Abstract

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.

A genome assembly of the sterlet, Acipenser ruthenus, reveals a whole-genome duplication early in the evolution of the entire sturgeon lineage and provides details about the rediploidization of the genome.

Details

Title
The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization
Author
Du, Kang 1 ; Stöck Matthias 2   VIAFID ORCID Logo  ; Kneitz Susanne 3 ; Klopp Christophe 4   VIAFID ORCID Logo  ; Woltering, Joost M 5 ; Adolfi Mateus Contar 3 ; Feron Romain 6   VIAFID ORCID Logo  ; Prokopov Dmitry 7   VIAFID ORCID Logo  ; Makunin Alexey 7   VIAFID ORCID Logo  ; Kichigin Ilya 7 ; Schmidt, Cornelia 3 ; Fischer, Petra 3 ; Kuhl Heiner 2 ; Wuertz Sven 2 ; Gessner Jörn 2 ; Kloas Werner 2 ; Cabau Cédric 4 ; Iampietro Carole 8 ; Parrinello Hugues 9 ; Tomlinson, Chad 10 ; Journot Laurent 9 ; Postlethwait, John H 11 ; Braasch Ingo 12 ; Trifonov, Vladimir 7 ; Warren, Wesley C 13 ; Meyer, Axel 5   VIAFID ORCID Logo  ; Guiguen Yann 14   VIAFID ORCID Logo  ; Schartl Manfred 15   VIAFID ORCID Logo 

1  University of Wuerzburg, Physiological Chemistry, Biocenter, Wuerzburg, Germany (GRID:grid.8379.5) (ISNI:0000 0001 1958 8658); University of Wuerzburg, Developmental Biochemistry, Biocenter, Wuerzburg, Germany (GRID:grid.8379.5) (ISNI:0000 0001 1958 8658) 
2  Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Berlin, Germany (GRID:grid.419247.d) (ISNI:0000 0001 2108 8097) 
3  University of Wuerzburg, Physiological Chemistry, Biocenter, Wuerzburg, Germany (GRID:grid.8379.5) (ISNI:0000 0001 1958 8658) 
4  Plate-forme Bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France (GRID:grid.507621.7); Université de Toulouse, INRA, ENVT, SIGENAE, GenPhySE, Castanet-Tolosan, France (GRID:grid.507621.7) 
5  University of Konstanz, Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, Konstanz, Germany (GRID:grid.9811.1) (ISNI:0000 0001 0658 7699) 
6  University of Lausanne, and Swiss Institute of Bioinformatics, Department of Ecology and Evolution, Lausanne, Switzerland (GRID:grid.9851.5) (ISNI:0000 0001 2165 4204) 
7  Novosibirsk State University, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia (GRID:grid.4605.7) (ISNI:0000000121896553) 
8  INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France (GRID:grid.507621.7) 
9  Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, Montpellier, France (GRID:grid.461890.2) (ISNI:0000 0004 0383 2080) 
10  Washington University School of Medicine, McDonnell Genome Institute, St. Louis, USA (GRID:grid.4367.6) (ISNI:0000 0001 2355 7002) 
11  University of Oregon, Institute of Neuroscience, Eugene, USA (GRID:grid.170202.6) (ISNI:0000 0004 1936 8008) 
12  Michigan State University, Department of Integrative Biology, East Lansing, USA (GRID:grid.17088.36) (ISNI:0000 0001 2150 1785) 
13  University of Missouri, Bond Life Sciences Center, Columbia, USA (GRID:grid.134936.a) (ISNI:0000 0001 2162 3504) 
14  INRA, UR1037 LPGP, Fish Physiology and Genomics, Rennes, France (GRID:grid.460202.2) 
15  University of Wuerzburg, Developmental Biochemistry, Biocenter, Wuerzburg, Germany (GRID:grid.8379.5) (ISNI:0000 0001 1958 8658); Department of Chemistry and Biochemistry, Texas State University, The Xiphophorus Genetic Stock Center, San Marcos, USA (GRID:grid.264772.2) (ISNI:0000 0001 0682 245X); Texas A&M University, Hagler Institute for Advanced Study and Department of Biology, College Station, USA (GRID:grid.264756.4) (ISNI:0000 0004 4687 2082) 
Pages
841-852
Publication year
2020
Publication date
Jun 2020
Publisher
Nature Publishing Group
e-ISSN
2397334X
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41559-020-1166-x
ProQuest document ID
2409174240
Copyright
© The Author(s) 2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.