The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization

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

doi:10.1038/s41559-020-1166-x

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.

Highlights

Sturgeons seem to be frozen in time
We sequenced the sterlet sturgeon, Acipenser Syntax Warning: Invalid Font Weight ruthenus, a species with only 120 chromosomes, and present here an annotated chromosome-scale genome assembly. We found that this genome represents an ancient whole-genome duplications (WGDs), which remained close to tetraploidy owing to the slow evolutionary rate and serves as a good representative of the ancestral actinopterygian genome
Our results show that the sterlet lineage branched from the vertebrate tree of life about 345 million years ago (Ma), shortly after the basal split between the linage of ray-finned fish and that of lungfish, coelacanth and land vertebrates happened

Summary

Introduction

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. The evolutionary history of the ~30,000 species of teleost fish, which make up more than 99% of all ray-finned fishes (Actinopterygia), is defined by a third WGD (3R) that occurred in their common ancestor about 320 million years ago (Ma), but not in the basal fish (bichirs, reedfish, sturgeons, paddlefishes, bowfins and gars), the land vertebrates or their sarcopterygian forbearing relatives (coelacanths and lungfishes). On the basis of some cytogenetic and microsatellite data, others have considered sturgeons to be functional diploids[10] as result of an evolutionary process, where the gene content of a tetraploid species degenerates to become functionally diploid but maintains twice as many chromosomes, which form regulaSyntax Warning: Invalid Font Weight r bivalents[11] Such far-reaching redundancy reduction leads one to question their polyploidy state[12]

Methods

Results

Conclusion