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

作者：Ingo Braasch, Andrew R. Gehrke, Jeramiah J. Smith, Kazuhiko Kawasaki, Tereza Manousaki, Jérémy Pasquier, Angel Amores, Thomas Desvignes, Peter Batzel, Julian Catchen, Aaron M. Berlin, Michael S. Campbell, Daniel Barrell, Kyle J. Martin, John F. Mulley, Vydianathan Ravi, Alison Lee, Tetsuya Nakamura, Domitille Chalopin, Shaohua Fan, Dustin J. Wcisel, Cristian Cañestro, Jason Sydes, Felix E.G. Beaudry, Yi Sun, Jana Hertel, Michael J. Beam, Mario Fasold, Mikio Ishiyama, Jeremy Johnson, Steffi Kehr, Marcia Lara, John Letaw, Gary W. Litman, Ronda T. Litman, Masato Mikami, Tatsuya Ota, Nil Ratan Saha, Louise Williams, Peter F. Stadler, Han Wang, John S. Taylor, Quenton Fontenot, Allyse Ferrara, Stephen M. J. Searle, Bronwen Aken, Mark Yandell, Igor Schneider, Jeffrey A. Yoder, Jean‐Nicolas Volff, Axel Meyer, Chris T. Amemiya, Byrappa Venkatesh, Peter W H Holland, Yann Guiguen, Julien Bobe, Neil H. Shubin, Federica Di Palma, Jessica Alföldi, Kerstin Lindblad‐Toh, John H. Postlethwait · 发表于：Nature Genetics · 年份：2016 · DOI：10.1038/ng.3526 · 被引用次数：689 · 研究领域：Cancer-related molecular mechanisms research、RNA Research and Splicing、interferon and immune responses

Ingo Braasch, John Postlethwait and colleagues report the genome of the spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before genome duplication. Their data provide insights into the evolution of genes involved in immunity, mineralization and development and facilitate the comparison of cis-regulatory elements between teleosts and humans. 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 ...