Population Genomics of Paramecium Species

Abstract

Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such analyses for unicellular eukaryotes prompted us to assess genomic variation in Paramecium, one of the most well-studied ciliate genera. The Paramecium aurelia complex consists of ∼15 morphologically indistinguishable species that diverged subsequent to two rounds of whole-genome duplications (WGDs, as long as 320 MYA) and possess extremely streamlined genomes. We examine patterns of both nuclear and mitochondrial polymorphism, by sequencing whole genomes of 10-13 worldwide isolates of each of three species belonging to the P. aurelia complex: P. tetraurelia, P. biaurelia, P. sexaurelia, as well as two outgroup species that do not share the WGDs: P. caudatum and P. multimicronucleatum. An apparent absence of global geographic population structure suggests continuous or recent dispersal of Paramecium over long distances. Intergenic regions are highly constrained relative to coding sequences, especially in P. caudatum and P. multimicronucleatum that have shorter intergenic distances. Sequence diversity and divergence are reduced up to ∼100-150 bp both upstream and downstream of genes, suggesting strong constraints imposed by the presence of densely packed regulatory modules. In addition, comparison of sequence variation at non-synonymous and synonymous sites suggests similar recent selective pressures on paralogs within and orthologs across the deeply diverging species. This study presents the first genome-wide population-genomic analysis in ciliates and provides a valuable resource for future studies in evolutionary and functional genetics in Paramecium.

Worldwide sampling reveals low genetic variability in populations of the freshwater ciliate Paramecium biaurelia (P. aurelia species complex, Ciliophora, Protozoa)

“…4) after careful sampling of these areas. The observed distinctiveness of P. biaurelia collected in both Americas (haplotypes Pa2COI_05, Pa2COI_09, Pa2COI_11) is in concordance with a previous analysis of genomic data (883 genes) of 11 strains that suggested a USA-Europe separation (Johri et al 2017). However, our results, similarly to (Pawlowski et al 2007), showed that despite isolation by distance, gene flow is still possible between populations from different ecozones.…”

The importance of the Neutral Theory in 1968 and 50 years on: A response to Kern and Hahn 2018

“…Importantly, observations from eukaryotic genomes, including humans and mice, show that levels of polymorphism are low in the neighborhood of coding or conserved noncoding sequences and increase approximately monotonically away from them (Cutter and Payseur ; Johri et al. ; Lynch et al. ).…”

“…Importantly, observations from eukaryotic genomes, including humans and mice, show that levels of polymorphism are low in the neighborhood of coding or conserved noncoding sequences and increase approximately monotonically away from them (Cutter and Payseur 2013;Johri et al 2017;Lynch et al 2017). While selective sweeps may contribute to this pattern, and are indeed required to explain other observations (Campos et al 2017), these findings imply that any selective sweeps involved must have rather local effects.…”

Population genetics ofParameciummitochondrial genomes: recombination, mutational spectrum, and efficacy of selection

“…We assembled complete mitochondrial genomes of seven species belonging to the P. aurelia complex: P. biaurelia , P. tetraurelia , P. sexaurelia , P. octaurelia , P. novaurelia , P. decaurelia , P. dodecaurelia , P. quadecaurelia , and P. jenningsi . In addition, we analyzed previously reported complete mitochondrial genomes of P. tetraurelia and P. sexaurelia belonging to the P. aurelia complex , as well as four outgroup species: P. caudatum, P. caudatum-C026, P. multimicronucleatum , and P. multimicronucleatum-Peniche3I (Figure 1; isolates sequenced in Johri et al, 2017). We note that P. caudatum-C026 and P. multimicronucleatum-Peniche3I were initially sampled as individual isolates belonging to the P. caudatum and P. multimicronucleatum species (based on morphological criteria), respectively.…”