Symmetric expression of ohnologs encoding conserved antiviral responses in tetraploid common carp suggest absence of subgenome dominance after whole genome duplication

Allopolyploids often experience subgenome dominance, with one subgenome showing higher levels of gene expression and greater gene retention. Here, we address the functionality of both subgenomes of allotetraploid common carp (Cyprinus carpio) by analysing a functional network of interferon-stimulate...

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Bibliographic Details
Published in:	Genomics (San Diego, Calif.) Vol. 115; no. 6; p. 110723
Main Authors:	Blasweiler, A., Megens, H.-J., Goldman, M.R.G., Tadmor-Levi, R., Lighten, J., Groenen, M.A.M., Dirks, R.P., Jansen, H.J., Spaink, H.P., David, L., Boudinot, P., Wiegertjes, G.F.
Format:	Journal Article
Language:	English
Published:	United States Elsevier Inc 01-11-2023 Elsevier
Subjects:	Antiviral response Common carp Life Sciences Ohnolog expression Subgenome dominance Whole genome duplication Common carp Antiviral response Whole genome duplication Subgenome dominance Ohnolog expression
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Summary:	Allopolyploids often experience subgenome dominance, with one subgenome showing higher levels of gene expression and greater gene retention. Here, we address the functionality of both subgenomes of allotetraploid common carp (Cyprinus carpio) by analysing a functional network of interferon-stimulated genes (ISGs) crucial in anti-viral immune defence. As an indicator of subgenome dominance we investigated retainment of a core set of ohnologous ISGs. To facilitate our functional genomic analysis a high quality genome was assembled (WagV4.0). Transcriptome data from an in vitro experiment mimicking a viral infection was used to infer ISG expression. Transcriptome analysis confirmed induction of 88 ISG ohnologs on both subgenomes. In both control and infected states, average expression of ISG ohnologs was comparable between the two subgenomes. Also, the highest expressing and most inducible gene copies of an ohnolog pair could be derived from either subgenome. We found no strong evidence of subgenome dominance for common carp. •Allopolyploid common carp model species for studying subgenome functionality.•First chromosomal level genome of European common carp strain R3xR8.•Annotation of conserved ISG set of 72 orthologous groups in carp.•ISG ohnologs used to directly relate gene expression to function•Transcriptomic analysis of ohnologs to evaluate functional contributions of subgenomes.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0888-7543 1089-8646 1089-8646
DOI:	10.1016/j.ygeno.2023.110723