Elephant shark genome provides unique insights into gnathostome evolution

Byrappa Venkatesh (), Alison P. Lee, Vydianathan Ravi, Ashish K. Maurya, Michelle M. Lian, Jeremy B. Swann, Yuko Ohta, Martin F. Flajnik, Yoichi Sutoh, Masanori Kasahara, Shawn Hoon, Vamshidhar Gangu, Scott W. Roy, Manuel Irimia, Vladimir Korzh, Igor Kondrychyn, Zhi Wei Lim, Boon-Hui Tay, Sumanty Tohari, Kiat Whye Kong, Shufen Ho, Belen Lorente-Galdos, Javier Quilez, Tomas Marques-Bonet, Brian J. Raney, Philip W. Ingham, Alice Tay, LaDeana W. Hillier, Patrick Minx, Thomas Boehm, Richard K. Wilson, Sydney Brenner and Wesley C. Warren ()
Additional contact information
Byrappa Venkatesh: Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673
Alison P. Lee: Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673
Vydianathan Ravi: Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673
Ashish K. Maurya: Developmental and Biomedical Genetics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673
Michelle M. Lian: Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673
Jeremy B. Swann: Max-Planck-Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
Yuko Ohta: University of Maryland
Martin F. Flajnik: University of Maryland
Yoichi Sutoh: Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
Masanori Kasahara: Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
Shawn Hoon: Molecular Engineering Laboratory, Biomedical Sciences Institutes, A*STAR, Biopolis, Singapore 138673
Vamshidhar Gangu: Molecular Engineering Laboratory, Biomedical Sciences Institutes, A*STAR, Biopolis, Singapore 138673
Scott W. Roy: San Francisco State University
Manuel Irimia: University of Toronto, Toronto, Ontario M5S 3E1, Canada
Vladimir Korzh: Fish Developmental Biology Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673
Igor Kondrychyn: Fish Developmental Biology Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673
Zhi Wei Lim: Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673
Boon-Hui Tay: Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673
Sumanty Tohari: Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673
Kiat Whye Kong: Molecular Engineering Laboratory, Biomedical Sciences Institutes, A*STAR, Biopolis, Singapore 138673
Shufen Ho: Molecular Engineering Laboratory, Biomedical Sciences Institutes, A*STAR, Biopolis, Singapore 138673
Belen Lorente-Galdos: Institut de Biologia Evolutiva (UPF-CSIC), PRBB, 08003 Barcelona, Spain
Javier Quilez: Institut de Biologia Evolutiva (UPF-CSIC), PRBB, 08003 Barcelona, Spain
Tomas Marques-Bonet: Institut de Biologia Evolutiva (UPF-CSIC), PRBB, 08003 Barcelona, Spain
Brian J. Raney: Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz
Philip W. Ingham: Developmental and Biomedical Genetics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673
Alice Tay: Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673
LaDeana W. Hillier: The Genome Institute at Washington University
Patrick Minx: The Genome Institute at Washington University
Thomas Boehm: Max-Planck-Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
Richard K. Wilson: The Genome Institute at Washington University
Sydney Brenner: Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673
Wesley C. Warren: The Genome Institute at Washington University

Nature, 2014, vol. 505, issue 7482, 174-179

Abstract: Abstract The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes and the bony vertebrates. Here we report the whole-genome analysis of a cartilaginous fish, the elephant shark (Callorhinchus milii). We find that the C. milii genome is the slowest evolving of all known vertebrates, including the ‘living fossil’ coelacanth, and features extensive synteny conservation with tetrapod genomes, making it a good model for comparative analyses of gnathostome genomes. Our functional studies suggest that the lack of genes encoding secreted calcium-binding phosphoproteins in cartilaginous fishes explains the absence of bone in their endoskeleton. Furthermore, the adaptive immune system of cartilaginous fishes is unusual: it lacks the canonical CD4 co-receptor and most transcription factors, cytokines and cytokine receptors related to the CD4 lineage, despite the presence of polymorphic major histocompatibility complex class II molecules. It thus presents a new model for understanding the origin of adaptive immunity.

Date: 2014
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DOI: 10.1038/nature12826

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