Statistical distributions of gene expression levels in the non-model ciliate Colpoda across strains and genes using transcriptome sequencing.

Gene expression variation is a key driver of phenotypic diversity and evolution. However, its role in free-living ciliates, particularly in non-model species, remains largely unexplored. In this study, we analyzed gene expression variation in Colpoda steinii and C. inflata strains, mostly from mainland China. These two species are dominant ciliates in the soil microbial loop, cosmopolitan in distribution, and beneficial for promoting crop growth. Through population transcriptome sequencing and rigorous quality control filtering of 56 C. steinii and 31 C. inflata strains, we identified expressed genes to characterize the statistical distributions of gene expression levels. In both species, gene expression across most strains followed lognormal or skewed-lognormal distributions, suggesting stable gene regulation and supporting the use of the geometric mean of expression levels to estimate gene activity. However, some strains showed bimodal distributions, which were possibly associated with strain-specific genetic differences. Highly expressed genes related to cell maintenance and stress response were overrepresented in these bimodal distributions. These findings highlight the robust regulation of gene expression in Colpoda species, with implications for understanding their ecological and evolutionary dynamics. Our study provides a statistical framework to quantify biological traits and their distributions, contributing to the biometrics of protists and broader biological applications.