Genome analysis of the unicellular eukaryote Euplotes vannus reveals molecular basis for sex determination and tolerance to environmental stresses

Background: The genus Euplotes is a clade of free-living and cosmopolitan ciliated protists. As a model organism in studies of cell and environmental biology, Euplotes vannus has more than ten mating types (sexes) and shows strong resistance to environmental stresses such as low temperature and high salinity. However, the molecular basis of its mating type determination mechanism and how the cell responds to stress are still largely unknown. Here we focus on these topics by genome analysis of different mating types of Euplotes vannus. Results: This work combines analysis of de novo assembled high-quality macronucleus (MAC; i.e. somatic) genome and partial micronucleus (MIC; i.e. germline) genome of Euplotes vannus. MAC genomic and transcriptomic data from several mating types of E. vannus were investigated and gene expression levels were profiled under different environmental stresses, including stresses from nutrient scarcity, extreme temperature, salinity and the presence of free ammonia. The results indicate that: 1) E. vannus, which possesses "gene-sized" nanochromosomes in its MAC, shares a similar pattern on frameshifting and stop codon usage as Euplotes octocarinatus and may be undergoing incipient sympatric speciation with Euplotes crassus; 2) E. vannus possesses two Type-I and four Type-II pheromones, including two novel alleles Ev-4 and Ev-beta, based on the genome investigation of six mating types; 3) the coding regions of pheromone genes in the MAC genome of E. vannus consist of multiple macronuclear destined sequences (MDS) regions in the MIC; 4) different mating types of E. vannus have mating type-specific chromatin and expression profiling of Type-II pheromone loci; 5) the HSP70 gene of E. vannus does not carry either unique amino acid substitutions of potential significance for cold adaptation nor mRNA destabilization ARE elements in its 39 regulatory region. Additionally, the genome resources generated in this study are available online at Euplotes vannus DB (http://evan.ciliate.org). Conclusions: Based on the results of the current study, the following conclusions are put forward: 1) the high similarity of the pheromones of E. vannus and E. crassus reveals the molecular basis of hybridization between these two "morphospecies" under laboratory conditions; 2) somatic pheromone loci of E. vannus are generated from programmed DNA rearrangements of multiple germline MDS segments, which are similar to the complex rearrangements of mating type determination in Tetrahymena; 3) however, unlike Tetrahymena, E. vannus does not possess mating type-specific genes. Instead, the mating types are distinguished by the different combinations of pheromone loci. This finding supports the allelic codominance or non-hierarchical dominance relationship among pheromone loci during Euplotes pheromone-mediated cell-cell signaling and cross-mating; 4) as a common species in global waters, the HSP70 gene of E. vannus has evolved to be insensitive to environmental temperature change.