2μ plasmid in Saccharomyces species and in Saccharomyces cerevisiae

Abstract

We determined that extrachromosomal 2μ plasmid was present in 67 of the Saccharomyces cerevisiae 100-genome strains; in addition to variation in the size and copy number of 2μ, we identified three distinct classes of 2μ. We identified 2μ presence/absence and class associations with populations, clinical origin and nuclear genotypes. We also screened genome sequences of S. paradoxus, S. kudriavzevii, S. uvarum, S. eubayanus, S. mikatae, S. arboricolus and S. bayanus strains for both integrated and extrachromosomal 2μ. Similar to S. cerevisiae, we found no integrated 2μ sequences in any S. paradoxus strains. However, we identified part of 2μ integrated into the genomes of some S. uvarum, S. kudriavzevii, S. mikatae and S. bayanus strains, which were distinct from each other and from all extrachromosomal 2μ. We identified extrachromosomal 2μ in one S. paradoxus, one S. eubayanus, two S. bayanus and 13 S. uvarum strains. The extrachromosomal 2μ in S. paradoxus, S. eubayanus and S. cerevisiae were distinct from each other. In contrast, the extrachromosomal 2μ in S. bayanus and S. uvarum strains were identical with each other and with one of the three classes of S. cerevisiae 2μ, consistent with interspecific transfer.

Keywords: 2-micron plasmid; 2μ plasmid; Saccharomyces cerevisiae; Saccharomyces genus; population genomics; selfish genetic elements.

Graphical Abstract Figure.

We show extensive 2μ sequence variation in Saccharomyces cerevisiae and in other species of Saccharomyces and 2μ associations with S. cerevisiae populations, clinical origin and genotypes.

Figure 1.

The class A (red), class C (blue) and recombinant class B (red and blue) extrachromosomal 2μ sequences found in the 100-genomes S. cerevisiae strains.

Figure 2.

Phylogeny of 2μ sequences in S. cerevisiae and other Saccharomyces species. (A) Extrachromosomal and integrated REP1–RAF1 2μ sequences. Red taxa belong to class A and blue taxa belong to class B and C. (B) Extrachromosomal and integrated REP2–FLP1 2μ sequences. Red taxa belong to classes A and B, and blue taxa belong to class C. The previously identified nuclearly integrated 2μ sequences REP1–RAF1 from S. uvarum, S. bayanus and S. kudriavzevii, and REP2–FLP1 from S. mikatae (Frank and Wolfe 2009) are included in the respective clades.