Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp

Heiner Kuhl, Kang Du, Manfred Schartl, Lukáš Kalous, Matthias Stöck () and Dunja K. Lamatsch ()
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Heiner Kuhl: Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin)
Kang Du: University of Würzburg, Developmental Biochemistry, Biocenter
Manfred Schartl: University of Würzburg, Developmental Biochemistry, Biocenter
Lukáš Kalous: Czech University of Life Sciences Prague
Matthias Stöck: Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin)
Dunja K. Lamatsch: University of Innsbruck

Nature Communications, 2022, vol. 13, issue 1, 1-11

Abstract: Abstract Understanding genome evolution of polyploids requires dissection of their often highly similar subgenomes and haplotypes. Polyploid animal genome assemblies so far restricted homologous chromosomes to a ‘collapsed’ representation. Here, we sequenced the genome of the asexual Prussian carp, which is a close relative of the goldfish, and present a haplotype-resolved chromosome-scale assembly of a hexaploid animal. Genome-wide comparisons of the 150 chromosomes with those of two ancestral diploid cyprinids and the allotetraploid goldfish and common carp revealed the genomic structure, phylogeny and genome duplication history of its genome. It consists of 25 syntenic, homeologous chromosome groups and evolved by a recent autoploid addition to an allotetraploid ancestor. We show that de-polyploidization of the alloploid subgenomes on the individual gene level occurred in an equilibrated fashion. Analysis of the highly conserved actinopterygian gene set uncovered a subgenome dominance in duplicate gene loss of one ancestral chromosome set.

Date: 2022
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DOI: 10.1038/s41467-022-31515-w

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