Jessen
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authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Eiichi
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authors.lastname: Shoguchi
authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Fuki
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authors.affiliation: Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas 77005, USA.
authors.forename: Jia-Xing
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authors.affiliation: Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
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authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Robert M
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authors.affiliation: Marine Biological Laboratory, Graduate School of Science, Hiroshima University, Onomichi, Hiroshima 722-0073, Japan.
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authors.lastname: Sasaki
authors.affiliation: Natural Science Center for Basic Research and Development, Gene Science Division, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8527, Japan.
authors.forename: Tomoe
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authors.lastname: Hikosaka-Katayama
authors.affiliation: Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.
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authors.affiliation: DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
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authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
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authors.affiliation: Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA.
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authors.affiliation: Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA.
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authors.affiliation: Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA.
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authors.affiliation: DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
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authors.affiliation: DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
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authors.affiliation: DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
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authors.affiliation: DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
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authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
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authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
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authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
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authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
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authors.lastname: Dugan
authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
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authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
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authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
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authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
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authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
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authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
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authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
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authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
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authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
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authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
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authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
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authors.affiliation: Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.|Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA.|US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Daniel S
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authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA.
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mesh_terms: D000818:Animals; D002816:Chordata, Nonvertebrate / Q000145:classification / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D004447:Echinodermata / Q000145:classification / Q000235:genetics; D019143:Evolution, Molecular; D016678:Genome / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny; D015398:Signal Transduction; D026801:Synteny / Q000235:genetics; D016212:Transforming Growth Factor beta
chemical_list: D016212:Transforming Growth Factor beta