Schizosaccharomyces lindneri sp. nov., a fission yeast occurring in honey

Abstract

Two strains of fission yeast were isolated from honey. They differ from the type strain of Schizosaccharomyces octosporus by three substitutions in the D1/D2 domain of the nuclear 26S large subunit ribosomal RNA (rRNA) gene sequence, resulting in a 99.5% identity. In the internal transcribed spacer (ITS) region (consisting of ITS1, 5.8S rDNA, and ITS2), the strains differ from S. octosporus by 16 gaps and 91 substitutions, which is equivalent to an identity of 88.1%. Genome sequencing on one of the new strains revealed that the average nucleotide identity (ANI) between its genome and the reference genome of S. octosporus is 90.43% and there exist major genome rearrangements between the two genomes. Mating analysis revealed that S.octosporus and one of the new strains are completely reproductively separated. A strong prezygotic barrier exists and the few mating products consist of diploid hybrids that do not form recombinant ascospores. In the new strains, asci are either zygotic, arising from conjugation, or they develop without conjugation from asexual cells (azygotic). Compared to the currently recognized Schizosaccharomyces species, the spectrum of nutrients that are assimilated by the new strains is restricted. Of the 43 carbohydrates that were included in the physiological standard tests, only 7 were assimilated. According to the results of the genome sequence analysis, the mating trials, and the phenotypic characterization, the new species Schizosaccharomyces lindneri is described to accommodate the two strains (holotype: CBS 18203 T and ex-type: MUCL 58363; MycoBank no.: MB 847838).

Schizosaccharomyces versatilisrepresents a distinct evolutionary lineage

“…Using RelTree ML, the split was dated at 25.05 MYA (Figure 3) and using RelTree branch length, 24.69 MYA. Additionally, we removed the previously calculated split between S. octosporus and S. osmophilus from the tree to confirm that this dating-method recapitulated the previously calculated divergence time (Jia et al, 2023). RelTree ML and RelTree branch lengths dated this split at 16.27 MYA and 16.02 MYA respectively (and confirmed the S. japonicus and CBS5679 divergence time), closely reflecting the previously calculated divergence time of 15.7 MYA (Jia et al, 2023) (Supplementary Figure S1).…”

“…We downloaded publicly available (as of February 2023) genome assemblies of Schizosaccharomyces species as follows: S. octosporus -GCA_000150505.2 (Tong et al, 2019) S. osmophilus -GCA_027921745.1 (Jia et al, 2023) S. cryophilus -GCA_000004155.2 (Tong et al, 2019) S. pombe -PomBase (Harris et al, 2022) S. japonicus (FY16936) -Ensembl Fungi GCA_000149845.2 (Yates et al, 2022) S. japonicus (FY16936) -EI 1.0 GCA_956476325 Saitoella complicata (outgroup) -GCF_001661265.1 (Nishida, Hamamoto, & Sugiyama, 2011) For each assembly we ran BUSCO (v5.4.4) using the most up-to-date Ascomycota database (ascomycota_odb10) to identify single-copy orthologs in each assembly. We then took the intersect of orthologs that were found to be complete and in a single copy across all assemblies and created a BED-format file of all those genes across each assembly.…”

“…We then used SNP-sites (Page et al, 2016) to extract all variable sites where each nucleotide was either A, T, C, or G. Next, we used RelTree ML and RelTree Branch Lengths in MEGA (Stecher, Tamura, & Kumar, 2020;Tamura et al, 2012;Tamura, Tao, & Kumar, 2018) to date the CBS5679-FY16936 split, using the ortholog SNP-sites alignment data and the ML phylogeny. We used the following previously calculated divergence times (Jia et al, 2023;X. X. Shen et al, 2020) To compare our calculated divergence time with other previously calculated times, we ran RelTree ML and RelTree Branch Lengths, omitting Split 4 above (S. octosporus -S. osmophilus) and compared our predicted divergence time to that of the previously calculated divergence time (Jia et al, 2023).…”

“…We used the following previously calculated divergence times (Jia et al, 2023;X. X. Shen et al, 2020) To compare our calculated divergence time with other previously calculated times, we ran RelTree ML and RelTree Branch Lengths, omitting Split 4 above (S. octosporus -S. osmophilus) and compared our predicted divergence time to that of the previously calculated divergence time (Jia et al, 2023).…”

“…Advances in whole genome sequencing and assembly methods have made it possible to sequence and assemble the relatively small genomes of yeast species cheaply and quickly. All known species of fission yeast have now been sequenced (M. Brysch-Herzberg et al, 2023; Jia et al, 2023; Rhind et al, 2011; Wood et al, 2002). More recently, the availability of low-cost long-read sequencing combined with advances in genome assembly algorithms has allowed for chromosome-scale telomere-to-telomere sequencing to become achievable even for the most complex genomes (Belser et al, 2021; Nurk et al, 2022).…”