Abstract
BackgroundCiliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused genomes are extensively rearranged to generate functional minichromosomes. Interestingly, each ciliate species seems to have its way of processing genomes, providing a diversity of resources for studying genome plasticity and its regulation. Here, we sequenced and analyzed the macronuclear genome of different strains of Paramecium bursaria, a highly divergent species of the genus Paramecium which can stably establish endosymbioses with green algae.ResultsWe assembled a high-quality macronuclear genome of P. bursaria and further refined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that are potentially associated with endosymbiosis. Moreover, we observed an intensive chromosome breakage pattern that occurred during or shortly after sexual reproduction and contributed to highly variable gene dosage throughout the genome. However, patterns of copy number variation were highly correlated among genetically divergent strains, suggesting that copy number is adjusted by some regulatory mechanisms or natural selection. Further analysis showed that genes with low copy number variation among populations tended to function in basic cellular pathways, whereas highly variable genes were enriched in environmental response pathways.ConclusionsWe report programmed DNA rearrangements in the P. bursaria macronuclear genome that allow cells to adjust gene copy number globally according to individual gene functions. Our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments.
Highlights
Ciliates are an ancient and diverse eukaryotic group found in various environments
Most large-scale studies on Copy number variation (CNV) have been conducted on human populations, which show that de novo CNV frequently occurs in human genomes [9, 10] and accounts for 17.7% of altered gene expression among genes associated with CNV or Single nucleotide polymorphism (SNP) [11]
By comparing the genomes of different P. bursaria strains, we reveal that minichromosomes maintained in consistent copy numbers among strains are enriched with housekeeping genes, whereas those carrying environmental response genes exhibit pronounced CNV among strains
Summary
Ciliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. Most studies of phenotypic diversity focused on single nucleotide polymorphisms (SNPs), whereas the effects of CNV remain understudied [3]. The phenotypic outcomes of CNV have been investigated in other organisms, including domestication traits in animals and plants [13], chemical or disease resistance in insects and plants [14, 15], and environmental adaptation in microorganisms [3, 16]. These studies provide examples of how organismal phenotypes are influenced by CNV. It remains unclear to what extent CNV can be tolerated in a typical genome and if organisms systematically utilize CNV to adjust their physiologies under different environments
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