PT  - JOURNAL ARTICLE
AU  - Thomas Hackl
AU  - Sarah Duponchel
AU  - Karina Barenhoff
AU  - Alexa Weinmann
AU  - Matthias G. Fischer
TI  - Endogenous virophages populate the genomes of a marine heterotrophic flagellate
AID  - 10.1101/2020.11.30.404863
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.11.30.404863
4099  - http://biorxiv.org/content/early/2020/11/30/2020.11.30.404863.short
4100  - http://biorxiv.org/content/early/2020/11/30/2020.11.30.404863.full
AB  - Endogenous viral elements (EVEs) are frequently found in eukaryotic genomes, yet their integration dynamics and biological functions remain largely unknown. Unlike most other eukaryotic DNA viruses, the virophage mavirus integrates efficiently into the nuclear genome of its host, the marine heterotrophic flagellate Cafeteria burkhardae. Mavirus EVEs can reactivate upon superinfection with the lytic giant virus CroV and may act as an adaptive antiviral defense system, because mavirus increases host population survival during a coinfection with CroV. However, the prevalence of endogenous virophages in natural flagellate populations has not been explored. Here we report dozens of endogenous mavirus-like elements (EMALEs) in the nuclear genomes of four C. burkhardae strains. EMALEs were typically 20 kilobase pairs long and constituted 0.7% to 1.8% of each host genome. We analyzed 33 fully assembled EMALEs that fell into two main clusters and eight types based on GC-content, nucleotide similarity, and coding potential. Inter-strain comparison showed conservation of some EMALE insertion loci, whereas the majority of integration sites were unique to a given host strain. We also describe a group of tyrosine recombinase retrotransposons, some of which exhibited a strong preference for integration into EMALEs and represent yet another layer of parasitism in this microbial system. Our findings show that virophages are common, diverse, and dynamic genome components of the marine protist C. burkhardae, which implies important eco-evolutionary roles for these enigmatic viruses.Competing Interest StatementThe authors have declared no competing interest.