Public Release:  A*STAR scientists decipher genome code of a living fossil

An international team of researchers join forces to decode the genome of the once-thought-to-be-extinct African coelacanth

Agency for Science, Technology and Research (A*STAR), Singapore

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Credit: IMCB

1. An enigmatic prehistoric fish has brought scientists at A*STAR's Institute of Molecular and Cell Biology (IMCB) together with researchers from all over the world to crack its genomic code. Findings from the study are providing new insights into the evolutionary history of the African coelacanth (Figure 1) and possible clues as to how aquatic creatures transitioned to life on land.

2. Coelacanths resemble the fossilised skeletons of their ancestors from more than 300-million years ago (Figure 2). By sequencing its genome and comparing it to genes of other vertebrate species, the researchers have uncovered valuable information on genetic changes that may have helped aquatic animals to transition from water to land, and adapt to life on land. Their findings include many genes and regulatory elements that were gained and genes that were lost when vertebrates came on land. The research findings were published in the 18 April online issue of the prestigious journal, Nature.

3. The most interesting feature of the coelacanth is its fleshy fins, which resemble the limbs of land animals (Figure 3). The team has found several important regions of the genome used in the formation of limbs, which suggest that land animals (tetrapods) adopted these sequences from coelacanths to help them form limbs. The researchers also found that there are many regulatory changes that influence genes involved in the perception of smell, as creatures that transitioned to land needed new means of detecting chemicals in their environment.

4. While sequencing the genome of the coelacanth provides some answers, more information on how some vertebrates adapted to land while others remained in the water can be discerned from future research of coelacanth's physiological systems such as the immune system, respiratory system, and reproductive system.

5. Prof. Byrappa Venkatesh, Research Director IMCB, whose group was involved in the project said, "The coelacanth with its distinctive fleshy fins represents an intermediary phase in the evolution of land animals from aquatic fishes. By comparing the genomes of coelacanth, human and other vertebrates our group has been able to discover gene regulatory elements that played a key role in the development of our limbs and fingers as well as our ability to detect air-borne odorants. Mutations in these elements can potentially lead to genetic diseases."

6. Prof Hong Wan Jin, Executive Director IMCB, said, "This is the same IMCB group that sequenced the puffer fish genome in 2002 soon after the completion of the human genome and they are truly a pioneer in the field of comparative genomics. I am pleased to note that they are now part of yet another major international collaboration in genomics and are continuing to make significant contributions to our understanding of the structure, function and evolution of the human genome."

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Enclosed:

Annex A- Figures
Figure 1. African coelacanth
Figure 2. Coelacanth in the phylogenetic tree
Figure 3. Fleshy fins of the coelacanth

Notes for Editor:

The research findings described in this media release can be found in the 18 April online issue of Nature, under the title "Analysis of the African coelacanth genome sheds light on tetrapod evolution", by Chris T. Amemiya*1,2, Jessica Alföldi*3, Alison P. Lee4, Shaohua Fan5, Hervé Philippe6, Iain MacCallum3, Ingo Braasch7, Tereza Manousaki5,8, Igor Schneider9, Nicolas Rohner10, Chris Organ11, Domitille Chalopin12, Jeramiah J. Smith13, Mark Robinson1, Rosemary A. Dorrington14, Marco Gerdol15, Bronwen Aken16, Maria Assunta Biscotti17, Marco Barucca17, Denis Baurain18, Aaron M. Berlin3, Gregory L. Blatch14,19, Francesco Buonocore20, Thorsten Burmester21, Michael S. Campbell22, Adriana Canapa17, John P. Cannon23, Alan Christoffels24, Gianluca De Moro15, Adrienne L. Edkins14, Lin Fan3, Anna Maria Fausto20, Nathalie Feiner5,25, Mariko Forconi17, Junaid Gamieldien24, Sante Gnerre3, Andreas Gnirke3, Jared V. Goldstone26, Wilfried Haerty27, Mark E. Hahn26, Uljana Hesse24, Steve Hoffmann28, Jeremy Johnson3, Sibel I. Karchner26, Shigehiro Kuraku5,**, Marcia Lara3, Joshua Z. Levin3, Gary W. Litman23, Evan Mauceli3,***, Tsutomu Miyake29, M. Gail Mueller30, David R. Nelson31, Anne Nitsche32, Ettore Olmo17, Tatsuya Ota33, Alberto Pallavicini15, Sumir Panji24****, Barbara Picone24, Chris P. Ponting27, Sonja J. Prohaska34, Dariusz Przybylski3, Nil Ratan Saha1, Vydianathan Ravi4, Filipe J. Ribeiro3,*****, Tatjana Sauka-Spengler35, Giuseppe Scapigliati20, Stephen M. J. Searle16, Ted Sharpe3, Oleg Simakov5,36, Peter F. Stadler32, John J. Stegeman26, Kenta Sumiyama37, Diana Tabbaa3, Hakim Tafer32, Jason Turner-Maier3, Peter van Heusden24, Simon White16, Louise Williams3, Mark Yandell22, Henner Brinkmann6, Jean-Nicolas Volff12, Clifford J. Tabin10, Neil Shubin38, Manfred Schartl39, David Jaffe3, John H. Postlethwait7, Byrappa Venkatesh4, Federica Di Palma3, Eric S. Lander3, Axel Meyer5,8,25, Kerstin Lindblad-Toh3,40

1Molecular Genetics Program, Benaroya Research Institute, Seattle, WA, USA

2Department of Biology, University of Washington, Seattle, WA, USA

3Broad Institute of MIT and Harvard, Cambridge, MA, USA

4Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore

5Department of Biology, University of Konstanz, Konstanz, Germany

6Departement de Biochimie, Universite de Montreal, Centre Robert Cedergren, Montreal, Canada

7Institute of Neuroscience, University of Oregon, Eugene, OR, USA

8Konstanz Research School of Chemical Biology, University of Konstanz, Konstanz, Germany

9Instituto de Ciencias Biologicas, Universidade Federal do Para, Belem, Brazil

10Department of Genetics, Harvard Medical School, Boston, MA, USA

11Department of Anthropology, University of Utah, Salt Lake City, UT, USA

12Institut de Genomique Fonctionnelle de Lyon, Ecole Normale Superieure de Lyon, Lyon, France

13Department of Biology, University of Kentucky, Lexington, KY, USA

14Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry, Microbiology & Biotechnology, Rhodes University, Grahamstown, South Africa

15Department of Life Sciences, University of Trieste, Trieste, Italy

16Department of Informatics, Wellcome Trust Sanger Institute, Hinxton, UK

17Department of Life and Environmental Sciences, Polytechnic University of the Marche, Ancona, Italy

18Department of Life Sciences, University of Liege, Liege, Belgium

19College of Health and Biomedicine, Victoria University, Melbourne, Australia

20Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Viterbo, Italy

21Department of Biology, University of Hamburg, Hamburg, Germany

22Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA

23Department of Pediatrics, University of South Florida Morsani College of Medicine, Children's Research Institute, St. Petersburg, FL, USA

24South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa

25International Max-Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany

26Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA

27MRC Functional Genomics Unit, Oxford University, Oxford, UK

28Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany

29Graduate School of Science and Technology, Keio University, Yokohama, Japan

30Department of Molecular Genetics, All Children's Hospital, St. Petersburg, FL, USA

31Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA

32Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany

33Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Japan

34Computational EvoDevo Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany

35Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK

36European Molecular Biology Laboratory, Heidelberg, Germany

37Division of Population Genetics, National Institute of Genetics, Mishima, Japan

38University of Chicago, Chicago, IL, USA

39Department Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg Germany

40Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

Genome Resource and Analysis Unit, Center for Developmental Biology, RIKEN, Kobe, Japan

Boston Children's Hospital, Boston, MA

Computational Biology Unit, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Campus, Anzio Road, Observatory 7925, South Africa

New York Genome Center, New York, NY, USA

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About Institute of Molecular and Cell Biology (IMCB)

The Institute of Molecular and Cell Biology (IMCB) is a member of Singapore's Agency for Science, Technology and Research (A*STAR) and is funded through A*STAR's Biomedical Research Council (BMRC). It is a world-class research institute that focuses its activities on six major fields: Cell Biology, Developmental

Biology, Genomics, Structural Biology, Infectious Diseases, Cancer Biology and Translational Research, with core strengths in cell cycling, cell signalling, cell death, cell motility and protein trafficking. Its achievements include leading an international consortium that successfully sequenced the entire pufferfish (fugu) genome. The IMCB was awarded the Nikkei Prize 2000 for Technological Innovation in recognition of its growth into a leading international research centre and its collaboration with industry and research institutes worldwide. Established in 1987, the Institute currently has 26 independent research groups, eight core facilities and 300 researchers.

For more information about IMCB, please visit http://www.imcb.a-star.edu.sg. About the Agency for Science, Technology and Research (A*STAR)

The Agency for Science, Technology and Research (A*STAR) is the lead agency for fostering world-class scientific research and talent for a vibrant knowledge-based and innovation-driven Singapore. A*STAR oversees 14 biomedical sciences and physical sciences and engineering research institutes, and six consortia & centres, located in Biopolis and Fusionopolis as well as their immediate vicinity. A*STAR supports Singapore's key economic clusters by providing intellectual, human and industrial capital to its partners in industry. It also supports extramural research in the universities, and with other local and international partners. For more information about A*STAR, please visit http://www.a-star.edu.sg.

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