Evolutionary Genomics in Paramecium

Among the highly diverse microbial eukaryotes, the freshwater ciliate Paramecium has a unique genome architecture among all eukaryotes, but in common with all ciliate species. Every single cell holds at least one “germline” diploid micronucleus (MIC) and one “somatic” polyploid macronucleus (MAC).

During asexual division the MIC undergoes mitosis while the MAC simply cleaves (amitosis) into two new nuclei with a potentially unequal distribution of DNA, which may can lead to intraclonal MAC genome differences and different phenotypes. At the stage of sexual reproduction the MIC goes through meiosis while the MAC disintegrates during conjugation, and is newly formed by one of the MIC-originated, postzygotic nuclei. During the MAC development, zygotic chromosomes were fragmented, some sequences were eliminated and genes were amplified.

This exclusive fact of genome development displays the importance of ciliates in cell biology and evolution, but also denotes them as an interesting study system for a functional understanding of phenotype-genotype interactions.

The MAC genomes of several Paramecium species have been recently sequenced (hosted at the ParameciumDB) and can now be used to examine mechanisms of speciation, gene duplication events, chromosome losses, etc. by comparing portions of a number of Paramecium genomes. Recently, we have re-sequenced dozens of different strains of various Paramecium species, done in collaboration with peers from the Lynch lab (Indiana University Bloomington, USA) for comparative genomic and future population genomic approaches. The results have been published in Molecular Biology and Evolution, msx074.

In collaboration with Sandra Duharcourt and Frédéric Guérin (Institut Jacques-Monod, CNRS, University Paris Diderot, France) we are trying to sequence the larger MIC genome of Paramecium caudatum to detect differences between MIC and MAC genomes in respect to their different developments and functions. This is needed to get insights into e.g. the connection between genotypic and phenotypic as well as transcriptional changes and epigenetic mechanisms in response to changing environments. First results show that while the streamlined MAC genome of P. caudatum is relatively small with only ~30Mb, the MIC genome is about 1GB in size comprising huge amounts of highly repetitive DNA seqeunces.

Part of this cooparative work was supported by the COST action BM1102 - Ciliates as model systems to study genome evolution, mechanisms of non-Mendelian inheritance, and their roles in environmental adaptation.