The tiny germline chromosomes of Paramecium aurelia have anexceptionally high recombination rate and are capped by a new class of Helitrons

Arnaiz, O.; Guerin, F.; Couloux, A.; Miro-Pina, C.; Pellerin, G.; Nekrasova, I.; Amselem, J.; Aury, J.-M.; Bhullar, S.; Frapporti, A.; Lerat, E.; Luyten, I.; Malinsky, S.; Mathy, N.; Potekhin, A.; Regnier, V.; Sawka-Gadek, N.; Touzeau, A.; de Vanssay, A.; Zangarelli, C.; Quesneville, H.; Betermier, M.; Labadie, K.; Duret, L.; Meyer, E.; Duharcourt, S.; Sperling, L.

doi:10.1101/2025.11.06.686955

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bioRxiv · 10.1101/2025.11.06.686955

The tiny germline chromosomes of Paramecium aurelia have anexceptionally high recombination rate and are capped by a new class of Helitrons

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Abstract

BackgroundParamecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual generations. A polyploid transcriptionally active somatic macronucleus (MAC) develops at each sexual generation from a copy of the MIC through programmed DNA elimination (PDE) of > 30% of germline DNA. PDE requires the domesticated PiggyMac (Pgm) transposase. Assembly of Paramecium germline genomes has presented an enormous challenge owing to the difficulty of MIC isolation. ResultsWe report chromosome-scale short-read MIC assemblies for 7 species from the P. aurelia species complex. We discovered a novel clade of Helitrons, with 9-10 kb transposase ORFs under purifying selection, that have remained active in all P. aurelia lineages. A long-read assembly for P. tetraurelia together with a genetic linkage map provided a nearly telomere-to-telomere assembly. Conclusions.The genome consists of tiny (300 kb - 1.2 Mb) and numerous ([~]160) germline chromosomes with the highest recombination rate ever reported for a eukaryote (420 cM/Mb). The ends of the chromosomes consist of Helitrons inserted in telomeric C4A2 repeats, forming a distinct genomic compartment that is eliminated very early during MAC development in a Pgm-independent manner.

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Arnaiz, O., Guerin, F., Couloux, A., Miro-Pina, C., Pellerin, G., Nekrasova, I., Amselem, J., Aury, J.-M., Bhullar, S., Frapporti, A., Lerat, E., Luyten, I., Malinsky, S., Mathy, N., Potekhin, A., Regnier, V., Sawka-Gadek, N., Touzeau, A., de Vanssay, A., Zangarelli, C., Quesneville, H., Betermier, M., Labadie, K., Duret, L., Meyer, E., Duharcourt, S., Sperling, L.. 2025-11-07. The tiny germline chromosomes of Paramecium aurelia have anexceptionally high recombination rate and are capped by a new class of Helitrons. https://doi.org/10.1101/2025.11.06.686955

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