Haro, R. | Search bioRxiv

bioRxiv2026

Multiple origins of endogenous virophage and polinton-like virus in the halophilic protist Halocafeteria seosinensis

Virophages and Polinton-like Viruses (PLVs) are related viral elements classified within the supergroup Polisuviricotina. While virophages typically depend on large dsDNA viruses (Nucleocytoviricota) for replication in eukaryotic hosts, the replication strategies of most PLVs are unknown. While both virophages and PLVs can exist as stand-alone entities or be integrated into host genomes, their co-occurrence within a single eukaryotic genome is rare. We investigated the chromosome-scale nuclear genome assembly of the halophilic protist Halocafeteria seosinensis and discovered 41 endogenous PLVs and 36 virophage sequences, most of which are full-length elements; together they comprise 6.2% of the genome. These viral elements belong to six PLV and seven virophage subtypes. Notably, we found genes shared between H. seosinensis PLVs and virophages, suggesting active genetic exchange between them. We also observed supraparasitism, with MULE DNA transposons and LINE retrotransposons frequently embedded within the viral genomes. Our study reveals dynamic interactions between viral elements and host mobile DNA in a halophilic protist, expanding our understanding of viral diversity in extreme environments. SIGNIFICANCEVirophages and polinton-like viruses (PLVs) are enigmatic viral elements found in many aquatic habitats. Our understanding of their diversity stems mainly from analysis of environmental sequence data, but they have also been found integrated into the genomes of cultured protists. The evolutionary impacts of such integrations are poorly understood. In this study, we reveal the co-occurrence of multiple PLV and virophage subtypes that together constitute a substantial fraction of the genome of the halophilic protist Halocafeteria seosinensis. These distantly related viral lineages coexist within the same genome and share a common gene pool, forming chimeric arrangements with host transposons and with one another. The H. seosinensis genome thus serves as a dynamic arena for viral gene exchange and genome remodelling, reshaping host genome architecture and potentially conferring immunity to giant viruses.

genomics↗

bioRxiv2026

Sequencing, Chromosome-scale Assembly, and Annotation of the Genome of the Halophilic Nanoflagellate Halocafeteria seosinensis

Compared with bacterial and archaeal extremophiles, single-celled eukaryotes living in extreme habitats are understudied and underrepresented in genomic databases. An exception is the obligately halophilic stramenopile Halocafeteria seosinensis strain EHF34. A transcriptome-focused analysis of this extremophilic protists revealed the importance of organic osmolyte regulation and transport in its adaptation to hypersaline environments. However, genomic resources for H. seosinensis are currently limited to a highly fragmented assembly generated by short-read sequencing, which has hindered further investigation of the genome biology and evolution of this fascinating organism. Here, we used long-read Oxford Nanopore sequencing to generate a highly contiguous, chromosome-scale genome assembly for H. seosinensis. The assembly is 38.8 megabase pairs (Mbp) in size and contains 60 nuclear contigs, making it the most contiguous genome for a member of the order Bicosoecida. Approximately 19% of the genome is comprised of transposable elements. Of the 11,684 predicted protein-coding genes, many appear to be associated with DNA mobility-related functions, and several may be linked to adaptation to a hypersaline environment. Analysis of the H. seosinensis long-read genome assembly presented herein will facilitate our understanding of the ways in which protists have adapted to extreme environments. SignificanceHalocafeteria seosinensis is an extremophilic protist adapted to hypersaline environments. Previous analyses of a transcriptome and short-read draft genome assembly for this organism provided insights into the molecular mechanisms underlying osmotic regulation, which facilitate its adaptation to high-salt conditions. However, the lack of contiguity and quality of the draft assembly prevented the characterization of complex genomic regions, including transposable elements and viral insertions, as well as genomic comparisons with related species. Here we present a highly contiguous, chromosome-scale genome assembly for H. seosinensis that enables accurate gene prediction, detailed analysis of repeat content, and comparative genomic analysis. This long-read genome assembly will serve as a valuable resource for studying one of the few tractable halophilic protists sequenced to date.

genomics↗