A high-quality reference genome for the fission yeast <i>Schizosaccharomyces osmophilus</i>

Jia, Guo‐Song; Zhang, Wencai; Liang, Yue; Liu, Xi-Han; Rhind, Nicholas; Pidoux, Alison L.; Brysch‐Herzberg, Michael; Du, Li-Lin

doi:10.1093/g3journal/jkad028

Cited by 17 publications

(35 citation statements)

References 204 publications

(336 reference statements)

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“…nov. draft nuclear genome, 1225 (93.16%) of the BUSCO genes are “complete and single copy” and 37 (2.81%) of the BUSCO genes are “complete and duplicated” (Supporting Information: Table ). Such a level of BUSCO gene completeness is similar to those of the published reference genomes of other fission yeast species (Jia et al, 2023).…”

Section: Resultssupporting

confidence: 81%

“…The total length of the S. lindneri sp. nov. draft nuclear genome (10.87 Mb) is slightly smaller than the lengths of the reference nuclear genomes of the five previously recognized fission yeast species (12.57, 11.27, 11.52, 11.13, and 11.42 Mb for S. pombe , S. octosporus , S. cryophilus , S. japonicus , and S. osmophilus , respectively) (Jia et al, 2023; Rhind et al, 2011; Wood et al, 2002), presumably because the repetitive regions are underrepresented in the S. lindneri sp. nov. draft nuclear genome owing to the limitation of the short‐read sequencing technology.…”

Section: Resultsmentioning

confidence: 82%

“…To obtain pairwise ANI values for all combinations of the type strains of fission yeast species, we employed the OrthoANIu (OAU) tool (v1.2, http://www.ezbiocloud.net/tools/orthoaniu) (Yoon et al, 2017). The genome assemblies used as input for the OAU analysis are as follows: S. pombe type strain (CBS 356 T = JB861) assembly from https://figshare.com/articles/dataset/SGA_de_novo_assemblies_of_all_wild_strains/3978279 (Jeffares et al, 2015), S. octosporus type strain (CBS 371 T = ATCC 420 T = yFS286) assembly and S. cryophilus type strain (CBS 11777 T = OY26) assembly from http://bifx-core.bio.ed.ac.uk/%7Eptong/genome_assembly/ (Tong et al, 2019), S. japonicus type strain (CBS 354 T = IFO 1609 T = yFS275) assembly from the Ensembl‐Fungi database (http://fungi.ensembl.org/Schizosaccharomyces_japonicus/Info/Index) (Rhind et al, 2011), S. osmophilus type strain (CBS 15793 T ) assembly from the NCBI GenBank database (https://www.ncbi.nlm.nih.gov/assembly/GCA_027921745.1/) (Jia et al, 2022), and the S. lindneri sp. nov. type strain (CBS 18203 T ) draft nuclear genome obtained in this study.…”

Section: Methodsmentioning

confidence: 99%

“…S. complicata served as the outgroup in the analysis. We used the following calibration nodes: the S. japonicus – S. pombe split (207.2 million years ago), the S. pombe – S. octosporus split (108.2 million years ago), the S. octosporus – S. cryophilus split (29.4 million years ago) (Shen et al, 2020), and the S. octosporus – S. osmophilus split (15.7 million years ago) (Jia et al, 2023). The time‐calibrated phylogenetic tree was visualized in FigTree (v1.4.4, http://tree.bio.ed.ac.uk/software/figtree/) and the branch of the outgroup species S. complicata was removed manually in Adobe Illustrator.…”

Section: Methodsmentioning

confidence: 99%

“…To perform genome-based phylogenetic analysis, we used single-copy Benchmarking Universal Single-Copy Orthologs (BUSCO) genes for species tree estimation as previously described (Jia et al, 2023). We firstly submitted the S. lindneri sp.…”

Section: Species Tree Inference and Divergence Time Estimationmentioning

confidence: 99%

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Schizosaccharomyces lindnerisp. nov., a fission yeast occurring in honey

Brysch‐Herzberg

Jia

Sipiczki

et al. 2023

Yeast

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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).

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Section: Resultssupporting

confidence: 81%

Section: Resultsmentioning

confidence: 82%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Species Tree Inference and Divergence Time Estimationmentioning

confidence: 99%

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Schizosaccharomyces lindnerisp. nov., a fission yeast occurring in honey

Brysch‐Herzberg

Jia

Sipiczki

et al. 2023

Yeast

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Schizosaccharomyces pombe as a fundamental model for research on mitochondrial gene expression: Progress, achievements and outlooks

Dinh,

Bonnefoy

2023

IUBMB Life

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Schizosaccharomyces pombe (fission yeast) is an attractive model for mitochondrial research. The organism resembles human cells in terms of mitochondrial inheritance, mitochondrial transport, sugar metabolism, mitogenome structure and dependence of viability on the mitogenome (the petite‐negative phenotype). Transcriptions of these genomes produce only a few polycistronic transcripts, which then undergo processing as per the tRNA punctuation model. In general, the machinery for mitochondrial gene expression is structurally and functionally conserved between fission yeast and humans. Furthermore, molecular research on S. pombe is supported by a considerable number of experimental techniques and database resources. Owing to these advantages, fission yeast has significantly contributed to biomedical and fundamental research. Here, we review the current state of knowledge regarding S. pombe mitochondrial gene expression, and emphasise the pertinence of fission yeast as both a model and tool, especially for studies on mitochondrial translation.

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Telomere‐to‐telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features

Etherington,

Wu,

Oliferenko

et al. 2024

Yeast

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Schizosaccharomyces japonicus belongs to the single‐genus class Schizosaccharomycetes, otherwise known as “fission yeasts.” As part of a composite model system with its widely studied S. pombe sister species, S. japonicus has provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makes S. japonicus a valuable model organism in its own right. However, the currently available genome assembly contains gaps and has been unable to resolve centromeres and other repeat‐rich chromosomal regions. Here we present a telomere‐to‐telomere long‐read genome assembly of the S. japonicus genome. This includes the three megabase‐length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNA genes, transfer RNA genes, long terminal repeats, and short repeats. We identify a gene‐sparse region on chromosome 2 that resembles a 331 kb centromeric duplication. We revise the genome size of S. japonicus to at least 16.6 Mb and possibly up to 18.12 Mb, at least 30% larger than previous estimates. Our whole genome assembly will support the growing S. japonicus research community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics.

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A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus

Cited by 17 publications

References 204 publications

Schizosaccharomyces lindnerisp. nov., a fission yeast occurring in honey

Schizosaccharomyces lindnerisp. nov., a fission yeast occurring in honey

Schizosaccharomyces pombe as a fundamental model for research on mitochondrial gene expression: Progress, achievements and outlooks

Telomere‐to‐telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features

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