ArticleNature2015
Hemichordate genomes and deuterostome origins.
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Article in Nature, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers.
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114citing papers in PubMed
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114 citing papers in PubMed.
- Tunable AMPA receptor function via recurrent evolution of heterotetramers.The Journal of general physiology · 2026Article
- Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods.Nature communications · 2026Article
- Gills are not the primary site of gas exchange in the suspension-feeding hemichordate Protoglossus graveolens.The Journal of experimental biology · 2026Article
- Distinct cell states define larval and adult body plans in a hemichordate.Nature communications · 2026Article
- Topological mixing and irreversibility in animal chromosome evolution.Science advances · 2026Article
- Insights into cephalochordate genome and gene evolution from the early-diverging amphioxusProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Shared competence forms the basis of gill arch and paired fin serial homology.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes.Nature ecology & evolution · 2026Article
- Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes.iScience · 2025Article
- NALCN/Cch1 channelosome subunits originated in early eukaryotes.The Journal of general physiology · 2025Article
- The inbred newt genome unveils molecular mechanisms of behavior, development, and regeneration in urodele amphibians.iScience · 2025Article
- Article
- Evolutionary Origins and Functional Diversification of 2'-O-Methyltransferases: Insights from Phylogenetic and Structural Analysis.International journal of molecular sciences · 2025Article
- Why sequence the genome of every species? A view from evolutionary biology.Journal of the Marine Biological Association of the United Kingdom. Marine Biological Association of the United Kingdom · 2025Article
- Single-cell profiling of the amphioxus digestive tract reveals conservation of endocrine cells in chordates.Science advances · 2024Article
- Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes.Nature ecology & evolution · 2024Article
- Evolution of the Cdk4/6-Cdkn2 system in invertebrates.Genes to cells : devoted to molecular & cellular mechanisms · 2024Article
- A pre-vertebrate endodermal origin of calcitonin-producing neuroendocrine cells.Development (Cambridge, England) · 2024Article
- The evolution of tenascins.BMC ecology and evolution · 2024Article
- Article
54 more citing papers are in PubMed but not listed here.
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Authors and funding
61 authors.
Oleg SimakovMolecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Takeshi KawashimaMarine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Ferdinand MarlétazDepartment of Zoology, University of Oxford, Oxford OX1 3PS, UK.
Jerry JenkinsHudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA.
Ryo KoyanagiDNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Therese MitrosDepartment of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA.
Kanako HisataMarine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Jessen BredesonDepartment of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA.
Eiichi ShoguchiMarine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Fuki GyojaMarine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Jia-Xing YueDepartment of Ecology and Evolutionary Biology, Rice University, Houston, Texas 77005, USA.
Yi-Chih ChenInstitute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
Robert M FreemanDepartment of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
Akane SasakiMarine Biological Laboratory, Graduate School of Science, Hiroshima University, Onomichi, Hiroshima 722-0073, Japan.
Tomoe Hikosaka-KatayamaNatural Science Center for Basic Research and Development, Gene Science Division, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8527, Japan.
Atsuko SatoMarine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.
Manabu FujieDNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Kenneth W BaughmanMarine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Judith LevineDepartment of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA.
Paul GonzalezDepartment of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA.
Christopher CameronDépartment de sciences biologiques, University of Montreal, Quebec H3C 3J7, Canada.
Jens H FritzenwankerDepartment of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA.
Ariel M PaniUniversity of North Caroline at Chapel Hill, North Carolina 27599, USA.
Hiroki GotoDNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Miyuki KandaDNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Nana ArakakiDNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Shinichi YamasakiDNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Jiaxin QuHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Andrew CreeHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Yan DingHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Huyen H DinhHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Shannon DuganHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Michael HolderHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Shalini N JhangianiHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Christie L KovarHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Sandra L LeeHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Lora R LewisHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Donna MortonHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Lynne V NazarethHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Geoffrey OkwuonuHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Jireh SantibanezHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Rui ChenHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Stephen RichardsHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Donna M MuznyHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Andrew GillisDepartment of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
Leonid PeshkinDepartment of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
Michael WuDepartment of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA.
Tom HumphreysInstitute for Biogenesis Research, University of Hawaii, Hawaii 96822, USA.
Yi-Hsien SuInstitute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
Nicholas H PutnamDepartment of Ecology and Evolutionary Biology, Rice University, Houston, Texas 77005, USA.
Jeremy SchmutzHudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA.
Asao FujiyamaNational Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
Jr-Kai YuInstitute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
Kunifumi TagawaMarine Biological Laboratory, Graduate School of Science, Hiroshima University, Onomichi, Hiroshima 722-0073, Japan.
Kim C WorleyHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Richard A GibbsHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA.
Marc W KirschnerDepartment of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
Christopher J LoweDepartment of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA.
Noriyuki SatohMarine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Daniel S RokhsarMolecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
John GerhartDepartment of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA.
Funding
The Human Genome Sequencing CenterU54HG003273 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2004 to 2015
$341.3MSystems Analysis of cell type differentiation in Xenopus developmentR01HD073104 · NICHD · HARVARD MEDICAL SCHOOL · PI KIRSCHNER, MARC WALLACE, PESHKIN, LEON · 2012 to 2022
$6.7MDEVELOPMENTAL CIRCUITS IN GASTRULATION AND NEURULATIONR01HD037277 · NICHD · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI KIRSCHNER, MARC WALLACE · 1999 to 2008
$4.5MTraining Program in Developmental BiologyT32HD055164 · NICHD · UNIVERSITY OF CHICAGO · PI Sally Horne-Badovinac, Paschalis Kratsios · 2008 to 2026
$3.6MHemichordates and the Origin of ChordatesR01HD042724 · NICHD · UNIVERSITY OF CALIFORNIA BERKELEY · PI GERHART, JOHN C · 2002 to 2009
$1.7MInvestigating FGF/sFRP interactions during forebrain evolution and developmentF31NS074738 · NINDS · UNIVERSITY OF CHICAGO · PI PANI, ARIEL MATTHEW · 2011 to 2012
$39kNHGRI NIH HHS U54 HG003273NICHD NIH HHS HD37277NICHD NIH HHS HD42724NICHD NIH HHS R01 HD037277NICHD NIH HHS R01 HD042724NICHD NIH HHS R01 HD073104NICHD NIH HHS R01HD073104NICHD NIH HHS T32 HD055164NINDS NIH HHS F31 NS074738
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.
Indexed as
Evolution, MolecularAnimalsChordata, NonvertebrateConserved SequenceEchinodermataGenomeMultigene FamilyPhylogenySignal TransductionSyntenyTransforming Growth Factor betaTransforming Growth Factor beta
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