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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. 

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. 

Abstract The Viridiplantae comprise two main clades, the Chlorophyta (including a diverse array of marine and freshwater green algae) and the Streptophyta (consisting of the freshwater charophytes and the land plants). Lineages sister to core Chlorophyta, informally refer to as prasinophytes, form a grade of mainly planktonic green algae. Recently, one of these lineages, Prasinodermophyta, which is previously grouped with prasinophytes, has been identified as the sister lineage to both Chlorophyta and Streptophyta. Resolving the deep relationships among green plants is crucial for understanding the historical impact of green algal diversity on marine ecology and geochemistry, but has been proven difficult given the ancient timing of the diversification events. Through extensive taxon and gene sampling, we conduct large-scale phylogenomic analyses to resolve deep relationships and reveal the Prasinodermophyta as the lineage sister to Chlorophyta, raising questions about the necessity of classifying the Prasinodermophyta as a distinct phylum. We unveil that incomplete lineage sorting is the main cause of discordance regarding the placement of Prasinodermophyta. Molecular dating analyses suggest that crown-group green plants and crown-group Prasinodermophyta date back to the Paleoproterozoic-Mesoproterozoic. Our study establishes a plausible link between oxygen levels in the Paleoproterozoic-Mesoproterozoic and the origin of Viridiplantae.