The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization.
Du KPhysiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany.
Stöck MLeibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Berlin, Germany. matthias.stoeck@igb-berlin.de.
Kneitz SPhysiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany.
Klopp CPlate-forme Bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France.
Woltering JMLehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.
Adolfi MCPhysiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany.
Feron RDepartment of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Prokopov DInstitute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk State University, Novosibirsk, Russia.
Makunin AInstitute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk State University, Novosibirsk, Russia.
Kichigin IInstitute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk State University, Novosibirsk, Russia.
Schmidt CPhysiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany.
Fischer PPhysiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany.
Kuhl HLeibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Berlin, Germany.
Wuertz SLeibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Berlin, Germany.
Gessner JLeibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Berlin, Germany.
Kloas WLeibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Berlin, Germany.
Cabau CPlate-forme Bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France.
Iampietro CINRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France.
Parrinello HMontpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, Montpellier, France.
Tomlinson CMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
Journot LMontpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, Montpellier, France.
Postlethwait JHInstitute of Neuroscience, University of Oregon, Eugene, OR, USA.
Braasch IDepartment of Integrative Biology, Michigan State University, East Lansing, MI, USA.
Trifonov VInstitute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk State University, Novosibirsk, Russia.
Warren WCBond Life Sciences Center, University of Missouri, Columbia, MO, USA.
Meyer ALehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.
Guiguen YINRA, UR1037 LPGP, Fish Physiology and Genomics, Rennes, France.
Schartl MDevelopmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany. phch1@biozentrum.uni-wuerzburg.de.
English
Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the ~30,000 modern teleost fish species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities to investigate the evolution of polyploid genomes. We assembled a high-quality chromosome-level reference genome for the sterlet, Acipenser ruthenus. Our analysis revealed a very low protein evolution rate that is at least as slow as in other deep branches of the vertebrate tree, such as that of the coelacanth. We uncovered a whole-genome duplication that occurred in the Jurassic, early in the evolution of the entire sturgeon lineage. Following this polyploidization, the rediploidization of the genome included the loss of whole chromosomes in a segmental deduplication process. While known adaptive processes helped conserve a high degree of structural and functional tetraploidy over more than 180 million years, the reduction of redundancy of the polyploid genome seems to have been remarkably random.