Genome plasticity in Paramecium bursaria revealed by population genomics
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RESEARCH ARTICLE
Open Access
Genome plasticity in Paramecium bursaria revealed by population genomics Yu-Hsuan Cheng1,2, Chien-Fu Jeff Liu2, Yen-Hsin Yu2, Yu-Ting Jhou2, Masahiro Fujishima4, Isheng Jason Tsai1,3 and Jun-Yi Leu1,2*
Abstract Background: 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. 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. Results: We 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. Conclusions: We 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. Keywords: Ciliate, Paramecium, Copy number variation, Programmed DNA rearrangement, Comparative genomics, Minichromosomes
* Correspondence: [email protected] 1 Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 106, Taiwan 2 Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei 115, Taiwan Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the
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