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

A. Blasweiler*, H. J. Megens, M. R.G. Goldman, R. Tadmor-Levi, J. Lighten, M. A.M. Groenen, R. P. Dirks, H. J. Jansen, H. P. Spaink, L. David, P. Boudinot, G. F. Wiegertjes

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

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.

Original languageAmerican English
Article number110723
JournalGenomics
Volume115
Issue number6
DOIs
StatePublished - Nov 2023

Bibliographical note

Publisher Copyright:
© 2023 The Authors

Keywords

  • Antiviral response
  • Common carp
  • Ohnolog expression
  • Subgenome dominance
  • Whole genome duplication

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