Dataset Information

The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization.

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.

SUBMITTER: Du K

PROVIDER: S-EPMC7269910 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization.

Du Kang K Stöck Matthias M Kneitz Susanne S Klopp Christophe C Woltering Joost M JM Adolfi Mateus Contar MC Feron Romain R Prokopov Dmitry D Makunin Alexey A Kichigin Ilya I Schmidt Cornelia C Fischer Petra P Kuhl Heiner H Wuertz Sven S Gessner Jörn J Kloas Werner W Cabau Cédric C Iampietro Carole C Parrinello Hugues H Tomlinson Chad C Journot Laurent L Postlethwait John H JH Braasch Ingo I Trifonov Vladimir V Warren Wesley C WC Meyer Axel A Guiguen Yann Y Schartl Manfred M

Nature ecology & evolution 20200330 6

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 a ...[more]

PMID: 32231327

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Project description:BackgroundThe Brassica species, related to Arabidopsis thaliana, include an important group of crops and represent an excellent system for studying the evolutionary consequences of polyploidy. Previous studies have led to a proposed structure for an ancestral karyotype and models for the evolution of the B. rapa genome by triplication and segmental rearrangement, but these have not been validated at the sequence level.ResultsWe developed computational tools to analyse the public collection of B. rapa BAC end sequence, in order to identify candidates for representing collinearity discontinuities between the genomes of B. rapa and A. thaliana. For each putative discontinuity, one of the BACs was sequenced and analysed for collinearity with the genome of A. thaliana. Additional BAC clones were identified and sequenced as part of ongoing efforts to sequence four chromosomes of B. rapa. Strikingly few of the 19 inter-chromosomal rearrangements corresponded to the set of collinearity discontinuities anticipated on the basis of previous studies. Our analyses revealed numerous instances of newly detected collinearity blocks. For B. rapa linkage group A8, we were able to develop a model for the derivation of the chromosome from the ancestral karyotype. We were also able to identify a rearrangement event in the ancestor of B. rapa that was not shared with the ancestor of A. thaliana, and is represented in triplicate in the B. rapa genome. In addition to inter-chromosomal rearrangements, we identified and analysed 32 BACs containing the end points of segmental inversion events.ConclusionOur results show that previous studies of segmental collinearity between the A. thaliana, Brassica and ancestral karyotype genomes, although very useful, represent over-simplifications of their true relationships. The presence of numerous cryptic collinear genome segments and the frequent occurrence of segmental inversions mean that inference of the positions of genes in B. rapa based on the locations of orthologues in A. thaliana can be misleading. Our results will be of relevance to a wide range of plants that have polyploid genomes, many of which are being considered according to a paradigm of comprising conserved synteny blocks with respect to sequenced, related genomes.

Dataset Information

The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization.

Publications

The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization.

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