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Asymmetric genome merging leads to gene expression novelty through nucleo‐cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

Lucas Prost Boxoen (UGent) , Quinten Bafort (UGent) , Antoine Van de Vloet (UGent) , Fabricio De Almeida Silva (UGent) , Yunn Thet Paing (UGent) , Griet Casteleyn (UGent) , Sofie D'hondt (UGent) , Olivier De Clerck (UGent) and Yves Van de Peer (UGent)
(2025) NEW PHYTOLOGIST. 245(22). p.869-884
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Abstract
Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well-understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression-level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression-level dominance and a pattern of 'functional dominance' from the haploid parent was observed. Despite major genomic and nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.
Keywords
Chlamydomonas reinhardtii, RNA‐Seq, allopolyploidy, experimental evolution laboratory natural selection (LNS), genome merging, transcriptomics, RNA-Seq, EVOLUTIONARY CONSEQUENCES, TRAGOPOGON-MISCELLUS, SYNTHETIC POLYPLOIDS, CHLOROPLAST DNA, LEVEL DOMINANCE, RNA-SEQ, ANEUPLOIDY, PATTERNS, PLOIDY, INSTABILITY

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Citation

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MLA
Prost, Lucas, et al. “Asymmetric Genome Merging Leads to Gene Expression Novelty through Nucleo‐cytoplasmic Disruptions and Transcriptomic Shock in Chlamydomonas Triploids.” NEW PHYTOLOGIST, vol. 245, no. 22, 2025, pp. 869–84, doi:10.1111/nph.20249.
APA
Prost, L., Bafort, Q., Van de Vloet, A., De Almeida Silva, F., Yunn Thet Paing, Casteleyn, G., … Van de Peer, Y. (2025). Asymmetric genome merging leads to gene expression novelty through nucleo‐cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids. NEW PHYTOLOGIST, 245(22), 869–884. https://doi.org/10.1111/nph.20249
Chicago author-date
Prost, Lucas, Quinten Bafort, Antoine Van de Vloet, Fabricio De Almeida Silva, Yunn Thet Paing, Griet Casteleyn, Sofie D’hondt, Olivier De Clerck, and Yves Van de Peer. 2025. “Asymmetric Genome Merging Leads to Gene Expression Novelty through Nucleo‐cytoplasmic Disruptions and Transcriptomic Shock in Chlamydomonas Triploids.” NEW PHYTOLOGIST 245 (22): 869–84. https://doi.org/10.1111/nph.20249.
Chicago author-date (all authors)
Prost, Lucas, Quinten Bafort, Antoine Van de Vloet, Fabricio De Almeida Silva, Yunn Thet Paing, Griet Casteleyn, Sofie D’hondt, Olivier De Clerck, and Yves Van de Peer. 2025. “Asymmetric Genome Merging Leads to Gene Expression Novelty through Nucleo‐cytoplasmic Disruptions and Transcriptomic Shock in Chlamydomonas Triploids.” NEW PHYTOLOGIST 245 (22): 869–884. doi:10.1111/nph.20249.
Vancouver
1.
Prost L, Bafort Q, Van de Vloet A, De Almeida Silva F, Yunn Thet Paing, Casteleyn G, et al. Asymmetric genome merging leads to gene expression novelty through nucleo‐cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids. NEW PHYTOLOGIST. 2025;245(22):869–84.
IEEE
[1]
L. Prost et al., “Asymmetric genome merging leads to gene expression novelty through nucleo‐cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids,” NEW PHYTOLOGIST, vol. 245, no. 22, pp. 869–884, 2025.
@article{01JCFR8S9NY9WXK4MJ1RB708WV,
  abstract     = {{Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well-understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression-level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression-level dominance and a pattern of 'functional dominance' from the haploid parent was observed. Despite major genomic and nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.}},
  author       = {{Prost Boxoen, Lucas and Bafort, Quinten and Van de Vloet, Antoine and De Almeida Silva, Fabricio and Yunn Thet Paing and Casteleyn, Griet and D'hondt, Sofie and De Clerck, Olivier and Van de Peer, Yves}},
  issn         = {{0028-646X}},
  journal      = {{NEW PHYTOLOGIST}},
  keywords     = {{Chlamydomonas reinhardtii,RNA‐Seq,allopolyploidy,experimental evolution laboratory natural selection (LNS),genome merging,transcriptomics,RNA-Seq,EVOLUTIONARY CONSEQUENCES,TRAGOPOGON-MISCELLUS,SYNTHETIC POLYPLOIDS,CHLOROPLAST DNA,LEVEL DOMINANCE,RNA-SEQ,ANEUPLOIDY,PATTERNS,PLOIDY,INSTABILITY}},
  language     = {{eng}},
  number       = {{22}},
  pages        = {{869--884}},
  title        = {{Asymmetric genome merging leads to gene expression novelty through nucleo‐cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids}},
  url          = {{http://doi.org/10.1111/nph.20249}},
  volume       = {{245}},
  year         = {{2025}},
}
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