Whole Genome Sequencing,de NovoAssembly and Phenotypic Profiling for the New Budding Yeast SpeciesSaccharomyces jurei

Abstract

Saccharomyces sensu stricto complex consist of yeast species, which are not only important in the fermentation industry but are also model systems for genomic and ecological analysis. Here, we present the complete genome assemblies of Saccharomyces jurei, a newly discovered Saccharomyces sensu stricto species from high altitude oaks. Phylogenetic and phenotypic analysis revealed that S. jurei is more closely related to S. mikatae, than S. cerevisiae, and S. paradoxus. The karyotype of S. jurei presents two reciprocal chromosomal translocations between chromosome VI/VII and I/XIII when compared to the S. cerevisiae genome. Interestingly, while the rearrangement I/XIII is unique to S. jurei, the other is in common with S. mikatae strain IFO1815, suggesting shared evolutionary history of this species after the split between S. cerevisiae and S. mikatae. The number of Ty elements differed in the new species, with a higher number of Ty elements present in S. jurei than in S. cerevisiae. Phenotypically, the S. jurei strain NCYC 3962 has relatively higher fitness than the other strain NCYC 3947T under most of the environmental stress conditions tested and showed remarkably increased fitness in higher concentration of acetic acid compared to the other sensu stricto species. Both strains were found to be better adapted to lower temperatures compared to S. cerevisiae.

Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination

“…Additionally, we generated and included PacBio assemblies for three S. cerevisiae strains isolated from ancestral oak habitats in North America, Europe and Japan (SDO2s1, ZP568s1, ZP655.1A) to better sample Ty1 content in geographically-diverse wild S. cerevisiae lineages [49,50]. Ty1 sequences from PacBio assemblies of two S. jurei strains (NCYC 3947, NCYC 3962) reported in Naseeb et al [43] were used to root trees and polarize changes on the S. cerevisiae and S. paradoxus lineages. Ty elements in these genomes were detected as described above and Ty content for all strains can be found in S1 File.…”

“…HGAP assemblies for the genomes reported here plus a complementary set of HGAP assemblies from S. cerevisiae, S. paradoxus, and the outgroup species S. jurei [18,43] were used to identify Ty elements using a modified strategy similar to Carr et al [13]. RepeatMasker (version 4.0.5; options: -e wublast -s -xsmall -nolow -no_is) (http://repeatmasker.org) was used to find all Ty fragments with similarity to a custom database of canonical Ty sequences derived from those reported in Carr et al [13] that was updated to fix several small errors and include a version of the Tsu4 element from S. paradoxus [19] (S6 File).…”

“…Assembly statistics and Ty content in PacBio assemblies of Saccharomyces species. Strains from the current work are labeled Czaja; strains from published assemblies are labeled by the last name of the first author of the respective paper [18,42,43]. Counts of Ty elements are based on structural classification of fragments from the same RepeatMasker annotation: full-length (internal region present and total length >95% of canonical length), truncated (internal region present and total length <95% of canonical length), or solo LTRs (LTR present but no match to internal region).…”

“…We show that "permissive" strains with high Ty1-H3 mobility can be converted to "restrictive" strains with low Ty1-H3 mobility by experimentally introducing multiple Ty1-H3 elements into permissive genomes, implying that permissive strains are competent to express Ty1 CNC. Additionally, we investigated the genomic basis of variation in Ty1-H3 mobility using whole genome PacBio long-read assemblies that yield complete sequence information of transposable elements in their native chromosomal locations [18,42,43]. By comparing Ty1 copy number and sequence composition with mobility frequency, we infer that restrictive strains in both S. cerevisiae and S. paradoxus contain fulllength Ty1 elements with a canonical form of gag.…”

A natural variant of the essential host geneMMS21restricts the parasitic 2-micron plasmid inSaccharomyces cerevisiae

“…Sequence of MMS21 codon 69 across the Saccharomyces sensu stricto clade, as well as selected S. cerevisiae strains and two outgroup Naumovozyma species. Species cladogram was adapted from previous studies111,112 . This analysis shows that the Thr69 allele of MMS21 is ancestral in S. cerevisiae but is not universally conserved in closely-related species.…”