The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization
Kang Du, Matthias Stöck, Susanne Kneitz, Christophe Klopp, Joost M. Woltering, Mateus Contar Adolfi, Romain Feron, Dmitry Prokopov, Alex Makunin, Ilya G. Kichigin, Cornelia Schmidt, Petra Fischer, Heiner Kuhl, Sven Wuertz, Jörn Geßner, Werner Kloas, Cédric Cabau, Carole Iampietro, Hugues Parrinello, Chad Tomlinson, Laurent Journot, John H. Postlethwait, Ingo Braasch, Vladimir A. Trifonov, Wesley C. Warren, Axel Meyer, Yann Guiguen, Manfred Schartl
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.