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Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection. J Fungi (Basel) 2021; 7:jof7100864. [PMID: 34682285 PMCID: PMC8537764 DOI: 10.3390/jof7100864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Abstract
Fission yeasts have a unique life history and exhibit distinct evolutionary patterns from other yeasts. Besides, the species demonstrate stable genome structures despite the relatively fast evolution of their genomic sequences. To reveal what could be the reason for that, comparative genomic analyses were carried out. Our results provided evidence that the structural and sequence evolution of the fission yeasts were correlated. Moreover, we revealed ancestral locally collinear blocks (aLCBs), which could have been inherited from their last common ancestor. These aLCBs proved to be the most conserved regions of the genomes as the aLCBs contain almost eight genes/blocks on average in the same orientation and order across the species. Gene order of the aLCBs is mainly fission-yeast-specific but supports the idea of filamentous ancestors. Nevertheless, the sequences and gene structures within the aLCBs are as mutable as any sequences in other parts of the genomes. Although genes of certain Gene Ontology (GO) categories tend to cluster at the aLCBs, those GO enrichments are not related to biological functions or high co-expression rates, they are, rather, determined by the density of essential genes and Rec12 cleavage sites. These data and our simulations indicated that aLCBs might not only be remnants of ancestral gene order but are also maintained by natural selection.
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: diversity, taxonomy and phylogeny of the Fungi. Biol Rev Camb Philos Soc 2019; 94:2101-2137. [PMID: 31659870 PMCID: PMC6899921 DOI: 10.1111/brv.12550] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/11/2022]
Abstract
The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely unicellular monopolar organisms to highly complex syncitial filaments that may form macroscopic structures. Fungi emerged as a 'Third Kingdom', embracing organisms that were outside the classical dichotomy of animals versus vegetals. The taxonomy of this group has a turbulent history that is only now starting to be settled with the advent of genomics and phylogenomics. We here review the current status of the phylogeny and taxonomy of fungi, providing an overview of the main defined groups. Based on current knowledge, nine phylum-level clades can be defined: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Basidiomycota and Ascomycota. For each group, we discuss their main traits and their diversity, focusing on the evolutionary relationships among the main fungal clades. We also explore the diversity and phylogeny of several groups of uncertain affinities and the main phylogenetic and taxonomical controversies and hypotheses in the field.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
- Health and Experimental Sciences DepartmentUniversitat Pompeu Fabra (UPF)08003BarcelonaSpain
- ICREAPg. Lluís Companys 2308010BarcelonaSpain
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Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, Davey JW, Jeffares DC, Wolf JBW. Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast. Mol Biol Evol 2019; 36:1975-1989. [PMID: 31225876 PMCID: PMC6736153 DOI: 10.1093/molbev/msz126] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20-60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.
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Affiliation(s)
- Sergio Tusso
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Evolutionary Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Bart P S Nieuwenhuis
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - John W Davey
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | - Daniel C Jeffares
- Department of Biology, University of York, York, United Kingdom
- York Biomedical Research Institute (YBRI), University of York, York, United Kingdom
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Evolutionary Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: major ecological adaptations and evolutionary transitions. Biol Rev Camb Philos Soc 2019; 94:1443-1476. [PMID: 31021528 PMCID: PMC6850671 DOI: 10.1111/brv.12510] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
Abstract
Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF)08003BarcelonaSpain
- ICREA, Pg. Lluís Companys 2308010BarcelonaSpain
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Brysch-Herzberg M, Tobias A, Seidel M, Wittmann R, Wohlmann E, Fischer R, Dlauchy D, Peter G. Schizosaccharomyces osmophilus sp. nov., an osmophilic fission yeast occurring in bee bread of different solitary bee species. FEMS Yeast Res 2019; 19:5499025. [DOI: 10.1093/femsyr/foz038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 05/25/2019] [Indexed: 12/12/2022] Open
Affiliation(s)
- Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany
| | - Andrea Tobias
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Szent István University, Somlói út 14–16. H-1118 Budapest, Hungary
| | - Martin Seidel
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany
| | - Rupert Wittmann
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany
| | - Elke Wohlmann
- Karlsruhe Institute of Technology – KIT, Institute for Applied Bioscience, Department of Microbiology, Fritz-Haber-Weg 4, 76131 Karlsruhe, Germany
| | - Reinhard Fischer
- Karlsruhe Institute of Technology – KIT, Institute for Applied Bioscience, Department of Microbiology, Fritz-Haber-Weg 4, 76131 Karlsruhe, Germany
| | - Dénes Dlauchy
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Szent István University, Somlói út 14–16. H-1118 Budapest, Hungary
| | - Gabor Peter
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Szent István University, Somlói út 14–16. H-1118 Budapest, Hungary
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Assembly of Schizosaccharomyces cryophilus chromosomes and their comparative genomic analyses revealed principles of genome evolution of the haploid fission yeasts. Sci Rep 2018; 8:14629. [PMID: 30279451 PMCID: PMC6168568 DOI: 10.1038/s41598-018-32525-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/10/2018] [Indexed: 11/23/2022] Open
Abstract
The fission yeast clade, which has a distinct life history from other yeasts, can provide important clues about evolutionary changes. To reveal these changes the large S. cryophilus supercontigs were assembled into chromosomes using synteny relationships and the conserved pericentromeric, subtelomeric genes. Togetherness of the supercontigs was confirmed by PCR. Investigation of the gene order revealed localisation of the rDNA arrays, more than 300 new conserved orthologues and proved that S. cryophilus supercontigs were mosaics of collinear blocks. PFGE analysis showed that size of the S. cryophilus chromosomes differ from the S. pombe chromosomes. Comparative genomic analyses of the newly assembled chromosomes confirmed that the closest relative of S. cryophilus was S. octosporus not just in sequence similarity but also in a structural way, and revealed that preservation of the conserved regions did not arise from the lower number of chromosomal rearrangements. Translocations were more typical in the closely related species, while the number of inversions increased with the phylogenetic distances. Our data suggested that sites of the chromosomal rearrangements were not random and often associated with repetitive sequences, structural- and nucleotide evolution might correlate. Chromosomal rearrangements of the fission yeasts compared to other lineages were also discussed.
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Jeffares DC. The natural diversity and ecology of fission yeast. Yeast 2018; 35:253-260. [PMID: 29084364 DOI: 10.1002/yea.3293] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 10/12/2017] [Accepted: 10/13/2017] [Indexed: 12/17/2022] Open
Abstract
While the fission yeast is a powerful model of eukaryote biology, there have been few studies of quantitative genetics, phenotypic or genetic diversity. Here I survey the small collection of fission yeast diversity research. I discuss what we can infer about the ecology and origins of Schizosaccharomyces pombe from microbiology field studies and the few strains that have been collected.
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Affiliation(s)
- Daniel C Jeffares
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
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Hu W, Jiang ZD, Suo F, Zheng JX, He WZ, Du LL. A large gene family in fission yeast encodes spore killers that subvert Mendel's law. eLife 2017; 6:e26057. [PMID: 28631610 PMCID: PMC5478263 DOI: 10.7554/elife.26057] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/06/2017] [Indexed: 12/12/2022] Open
Abstract
Spore killers in fungi are selfish genetic elements that distort Mendelian segregation in their favor. It remains unclear how many species harbor them and how diverse their mechanisms are. Here, we discover two spore killers from a natural isolate of the fission yeast Schizosaccharomyces pombe. Both killers belong to the previously uncharacterized wtf gene family with 25 members in the reference genome. These two killers act in strain-background-independent and genome-location-independent manners to perturb the maturation of spores not inheriting them. Spores carrying one killer are protected from its killing effect but not that of the other killer. The killing and protecting activities can be uncoupled by mutation. The numbers and sequences of wtf genes vary considerably between S. pombe isolates, indicating rapid divergence. We propose that wtf genes contribute to the extensive intraspecific reproductive isolation in S. pombe, and represent ideal models for understanding how segregation-distorting elements act and evolve.
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Affiliation(s)
- Wen Hu
- National Institute of Biological Sciences, Beijing, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, Beijing, China
- PTN Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Jin-Xin Zheng
- National Institute of Biological Sciences, Beijing, China
| | - Wan-Zhong He
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
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Naumov GI, Kondratieva VI, Meshcheryakova EV, Naumova ES. Taxonomic genetics of methylotrophic yeast genus Komagataella: New biological species K. kurtzmanii. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416030108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Naumov GI. The yeast Komagataella: A genetic genus in accordance with interspecies hybridization. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715040141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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