Whole-genome duplications revealed by macronuclear genomes of five rare species of the model ciliates Paramecium.

Paramecium, a group of ciliates with a long evolutionary history, plays essential roles in freshwater ecosystems and has been model for genetic, cellular, and evolutionary studies for over a century. Despite the valuable contributions of genomic resources such as ParameciumDB, genomic data are still mostly limited to species in and near the P. aurelia group. This study addresses this gap by HiFi sequencing, assembling, and annotating the macronuclear genomes of five rare Paramecium species: P. calkinsi, P. duboscqui, P. nephridiatum, P. putrinum, and P. woodruffi. These genomes enable a comprehensive exploration of genomic diversity, genome evolution, and phylogenomic relationships within the genus Paramecium. The genome sizes range from 47.78 to 113.16 Mb, reflecting unexpected variation in genomic content, and genic features differ from those of other reported Paramecium genomes, such as larger intron sizes and higher GC content. Nonetheless, the de novo assemblies indicate that macronuclear genomes of all Paramecium are highly streamlined, with ~77% being protein-coding gene regions. Based on gene-duplication depths, synonymous mutations in paralogs, and phylogenomic relationships, we discovered that the five species experienced at least three whole-genome duplication (WGD) events, independent of those previously found in the P. aurelia complex. Using all available WGD data for Paramecium, we further explore the paralog dynamics after WGD events by modeling. This study contributed to a more comprehensive and deeper understanding of genome architecture and evolution in Paramecium.