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Summary 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 employedChlamydomonas reinhardtiias 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 inChlamydomonas reinhardtiiand possibly other systems.
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This content will become publicly available on May 1, 2026
Expanding the toolkit for ploidy manipulation in Chlamydomonas reinhardtii
Summary Whole‐genome duplications, widely observed in plant lineages, have significant evolutionary and ecological impacts. Yet, our current understanding of the direct implications of ploidy shifts on short‐ and long‐term plant evolution remains fragmentary, necessitating further investigations across multiple ploidy levels.Chlamydomonas reinhardtiiis a valuable model organism with profound potential to study the impact of ploidy increase on the longer term in a laboratory environment. This is partly due to the ability to increase the ploidy level.We developed a strategy to engineer ploidy inC. reinhardtiiusing noninterfering, antibiotic, selectable markers. This approach allows us to induce higher ploidy levels inC. reinhardtiiand is applicable to field isolates, which expands beyond specific auxotroph laboratory strains and broadens the genetic diversity of parental haploid strains that can be crossed. We implement flow cytometry for precise measurement of the genome size of strains of different ploidy.We demonstrate the creation of diploids, triploids, and tetraploids by engineering North American field isolates, broadening the application of synthetic biology principles inC. reinhardtii. However, our newly formed triploids and tetraploids show signs of rapid aneuploidization.Our study greatly facilitates the application ofC. reinhardtiito study polyploidy, in both fundamental and applied settings.
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- Award ID(s):
- 2320251
- PAR ID:
- 10591396
- Publisher / Repository:
- New Phytologist Foundation
- Date Published:
- Journal Name:
- New Phytologist
- Volume:
- 246
- Issue:
- 3
- ISSN:
- 0028-646X
- Page Range / eLocation ID:
- 1403 to 1412
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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