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The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

Braasch, I. and Gehrke, A.R. and Smith, J.J. and Kawasaki, K. and Manousaki, T. and Pasquier, J. and Amores, A. and Desvignes, T. and Batzel, P. and Catchen, J. and Berlin, A.M. and Campbell, M.S. and Barrell, D. and Martin, K.J. and Mulley, J.F. and Ravi, V. and Lee, A.P. and Nakamura, T. and Chalopin, D. and Fan, S. and Wcisel, D. and Cañestro, C. and Sydes, J. and Beaudry, F.E.G. and Sun, Y. and Hertel, J. and Beam, M.J. and Fasold, M. and Ishiyama, M. and Johnson, J. and Kehr, S. and Lara, M. and Letaw, J.H. and Litman, G.W. and Litman, R.T. and Mikami, M. and Ota, T. and Saha, N.R. and Williams, L. and Stadler, P.F. and Wang, H. and Taylor, J.S. and Fontenot, Q. and Ferrara, A. and Searle, S.M.J. and Aken, B. and Yandell, M. and Schneider, I. and Yoder, J.A. and Volff, J. and Meyer, A. and Amemiya, C.T. and Venkatesh, B. and Holland, P.W.H. and Guiguen, Y. and Bobe, J. and Shubin, N.H. and Di Palma, F. and Alföldi, J. and Lindblad-Toh, K. and Postlethwait, J.H. (2016) The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. DOI: 10.1038/ng.3526

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Abstract

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

Item Type: Article
Subjects: Research Publications
Departments: College of Natural Sciences > School of Biological Sciences
Date Deposited: 12 Mar 2016 03:13
Last Modified: 23 Mar 2016 13:28
ISSN: 1061-4036
URI: http://e.bangor.ac.uk/id/eprint/6322
Identification Number: DOI: 10.1038/ng.3526
Publisher: Nature Publishing Group
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