Byrappa Venkatesh1,2,*, Alison P. Lee1, Vydianathan Ravi1, Ashish K. Maurya31, Michelle M. Lian1, Jeremy B. Swann4, Yuko Ohta5, Martin F. Flajnik5, Yoichi Sutoh6, Masanori Kasahara6, Shawn Hoon7, Vamshidhar Gangu7, Scott W. Roy8, Manuel Irimia9, Vladimir Korzh10, Igor Kondrychyn10, Zhi Wei Lim1, Boon-Hui Tay1, Sumanty Tohari1, Kiat Whye Kong7, Shufen Ho7, Belen Lorente-Galdos11, Javier Quilez11, Tomas Marques-Bonet11, Brian J. Raney12, Philip W. Ingham3, Alice Tay1, LaDeana W. Hillier13, Patrick Minx13, Thomas Boehm4, Richard K. Wilson13, Sydney Brenner1 & Wesley C. Warren13,*
1 - Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore.
2 - Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
3 - Developmental and Biomedical Genetics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore.
4 - Department of Developmental Immunology, Max-Planck-Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany.
5 - Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201 USA.
6 - Department of Pathology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan.
7 - Molecular Engineering Laboratory, Biomedical Sciences Institutes, A*STAR, Biopolis, Singapore.
8 - Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
9 - Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada.
10-Fish Developmental Biology Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore.
11-Institut de Biologia Evolutiva, (UPF-CSIC), PRBB, 08003, Barcelona, Spain.
12-Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
13-The Genome Institute at Washington University, St. Louis, MO, USA.
Published in Nature on 9 January 2014 (Vol 505: 174-179).
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Elephant Shark Genome Project Website: http://esharkgenome.imcb.a-star.edu.sg/
The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates (agnatha) was accompanied by major morphological and physiological innovations, such as hinged jaws, true teeth, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes (Chondrichthyes) and the bony vertebrates (Osteichthyes). Here we report the first 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 (SCPPs) 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.
Elephant shark genome is the slowest evolving among known vertebrate genomes. A neutral tree of 13 chordates based on four-fold degenerate (4D) sites shows that the elephant shark possesses the slowest evolving vertebrate genome. The tree is based on 699 protein-coding sequences (strict one-to-one orthologues) from 13 species.
For more information on Byrappa VENKATESH's laboratory, please click here.