April 18, 2013

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

Singapore, Apr 18, 2013 - (ACN Newswire) - 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)(1) and possible clues as to how aquatic creatures transitioned to life on land.

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.

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.

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.

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."

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."

Press document (with Figures):

(1) A deep-sea cave dwelling, five-foot long fish with limb-like fins

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 Alfoldi*[3], Alison P. Lee[4], Shaohua Fan[5], Herve Philippe[6], Iain MacCallum[3], Ingo Braasch[7], Tereza Manousaki[5],[8], Igor Schneider[9], Nicolas Rohner[10], Chris Organ[11], Domitille Chalopin[12], Jeramiah J. Smith[13], Mark Robinson[1], Rosemary A. Dorrington[14], Marco Gerdol[15], Bronwen Aken[16], Maria Assunta Biscotti[17], Marco Barucca[17], Denis Baurain[18], Aaron M. Berlin[3], Gregory L. Blatch[14],[19], Francesco Buonocore[20], Thorsten Burmester[21], Michael S. Campbell[22], Adriana Canapa[17], John P. Cannon[23], Alan Christoffels[24], Gianluca De Moro[15], Adrienne L. Edkins[14], Lin Fan[3], Anna Maria Fausto[20], Nathalie Feiner[5],[25], Mariko Forconi[17], Junaid Gamieldien[24], Sante Gnerre[3], Andreas Gnirke[3], Jared V. Goldstone[26], Wilfried Haerty[27], Mark E. Hahn[26], Uljana Hesse[24], Steve Hoffmann[28], Jeremy Johnson[3], Sibel I. Karchner[26], Shigehiro Kuraku[5],**, Marcia Lara[3], Joshua Z. Levin[3], Gary W. Litman[23], Evan Mauceli[3],***, Tsutomu Miyake[29], M. Gail Mueller[30], David R. Nelson[31], Anne Nitsche[32], Ettore Olmo[17], Tatsuya Ota[33], Alberto Pallavicini[15], Sumir Panji[24]****, Barbara Picone[24], Chris P. Ponting[27], Sonja J. Prohaska[34], Dariusz Przybylski[3], Nil Ratan Saha1, Vydianathan Ravi[4], Filipe J. Ribeiro[3],*****, Tatjana Sauka-Spengler[35], Giuseppe Scapigliati[20], Stephen M. J. Searle[16], Ted Sharpe[3], Oleg Simakov[5],[36], Peter F. Stadler[32], John J. Stegeman[26], Kenta Sumiyama[37], Diana Tabbaa[3], Hakim Tafer[32], Jason Turner-Maier[3], Peter van Heusden[24], Simon White[16], Louise Williams[3], Mark Yandell[22], Henner Brinkmann[6], Jean-Nicolas Volff[12], Clifford J. Tabin[10], Neil Shubin[38], Manfred Schartl[39], David Jaffe[3], John H. Postlethwait[7], Byrappa Venkatesh[4], Federica Di Palma[3], Eric S. Lander[3], Axel Meyer[5],[8],[25], Kerstin Lindblad-Toh[3],[40]

[1] Molecular Genetics Program, Benaroya Research Institute, Seattle, WA, USA
[2] Department of Biology, University of Washington, Seattle, WA, USA
[3] Broad Institute of MIT and Harvard, Cambridge, MA, USA
[4] Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
[5] Department of Biology, University of Konstanz, Konstanz, Germany
[6] Departement de Biochimie, Universite de Montreal, Centre Robert Cedergren, Montreal, Canada
[7] Institute of Neuroscience, University of Oregon, Eugene, OR, USA
[8] Konstanz Research School of Chemical Biology, University of Konstanz, Konstanz, Germany
[9] Instituto de Ciencias Biologicas, Universidade Federal do Para, Belem, Brazil
[10] Department of Genetics, Harvard Medical School, Boston, MA, USA
[11] Department of Anthropology, University of Utah, Salt Lake City, UT, USA
[12] Institut de Genomique Fonctionnelle de Lyon, Ecole Normale Superieure de Lyon, Lyon, France
[13] Department of Biology, University of Kentucky, Lexington, KY, USA
[14] Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry, Microbiology & Biotechnology, Rhodes University, Grahamstown, South Africa
[15] Department of Life Sciences, University of Trieste, Trieste, Italy
[16] Department of Informatics, Wellcome Trust Sanger Institute, Hinxton, UK
[17] Department of Life and Environmental Sciences, Polytechnic University of the Marche, Ancona, Italy
[18] Department of Life Sciences, University of Liege, Liege, Belgium
[19] College of Health and Biomedicine, Victoria University, Melbourne, Australia
[20] Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Viterbo, Italy
[21] Department of Biology, University of Hamburg, Hamburg, Germany
[22] Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA
[23] Department of Pediatrics, University of South Florida Morsani College of Medicine, Children's Research Institute, St. Petersburg, FL, USA
[24] South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
[25] International Max-Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany
[26] Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
[27] MRC Functional Genomics Unit, Oxford University, Oxford, UK
[28] Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, Universitat Leipzig, Leipzig, Germany
[29] Graduate School of Science and Technology, Keio University, Yokohama, Japan
[30] Department of Molecular Genetics, All Children's Hospital, St. Petersburg, FL, USA
[31] Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
[32] Bioinformatics Group, Department of Computer Science, Universitt Leipzig, Leipzig, Germany
[33] Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Japan
[34] Computational EvoDevo Group, Department of Computer Science, Universitat Leipzig, Leipzig, Germany
[35] Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
[36] European Molecular Biology Laboratory, Heidelberg, Germany
[37] Division of Population Genetics, National Institute of Genetics, Mishima, Japan
[38] University of Chicago, Chicago, IL, USA
[39] Department Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg Germany
[40] Science 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

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 www.imcb.a-star.edu.sg .

About 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 www.a-star.edu.sg .

Source: A*STAR


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