The little skate genome and the evolutionary emergence of wing-like fins.

Autor: Marlétaz F; Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK. ferdinand.marletaz@gmail.com.; Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan. ferdinand.marletaz@gmail.com., de la Calle-Mustienes E; Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain., Acemel RD; Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain.; Epigenetics and Sex Development Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany., Paliou C; Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain., Naranjo S; Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain., Martínez-García PM; Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain., Cases I; Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain., Sleight VA; Department of Zoology, University of Cambridge, Cambridge, UK.; School of Biological Sciences, University of Aberdeen, Aberdeen, UK., Hirschberger C; Department of Zoology, University of Cambridge, Cambridge, UK., Marcet-Houben M; Barcelona Supercomputing Centre (BCS-CNS), Barcelona, Spain.; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain., Navon D; Department of Genetics, Rutgers the State University of New Jersey, Piscataway, NJ, USA., Andrescavage A; Department of Genetics, Rutgers the State University of New Jersey, Piscataway, NJ, USA., Skvortsova K; Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.; Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia., Duckett PE; Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia., González-Rajal Á; Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.; Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia., Bogdanovic O; Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia., Gibcus JH; Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA., Yang L; Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA., Gallardo-Fuentes L; Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain., Sospedra I; Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain., Lopez-Rios J; Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain., Darbellay F; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland., Visel A; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; US Department of Energy Joint Genome Institute, Berkeley, CA, USA.; School of Natural Sciences, University of California, Merced, CA, USA., Dekker J; Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.; Howard Hughes Medical Institute, Chevy Chase, MD, USA., Shubin N; Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA., Gabaldón T; Barcelona Supercomputing Centre (BCS-CNS), Barcelona, Spain.; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.; CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain., Nakamura T; Department of Genetics, Rutgers the State University of New Jersey, Piscataway, NJ, USA. nakamura@dls.rutgers.edu., Tena JJ; Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain. jjtenagu@upo.es., Lupiáñez DG; Epigenetics and Sex Development Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany. Dario.Lupianez@mdc-berlin.de., Rokhsar DS; Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan. dsrokhsar@gmail.com.; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. dsrokhsar@gmail.com.; Chan-Zuckerberg Biohub, San Francisco, CA, USA. dsrokhsar@gmail.com., Gómez-Skarmeta JL; Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain.
Jazyk: angličtina
Zdroj: Nature [Nature] 2023 Apr; Vol. 616 (7957), pp. 495-503. Date of Electronic Publication: 2023 Apr 12.
DOI: 10.1038/s41586-023-05868-1
Abstrakt: Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments 1,2 . However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins-including gene expression, chromatin occupancy and three-dimensional conformation-we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.
(© 2023. The Author(s).)
Databáze: MEDLINE
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