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Simakov O, Kawashima T, Marlétaz F, Jenkins J, Koyanagi R, Mitros T, Hisata K, Bredeson J, Shoguchi E, Gyoja F, Yue JX, Chen YC, Freeman RM, Sasaki A, Hikosaka-Katayama T, Sato A, Fujie M, Baughman KW, Levine J, Gonzalez P, Cameron C, Fritzenwanker JH, Pani AM, Goto H, Kanda M, Arakaki N, Yamasaki S, Qu J, Cree A, Ding Y, Dinh HH, Dugan S, Holder M, Jhangiani SN, Kovar CL, Lee SL, Lewis LR, Morton D, Nazareth LV, Okwuonu G, Santibanez J, Chen R, Richards S, Muzny DM, Gillis A, Peshkin L, Wu M, Humphreys T, Su YH, Putnam NH, Schmutz J, Fujiyama A, Yu JK, Tagawa K, Worley KC, Gibbs RA, Kirschner MW, Lowe CJ, Satoh N, Rokhsar DS, Gerhart J. Hemichordate genomes and deuterostome origins. Nature 2015; 527:459-65. [PMID: 26580012 PMCID: PMC4729200 DOI: 10.1038/nature16150] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/13/2015] [Indexed: 12/12/2022]
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.
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Affiliation(s)
- Oleg Simakov
- 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
| | - Takeshi Kawashima
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | | | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Ryo Koyanagi
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Therese Mitros
- Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Jessen Bredeson
- Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Fuki Gyoja
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Jia-Xing Yue
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas 77005, USA
| | - Yi-Chih Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Robert M Freeman
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Akane Sasaki
- Marine Biological Laboratory, Graduate School of Science, Hiroshima University, Onomichi, Hiroshima 722-0073, Japan
| | - Tomoe Hikosaka-Katayama
- Natural Science Center for Basic Research and Development, Gene Science Division, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Atsuko Sato
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Kenneth W Baughman
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Judith Levine
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA
| | - Paul Gonzalez
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA
| | - Christopher Cameron
- Départment de sciences biologiques, University of Montreal, Quebec H3C 3J7, Canada
| | - Jens H Fritzenwanker
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA
| | - Ariel M Pani
- University of North Caroline at Chapel Hill, North Carolina 27599, USA
| | - Hiroki Goto
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Miyuki Kanda
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Nana Arakaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Shinichi Yamasaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Andrew Cree
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Yan Ding
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Huyen H Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Michael Holder
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Lora R Lewis
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Donna Morton
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Lynne V Nazareth
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Geoffrey Okwuonu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Jireh Santibanez
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Rui Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Andrew Gillis
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michael Wu
- Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA
| | - Tom Humphreys
- Institute for Biogenesis Research, University of Hawaii, Hawaii 96822, USA
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Nicholas H Putnam
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas 77005, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Asao Fujiyama
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Kunifumi Tagawa
- Marine Biological Laboratory, Graduate School of Science, Hiroshima University, Onomichi, Hiroshima 722-0073, Japan
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Christopher J Lowe
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Daniel S Rokhsar
- 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
| | - John Gerhart
- Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA
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