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.
Description:
DATA AVAILABILITY : The RNA-Seq 3′ QuantSeq data generated in this study are available in the NCBI Sequence Read Archive (SRA) under the accession no. PRJNA1145893.
SUPPORTING INFORMATION : FIG. S1. Growth curves of the different experimental strains.
FIG. S2. Mean maximum growth rate of parental strains, ancestral triploid, and triploid lines pooled at generation time points (G225 and G425).
FIG. S3. Comparative flow cytometric analysis of propidium iodide-stained nuclei for genome size estimation.
FIG. S4. Conservation of expression patterns across three experimental evolution time points (G0, G225, and G425) in the triploid progeny lines.
FIG. S5. Summary statistics of coexpression modules for the network with all samples.
TABLE S1. Overrepresented KEGG pathways among persistent downregulated genes in the triploid.
TABLE S2. Overrepresented KEGG pathways among genes showing persistent expression level dominance toward the haploid parent (ELD1).
TABLE S3. Overrepresented Gene Ontology terms in Category II genes.
TABLE S4. Overrepresented Gene Ontology terms in Category XI genes.
TABLE S5. Overview of genes in the lightsteelblue module.
