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Dinh N, Bonnefoy N. Schizosaccharomyces pombe as a fundamental model for research on mitochondrial gene expression: Progress, achievements and outlooks. IUBMB Life 2024; 76:397-419. [PMID: 38117001 DOI: 10.1002/iub.2801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
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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Affiliation(s)
- Nhu Dinh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
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2
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Forsburg SL. The micromammals. G3 (BETHESDA, MD.) 2024; 14:jkae073. [PMID: 38837137 DOI: 10.1093/g3journal/jkae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
In this editorial, Senior Editor Susan Forsburg examines the reasons to keep studying eukaryotic microbes like S. pombe and S. cerevisiae—and other yeasts, algae, amoeba, and fungi—even as genetic and genomic technologies now allow manipulation and study of practically any organism. She explores the challenges and opportunities of working in these tiny organisms, pointing to the substantial biology their study has uncovered.
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Affiliation(s)
- Susan L Forsburg
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA
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3
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Etherington GJ, Wu PS, Oliferenko S, Uhlmann F, Nieduszynski CA. Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features. Yeast 2024; 41:73-86. [PMID: 38451028 DOI: 10.1002/yea.3912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 03/08/2024] Open
Abstract
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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Affiliation(s)
| | | | - Snezhana Oliferenko
- The Francis Crick Institute, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Frank Uhlmann
- The Francis Crick Institute, London, UK
- Cell Biology Centre, Institute of Innovative Research, Tokyo Institute of Technology, Kanagawa, Japan
| | - Conrad A Nieduszynski
- The Earlham Institute, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
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4
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Etherington GJ, Gil EG, Haerty W, Oliferenko S, Nieduszynski CA. Schizosaccharomyces versatilis represents a distinct evolutionary lineage of fission yeast. Yeast 2024; 41:95-107. [PMID: 38146786 DOI: 10.1002/yea.3919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023] Open
Abstract
The fission yeast species Schizosaccharomyces japonicus is currently divided into two varieties-S. japonicus var. japonicus and S. japonicus var. versatilis. Here we examine the var. versatilis isolate CBS5679. The CBS5679 genome shows 88% identity to the reference genome of S. japonicus var. japonicus at the coding sequence level, with phylogenetic analyses suggesting that it has split from the S. japonicus lineage 25 million years ago. The CBS5679 genome contains a reciprocal translocation between chromosomes 1 and 2, together with several large inversions. The products of genes linked to the major translocation are associated with 'metabolism' and 'cellular assembly' ontology terms. We further show that CBS5679 does not generate viable progeny with the reference strain of S. japonicus. Although CBS5679 shares closer similarity to the 'type' strain of var. versatilis as compared to S. japonicus, it is not identical to the type strain, suggesting population structure within var. versatilis. We recommend that the taxonomic status of S. japonicus var. versatilis is raised, with it being treated as a separate species, Schizosaccharomyces versatilis.
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Affiliation(s)
| | - Elisa Gomez Gil
- Oliferenko Lab, The Francis Crick Institute, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Wilfried Haerty
- Research Faculty, The Earlham Institute, Norwich Research Park, Norwich, UK
| | - Snezhana Oliferenko
- Oliferenko Lab, The Francis Crick Institute, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Conrad A Nieduszynski
- Research Faculty, The Earlham Institute, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
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5
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Brysch-Herzberg M, Jia GS, Sipiczki M, Seidel M, Zhang WC, Du LL. Reinstatement of the fission yeast species Schizosaccharomyces versatilis Wickerham et Duprat, a sibling species of Schizosaccharomyces japonicus. Yeast 2024; 41:108-127. [PMID: 38450805 DOI: 10.1002/yea.3922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 03/08/2024] Open
Abstract
Schizosaccharomyces japonicus Yukawa et Maki (1931) and Schizosaccharomyces versatilis Wickerham et Duprat (1945) have been treated as varieties of S. japonicus or as conspecific, based on various approaches including mating trials and nDNA/nDNA optical reassociation studies. However, the type strains of S. japonicus and S. versatilis differ by five substitutions (99.15% identity) and one 1-bp indel in the sequences of the D1/D2 domain of the 26S rRNA gene, and 23 substitutions (96.3% identity) and 31-bp indels in the sequences of internal transcribed spacer (ITS) of rRNA, suggesting that they may not be conspecific. To reassess their taxonomic status, we conducted mating trials and whole-genome analyses. Mating trials using the type strains showed a strong but incomplete prezygotic sterility barrier, yielding interspecies mating products at two orders of magnitude lower efficiency than intraspecies matings. These mating products, which were exclusively allodiploid hybrids, were unable to undergo the haplontic life cycle of the parents. We generated chromosome-level gap-less genome assemblies for both type strains. Whole genome sequences yielded an average nucleotide identity (ANI) of 86.4%, indicating clear separation of S. japonicus and S. versatilis. Based on these findings, we propose the reinstatement of S. versatilis as a distinct species (holotype strain: CBS 103T and ex-types: NRRL Y-1026, NBRC 1607, ATCC 9987, PYCC 7100; Mycobank no.: 847838).
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Affiliation(s)
- Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Heilbronn, Germany
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing, China
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
| | - Martin Seidel
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Heilbronn, Germany
| | - Wen-Cai Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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6
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D'Angiolo M, Bähler J. New species, genome assemblies, and tools shed fresh light on fission yeasts. Yeast 2024; 41:69-72. [PMID: 38466717 DOI: 10.1002/yea.3930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 03/13/2024] Open
Affiliation(s)
- Melania D'Angiolo
- Department of Genetics, Evolution & Environment, Institute of Healthy Ageing, University College London, London, UK
| | - Jürg Bähler
- Department of Genetics, Evolution & Environment, Institute of Healthy Ageing, University College London, London, UK
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7
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Miao Z, Wang H, Tu X, Huang Z, Huang S, Zhang X, Wang F, Huang Z, Li H, Jiao Y, Gao S, Zhou Z, Shan CM, Li J, Yue JX. GetPrimers: A generalized PCR-based genetic targeting primer designer enabling easy and standardized targeted gene modification across multiple systems. Yeast 2024; 41:19-34. [PMID: 38041528 DOI: 10.1002/yea.3916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023] Open
Abstract
Genetic targeting (e.g., gene knockout and tagging) based on polymerase chain reaction (PCR) is a simple yet powerful approach for studying gene functions. Although originally developed in classic budding and fission yeast models, the same principle applies to other eukaryotic systems with efficient homologous recombination. One-step PCR-based genetic targeting is conventionally used but the sizes of the homologous arms that it generates for recombination-mediated genetic targeting are usually limited. Alternatively, gene targeting can also be performed via fusion PCR, which can create homologous arms that are orders of magnitude larger, therefore substantially increasing the efficiency of recombination-mediated genetic targeting. Here, we present GetPrimers (https://www.evomicslab.org/app/getprimers/), a generalized computational framework and web tool to assist automatic targeting and verification primer design for both one-step PCR-based and fusion PCR-based genetic targeting experiments. Moreover, GetPrimers by design runs for any given genetic background of any species with full genome scalability. Therefore, GetPrimers is capable of empowering high-throughput functional genomic assays at multipopulation and multispecies levels. Comprehensive experimental validations have been performed for targeting and verification primers designed by GetPrimers across multiple organism systems and experimental setups. We anticipate GetPrimers to become a highly useful and popular tool to facilitate easy and standardized gene modification across multiple systems.
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Affiliation(s)
- Zepu Miao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Haiting Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xinyu Tu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhengshen Huang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shujing Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xinxin Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Fan Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhishen Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huihui Li
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yue Jiao
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhipeng Zhou
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chun-Min Shan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
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8
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Zheng JX, Du TY, Shao GC, Ma ZH, Jiang ZD, Hu W, Suo F, He W, Dong MQ, Du LL. Ubiquitination-mediated Golgi-to-endosome sorting determines the toxin-antidote duality of fission yeast wtf meiotic drivers. Nat Commun 2023; 14:8334. [PMID: 38097609 PMCID: PMC10721834 DOI: 10.1038/s41467-023-44151-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
Killer meiotic drivers (KMDs) skew allele transmission in their favor by killing meiotic progeny not inheriting the driver allele. Despite their widespread presence in eukaryotes, the molecular mechanisms behind their selfish behavior are poorly understood. In several fission yeast species, single-gene KMDs belonging to the wtf gene family exert selfish killing by expressing a toxin and an antidote through alternative transcription initiation. Here we investigate how the toxin and antidote products of a wtf-family KMD gene can act antagonistically. Both the toxin and the antidote are multi-transmembrane proteins, differing only in their N-terminal cytosolic tails. We find that the antidote employs PY motifs (Leu/Pro-Pro-X-Tyr) in its N-terminal cytosolic tail to bind Rsp5/NEDD4 family ubiquitin ligases, which ubiquitinate the antidote. Mutating PY motifs or attaching a deubiquitinating enzyme transforms the antidote into a toxic protein. Ubiquitination promotes the transport of the antidote from the trans-Golgi network to the endosome, thereby preventing it from causing toxicity. A physical interaction between the antidote and the toxin enables the ubiquitinated antidote to translocate the toxin to the endosome and neutralize its toxicity. We propose that post-translational modification-mediated protein localization and/or activity changes may be a common mechanism governing the antagonistic duality of single-gene KMDs.
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Affiliation(s)
- Jin-Xin Zheng
- National Institute of Biological Sciences, Beijing, 102206, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Tong-Yang Du
- National Institute of Biological Sciences, Beijing, 102206, China
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Guang-Can Shao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhu-Hui Ma
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Wen Hu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Wanzhong He
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China.
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9
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Lera-Ramírez M, Bähler J, Mata J, Rutherford K, Hoffman CS, Lambert S, Oliferenko S, Martin SG, Gould KL, Du LL, Sabatinos SA, Forsburg SL, Nielsen O, Nurse P, Wood V. Revised fission yeast gene and allele nomenclature guidelines for machine readability. Genetics 2023; 225:iyad143. [PMID: 37758508 PMCID: PMC10627252 DOI: 10.1093/genetics/iyad143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/24/2023] [Indexed: 09/30/2023] Open
Abstract
Standardized nomenclature for genes, gene products, and isoforms is crucial to prevent ambiguity and enable clear communication of scientific data, facilitating efficient biocuration and data sharing. Standardized genotype nomenclature, which describes alleles present in a specific strain that differ from those in the wild-type reference strain, is equally essential to maximize research impact and ensure that results linking genotypes to phenotypes are Findable, Accessible, Interoperable, and Reusable (FAIR). In this publication, we extend the fission yeast clade gene nomenclature guidelines to support the curation efforts at PomBase (www.pombase.org), the Schizosaccharomyces pombe Model Organism Database. This update introduces nomenclature guidelines for noncoding RNA genes, following those set forth by the Human Genome Organisation Gene Nomenclature Committee. Additionally, we provide a significant update to the allele and genotype nomenclature guidelines originally published in 1987, to standardize the diverse range of genetic modifications enabled by the fission yeast genetic toolbox. These updated guidelines reflect a community consensus between numerous fission yeast researchers. Adoption of these rules will improve consistency in gene and genotype nomenclature, and facilitate machine-readability and automated entity recognition of fission yeast genes and alleles in publications or datasets. In conclusion, our updated guidelines provide a valuable resource for the fission yeast research community, promoting consistency, clarity, and FAIRness in genetic data sharing and interpretation.
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Affiliation(s)
- Manuel Lera-Ramírez
- University College London, Department of Genetics Evolution and Environment, Darwin Building, 99-105 Gower Street, London WC1E 6BT, UK
| | - Jürg Bähler
- University College London, Department of Genetics Evolution and Environment, Darwin Building, 99-105 Gower Street, London WC1E 6BT, UK
| | - Juan Mata
- University of Cambridge, Department of Biochemistry, Cambridge CB2 1GA, UK
| | - Kim Rutherford
- University of Cambridge, Department of Biochemistry, Cambridge CB2 1GA, UK
| | | | - Sarah Lambert
- Institut Curie, Université Paris-Saclay, CNRS UMR3348, Orsay 91400, France
| | - Snezhana Oliferenko
- The Francis Crick Institute, London NW1 1AT, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London SE1 1UL, UK
| | - Sophie G Martin
- University of Geneva, Department of Molecular and Cellular Biology, Geneva 1211, Switzerland
| | - Kathleen L Gould
- Vanderbilt University School of Medicine, Department of Cell and Developmental Biology, Nashville, TN 37232, USA
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China
| | - Sarah A Sabatinos
- Toronto Metropolitan University, Department of Chemistry & Biology, Toronto M5B 2K3, Canada
| | - Susan L Forsburg
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Olaf Nielsen
- Department of Biology, Cell cycle and genome stability Group, University of Copenhagen, Copenhagen N DK2100, Denmark
| | - Paul Nurse
- The Francis Crick Institute, London NW1 1AT, UK
| | - Valerie Wood
- University of Cambridge, Department of Biochemistry, Cambridge CB2 1GA, UK
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10
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Brysch-Herzberg M, Jia GS, Sipiczki M, Seidel M, Li W, Assali I, Du LL. Schizosaccharomyces lindneri sp. nov., a fission yeast occurring in honey. Yeast 2023. [PMID: 37243506 DOI: 10.1002/yea.3857] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 05/29/2023] Open
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 18203T and ex-type: MUCL 58363; MycoBank no.: MB 847838).
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Affiliation(s)
- Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University of Applied Sciences, Heilbronn, Germany
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing, China
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
| | - Martin Seidel
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University of Applied Sciences, Heilbronn, Germany
| | - Wen Li
- National Institute of Biological Sciences, Beijing, China
| | - Imen Assali
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University of Applied Sciences, Heilbronn, Germany
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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