Genomic characterisation and diversity of dsRNA viruses and their killer satellites in a natural population of the yeast <i>Saccharomyces paradoxus</i>

Abstract Killer yeasts secrete protein toxins that inhibit other yeast strains, a trait often encoded by M satellites of L-A dsRNA viruses. These systems serve as important molecular models, yet their adaptive significance in natural settings remains unclear. This study surveyed 60 strains from a natural Saccharomyces paradoxus population in the UK to characterise dsRNA viral genomic diversity. Our survey revealed 27% of strains showed killer activity mediated by dsRNA viruses. Additionally, five of 18 non-killer strains also contained dsRNA viruses. Deep sequencing of pooled dsRNAs from 17 strains identified six distinct M satellite types, including three novel lineages, with single nucleotide and structural polymorphisms creating multiple variant sequences within types. Predicted preprotoxin proteins generally contained post-translational modification sites necessary for toxin maturation, although with variable numbers among different types, potentially affecting processing and expression. Eight L-A virus sequences were also assembled. These were all closely related to each other and clustered phylogenetically with viruses from other European S. paradoxus strains. Extended 5′ sequence analysis revealed novel structural features in both L-As and their M satellites, including a pair of inverted repeats ending in a pair of inverted conserved motifs (GA5–6 and corresponding U5–6C in Ms and GAAUA and corresponding UAUUC in L-As) which is in turn flanked by a pair of direct repeats. The pair of conserved motifs also exists in all described Saccharomyces cerevisiae M satellites. The observed diversity of dsRNA satellites within a single yeast population is a challenge to explain, with many evolutionary forces potentially contributing.