{"entity": "researcher", "timestamp": "2026-07-19T07:06:48.683Z", "family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "affiliations": ["Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596"}}, "publications": [{"entity": "publication", "iuid": "4cb1f3bbbd73476d85743dd1a3b24932", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4cb1f3bbbd73476d85743dd1a3b24932.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4cb1f3bbbd73476d85743dd1a3b24932"}}, "title": "Early germline sequestration in a basidiomycete fungus.", "authors": [{"family": "Thor\u00e9n", "given": "Markus Hiltunen", "initials": "MH", "orcid": "0000-0002-8880-872X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b54361528b4c7c8f5122d91d58b36d.json"}}, {"family": "Olsson", "given": "Boel", "initials": "B", "orcid": "0009-0006-4157-2664", "researcher": {"href": "https://publications.scilifelab.se/researcher/219a75999b65464ca3d405ac20898743.json"}}, {"family": "Vonk", "given": "Peter Jan", "initials": "PJ", "orcid": "0000-0001-5325-7430", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5684212a1f5478cab0943d5064e74a7.json"}}, {"family": "Siljestam", "given": "Mattias", "initials": "M", "orcid": "0000-0002-3720-4926", "researcher": {"href": "https://publications.scilifelab.se/researcher/653d5e0ec2bc4925a19db2697ad61a2d.json"}}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J", "orcid": "0000-0003-1518-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/db7ebacfd8764a988ee41f2e5ab23e50.json"}}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2025-08-14", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "389", "issue": "6761", "pages": "720-723"}, "abstract": "In sexual organisms, inheritance of new mutations is highly dependent on the timing of germline definition. Here, we used the fairy ring-forming fungus Marasmius oreades to challenge the general assumption of a late germline separation in the Fungi. We collected mushrooms from different parts of rings over a 7-year period and identified new mutations in different tissues by whole-genome sequencing. We found evidence that fertile and sterile tissues had accumulated different mutations, suggesting that the germ line, destined for spore production, is already defined in the mycelium in this species. Moreover, the germ line carried fewer mutations than sterile tissues, indicating a lower mutation rate. Our findings suggest that early germline sequestration is more widespread than previously considered across multicellular life.", "doi": "10.1126/science.adu8580", "pmid": "40811541", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-08-29T12:41:10.841Z", "modified": "2025-11-21T13:14:48.967Z"}, {"entity": "publication", "iuid": "f63d11ddb9954b36bf8215cceb32f618", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f63d11ddb9954b36bf8215cceb32f618.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f63d11ddb9954b36bf8215cceb32f618"}}, "title": "Evolution of a bipolar sexual compatibility system in Marasmius.", "authors": [{"family": "Hiltunen Thor\u00e9n", "given": "Markus", "initials": "M", "orcid": "0000-0002-8880-872X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b54361528b4c7c8f5122d91d58b36d.json"}}, {"family": "Stanojkovi\u0107", "given": "Aleksandar", "initials": "A", "orcid": "0000-0003-3252-2068", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb40f8115f064296a9b493e5aa9f11cd.json"}}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2024-12-11", "journal": {"title": "Mycologia", "issn": "1557-2536", "volume": "117", "issue": "1", "pages": "19-33", "issn-l": null}, "abstract": "Sexual compatibility in the Basidiomycota is governed by genetic identity at one or two loci, resulting in compatibility systems called bipolar and tetrapolar. The loci are known as HD and P/R, encoding homeodomain transcription factors and pheromone precursors and receptors, respectively. Bipolarity is known to evolve either by linkage of the two loci or by loss of mating-type determination of either the HD or the P/R locus. The ancestor to basidiomycete fungi is thought to have been tetrapolar, and many transitions to bipolarity have been described in different lineages. In the diverse genus Marasmius (Agaricales), both compatibility systems are found, and the system has been shown to follow the infrageneric sections of the genus, suggesting a single origin of bipolarity. Here, we tested this hypothesis using a comprehensive phylogenetic framework and investigated the mode by which bipolarity has evolved in this group. We utilized available genomic data and marker sequences to investigate evolution of sexual compatibility in Marasmius and allied genera. By generating a concatenated multilocus phylogeny, we found support for a single transition to known bipolarity within Marasmius. Furthermore, utilizing genomic data of the bipolar species Marasmius oreades, we found that the HD and P/R loci likely have remained unlinked through this transition. By comparing nucleotide diversity at the HD and P/R loci in Ma. oreades, we show that the HD locus has retained high diversity, and thus likely the function of determining sexual identity, as similarly in other bipolar mushroom-forming fungi. Finally, we describe the genomic architecture of the MAT loci of species of both sexual compatibility systems in Marasmiaceae and related families.", "doi": "10.1080/00275514.2024.2425583", "pmid": "39661443", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:48:29.256Z", "modified": "2025-11-28T10:48:29.419Z"}, {"entity": "publication", "iuid": "34b3ab08d6fb428d9a51611e76936c20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34b3ab08d6fb428d9a51611e76936c20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34b3ab08d6fb428d9a51611e76936c20"}}, "title": "High rate of gene family evolution in proximity to the origin of ectomycorrhizal symbiosis in Inocybaceae.", "authors": [{"family": "Khan", "given": "Faheema Kalsoom", "initials": "FK", "orcid": "0000-0002-4891-953X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3d13492ee8f4ad1b69ce59f21b09155.json"}}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M", "orcid": "0000-0002-0635-6281", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ccb3584fa144e178750ff2fc4666cfe.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "244", "issue": "1", "pages": "219-234", "issn-l": "0028-646X"}, "abstract": "The genomes of ectomycorrhizal (ECM) fungi have a reduced number of genes encoding Carbohydrate-Active EnZymes (CAZymes), expansions in transposable elements (TEs) and small secreted proteins (SSPs) compared with saprotrophs. Fewer genes for specific peptidases and lipases in ECM fungi are also reported. It is unclear whether these changes occur at the shift to the ECM habit or are more gradual throughout the evolution of ECM lineages. We generated a genomic dataset of 20 species in the ECM lineage Inocybaceae and compared them with six saprotrophic species. Inocybaceae genomes have fewer CAZymes, peptidases, lipases, secondary metabolite clusters and SSPs and higher TE content than their saprotrophic relatives. There was an increase in the rate of gene family evolution along the branch with the transition to the ECM lifestyle. This branch had very high rate of evolution in CAZymes and had the largest number of contractions. Other significant changes along this branch included expansions in transporters, transposons-related genes and communication genes such as fungal kinases. There is a high concentration of changes in proximity to the transition to the ECM lifestyle, which correspond to the identified key changes for the gain of this lifestyle.", "doi": "10.1111/nph.20007", "pmid": "39113397", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-09-17T11:56:17.664Z", "modified": "2025-02-28T14:20:41.968Z"}, {"entity": "publication", "iuid": "6dad922586f84341baf632ac55a61367", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6dad922586f84341baf632ac55a61367.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6dad922586f84341baf632ac55a61367"}}, "title": "High-Quality Genome Assemblies of 4 Members of the Podospora anserina Species Complex.", "authors": [{"family": "Ament-Vel\u00e1squez", "given": "S Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Vogan", "given": "Aaron A", "initials": "AA", "orcid": "0000-0003-2013-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/71c6d460e3b44712a1a9dc19066211a4.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Hartmann", "given": "Fanny E", "initials": "FE", "orcid": "0000-0002-9365-4008", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac8e717031aa4621925ab90684adecdc.json"}}, {"family": "Gautier", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Silar", "given": "Philippe", "initials": "P", "orcid": "0000-0003-0104-987X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a40756e83bc493ebc1d98d8c5c374da.json"}}, {"family": "Giraud", "given": "Tatiana", "initials": "T"}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2024-03-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "3", "issn-l": "1759-6653"}, "abstract": "The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of 7 closely related species. In addition to P. anserina, high-quality genomic resources are available for 2 of these taxa. Here, we provide chromosome-level annotated assemblies of the 4 remaining species of the complex, as well as a comprehensive data set of annotated assemblies from a total of 28 Podospora genomes. We find that all 7 species have genomes of around 35 Mb arranged in 7 chromosomes that are mostly collinear and less than 2% divergent from each other at genic regions. We further attempt to resolve their phylogenetic relationships, finding significant levels of phylogenetic conflict as expected from a rapid and recent diversification.", "doi": "10.1093/gbe/evae034", "pmid": "38386982", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10936905"}, {"db": "pii", "key": "7612620"}], "notes": [], "created": "2024-08-02T12:17:18.611Z", "modified": "2025-02-28T14:18:08.086Z"}, {"entity": "publication", "iuid": "af709cc9882b4b46851b735254ff5af0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af709cc9882b4b46851b735254ff5af0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af709cc9882b4b46851b735254ff5af0"}}, "title": "Stage-specific transposon activity in the life cycle of the fairy-ring mushroom <i>Marasmius oreades<\/i>.", "authors": [{"family": "Hiltunen", "given": "Markus", "initials": "M", "orcid": "0000-0002-8880-872X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b54361528b4c7c8f5122d91d58b36d.json"}}, {"family": "Ament-Vel\u00e1squez", "given": "Sandra Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2022-11-16", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "119", "issue": "46", "pages": "e2208575119"}, "abstract": "Genetic variability can be generated by different mechanisms, and across the life cycle. Many basidiomycete fungi have an extended somatic stage, during which each cell carries two genetically distinct haploid nuclei (dikaryosis), resulting from fusion of two compatible monokaryotic individuals. Recent findings have revealed remarkable genome stability at the nucleotide level during dikaryotic growth in these organisms, but whether this pattern extends to mutations affecting large genomic regions remains unknown. Furthermore, despite high genome integrity during dikaryosis, basidiomycete populations are not devoid of genetic diversity, begging the question of when this diversity is introduced. Here, we used a <i>Marasmius oreades<\/i> fairy ring to investigate the rise of large-scale variants during mono- and dikaryosis. By separating the two nuclear genotypes from four fruiting bodies and generating complete genome assemblies, we gained access to investigate genomic changes of any size. We found that during dikaryotic growth in nature the genome stayed intact, but after separating the nucleotypes into monokaryons, a considerable amount of structural variation started to accumulate, driven to large extent by transposons. Transposon insertions were also found in monokaryotic single-meiospore isolates. Hence, we show that genome integrity in basidiomycetes can be interrupted during monokaryosis, leading to genomic rearrangements and increased activity of transposable elements. We suggest that genetic diversification is disproportionate between life cycle stages in mushroom-forming fungi, so that the short-lived monokaryotic growth stage is more prone to genetic changes than the dikaryotic stage.", "doi": "10.1073/pnas.2208575119", "pmid": "36343254", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9674265"}], "notes": [], "created": "2022-11-21T09:59:53.450Z", "modified": "2024-01-16T13:48:34.455Z"}, {"entity": "publication", "iuid": "2cea4b166b6140d9959d018dcb7952da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2cea4b166b6140d9959d018dcb7952da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2cea4b166b6140d9959d018dcb7952da"}}, "title": "Meiotic drive is associated with sexual incompatibility in Neurospora.", "authors": [{"family": "Vogan", "given": "Aaron A", "initials": "AA", "orcid": "0000-0003-2013-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/71c6d460e3b44712a1a9dc19066211a4.json"}}, {"family": "Svedberg", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0951-3019", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d35216730c841d197a958bfa00a06a0.json"}}, {"family": "Grudzinska-Sterno", "given": "Magdalena", "initials": "M"}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2022-09-23", "journal": {"title": "Evolution", "issn": "1558-5646", "issn-l": "0014-3820"}, "abstract": "Evolution of Bateson-Dobzhansky-Muller (BDM) incompatibilities is thought to represent a key step in the formation of separate species. They are incompatible alleles that have evolved in separate populations and are exposed in hybrid offspring as hybrid sterility or lethality. In this study, we reveal a previously unconsidered mechanism promoting the formation of BDM incompatibilities, meiotic drive. Theoretical studies have evaluated the role that meiotic drive, the phenomenon whereby selfish elements bias their transmission to progeny at ratios above 50:50, plays in speciation, and have mostly concluded that drive could not result in speciation on its own. Using the model fungus Neurospora, we demonstrate that the large meiotic drive haplotypes, Sk-2 and Sk-3, contain putative sexual incompatibilities. Our experiments revealed that although crosses between Neurospora intermedia and Neurospora metzenbergii produce viable progeny at appreciable rates, when strains of N. intermedia carry Sk-2 or Sk-3 the proportion of viable progeny drops substantially. Additionally, it appears that Sk-2 and Sk-3 have accumulated different incompatibility phenotypes, consistent with their independent evolutionary history. This research illustrates how meiotic drive can contribute to reproductive isolation between populations, and thereby speciation.", "doi": "10.1111/evo.14630", "pmid": "36148939", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2022-11-09T15:40:35.685Z", "modified": "2024-01-16T13:48:34.990Z"}, {"entity": "publication", "iuid": "83170949a3664c28be863b7ae471fc06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83170949a3664c28be863b7ae471fc06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83170949a3664c28be863b7ae471fc06"}}, "title": "Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma.", "authors": [{"family": "Meunier", "given": "C\u00e9cile", "initials": "C"}, {"family": "Darolti", "given": "Iulia", "initials": "I"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Mank", "given": "Judith E", "initials": "JE", "orcid": "0000-0002-2450-513X", "researcher": {"href": "https://publications.scilifelab.se/researcher/42f3e1ac3beb4d9cb0c6687ec7d94c68.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2022-08-10", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "issn-l": "0962-8452", "volume": "289", "issue": "1980", "pages": "20220971"}, "abstract": "Heterokaryosis is a system in which genetically distinct nuclei coexist within the same cytoplasm. While heterokaryosis dominates the life cycle of many fungal species, the transcriptomic changes associated with the transition from homokaryosis to heterokaryosis is not well understood. Here, we analyse gene expression profiles of homokaryons and heterokaryons from three phylogenetically and reproductively isolated lineages of the filamentous ascomycete Neurospora tetrasperma. We show that heterokaryons are transcriptionally distinct from homokaryons in the sexual stage of development, but not in the vegetative stage, suggesting that the phenotypic switch to fertility in heterokaryons is associated with major changes in gene expression. Heterokaryon expression is predominantly defined by additive effects of its two nuclear components. Furthermore, allele-specific expression analysis of heterokaryons with varying nuclear ratios show patterns of expression ratios strongly dependent on nuclear ratios in the vegetative stage. By contrast, in the sexual stage, strong deviations of expression ratios indicate a co-regulation of nuclear gene expression in all three lineages. Taken together, our results show two levels of expression control: additive effects suggest a nuclear level of expression, whereas co-regulation of gene expression indicate a heterokaryon level of control.", "doi": "10.1098/rspb.2022.0971", "pmid": "35946150", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9363985"}], "notes": [], "created": "2022-08-12T11:13:21.820Z", "modified": "2024-01-16T13:48:35.404Z"}, {"entity": "publication", "iuid": "903a0d4b47c0422abb32f266006c4d51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/903a0d4b47c0422abb32f266006c4d51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/903a0d4b47c0422abb32f266006c4d51"}}, "title": "Allorecognition genes drive reproductive isolation in Podospora anserina.", "authors": [{"family": "Ament-Vel\u00e1squez", "given": "S Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Vogan", "given": "Aaron A", "initials": "AA", "orcid": "0000-0003-2013-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/71c6d460e3b44712a1a9dc19066211a4.json"}}, {"family": "Granger-Farbos", "given": "Alexandra", "initials": "A"}, {"family": "Bastiaans", "given": "Eric", "initials": "E", "orcid": "0000-0003-1502-0947", "researcher": {"href": "https://publications.scilifelab.se/researcher/870bd6035e54489187ef1d5131d14108.json"}}, {"family": "Martinossi-Allibert", "given": "Ivain", "initials": "I"}, {"family": "Saupe", "given": "Sven J", "initials": "SJ"}, {"family": "de Groot", "given": "Suzette", "initials": "S"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}, {"family": "Debets", "given": "Alfons J M", "initials": "AJM", "orcid": "0000-0002-1799-4617", "researcher": {"href": "https://publications.scilifelab.se/researcher/b95b282c02d44a1a9f4d3d2aa7578b8a.json"}}, {"family": "Clav\u00e9", "given": "Corinne", "initials": "C"}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "issn-l": "2397-334X", "volume": "6", "issue": "7", "pages": "910-923"}, "abstract": "Allorecognition, the capacity to discriminate self from conspecific non-self, is a ubiquitous organismal feature typically governed by genes evolving under balancing selection. Here, we show that in the fungus Podospora anserina, allorecognition loci controlling vegetative incompatibility (het genes), define two reproductively isolated groups through pleiotropic effects on sexual compatibility. These two groups emerge from the antagonistic interactions of the unlinked loci het-r (encoding a NOD-like receptor) and het-v (encoding a methyltransferase and an MLKL/HeLo domain protein). Using a combination of genetic and ecological data, supported by simulations, we provide a concrete and molecularly defined example whereby the origin and coexistence of reproductively isolated groups in sympatry is driven by pleiotropic genes under balancing selection.", "doi": "10.1038/s41559-022-01734-x", "pmid": "35551248", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-022-01734-x"}, {"db": "pmc", "key": "PMC9262711"}], "notes": [], "created": "2022-11-09T15:43:47.396Z", "modified": "2024-01-16T13:48:36.025Z"}, {"entity": "publication", "iuid": "5623f32746cb4b67a34293cad348214a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5623f32746cb4b67a34293cad348214a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5623f32746cb4b67a34293cad348214a"}}, "title": "The Enterprise, a massive transposon carrying Spok meiotic drive genes.", "authors": [{"family": "Vogan", "given": "Aaron A", "initials": "AA", "orcid": "0000-0003-2013-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/71c6d460e3b44712a1a9dc19066211a4.json"}}, {"family": "Ament-Vel\u00e1squez", "given": "S Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Bastiaans", "given": "Eric", "initials": "E", "orcid": "0000-0003-1502-0947", "researcher": {"href": "https://publications.scilifelab.se/researcher/870bd6035e54489187ef1d5131d14108.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Saupe", "given": "Sven J", "initials": "SJ"}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "31", "issue": "5", "pages": "789-798", "issn-l": "1088-9051"}, "abstract": "The genomes of eukaryotes are full of parasitic sequences known as transposable elements (TEs). Here, we report the discovery of a putative giant tyrosine-recombinase-mobilized DNA transposon, Enterprise, from the model fungus Podospora anserina Previously, we described a large genomic feature called the Spok block which is notable due to the presence of meiotic drive genes of the Spok gene family. The Spok block ranges from 110 kb to 247 kb and can be present in at least four different genomic locations within P. anserina, despite what is an otherwise highly conserved genome structure. We propose that the reason for its varying positions is that the Spok block is not only capable of meiotic drive but is also capable of transposition. More precisely, the Spok block represents a unique case where the Enterprise has captured the Spoks, thereby parasitizing a resident genomic parasite to become a genomic hyperparasite. Furthermore, we demonstrate that Enterprise (without the Spoks) is found in other fungal lineages, where it can be as large as 70 kb. Lastly, we provide experimental evidence that the Spok block is deleterious, with detrimental effects on spore production in strains which carry it. This union of meiotic drivers and a transposon has created a selfish element of impressive size in Podospora, challenging our perception of how TEs influence genome evolution and broadening the horizons in terms of what the upper limit of transposition may be.", "doi": "10.1101/gr.267609.120", "pmid": "33875482", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gr.267609.120"}, {"db": "pmc", "key": "PMC8092012"}], "notes": [], "created": "2021-06-01T20:57:51.352Z", "modified": "2024-01-16T13:48:39.850Z"}, {"entity": "publication", "iuid": "86f05d7bca134d87b5dd15cffe3d55dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86f05d7bca134d87b5dd15cffe3d55dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86f05d7bca134d87b5dd15cffe3d55dd"}}, "title": "An introgressed gene causes meiotic drive in Neurospora sitophila.", "authors": [{"family": "Svedberg", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0951-3019", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d35216730c841d197a958bfa00a06a0.json"}}, {"family": "Vogan", "given": "Aaron A", "initials": "AA"}, {"family": "Rhoades", "given": "Nicholas A", "initials": "NA"}, {"family": "Sarmarajeewa", "given": "Dilini", "initials": "D"}, {"family": "Jacobson", "given": "David J", "initials": "DJ"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}, {"family": "Hammond", "given": "Thomas M", "initials": "TM", "orcid": "0000-0002-0812-4759", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdc694cc4c4749ca821feadf727fe77b.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2021-04-27", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "17", "pages": "e2026605118", "issn-l": "0027-8424"}, "abstract": "Meiotic drive elements cause their own preferential transmission following meiosis. In fungi, this phenomenon takes the shape of spore killing, and in the filamentous ascomycete Neurospora sitophila, the Sk-1 spore killer element is found in many natural populations. In this study, we identify the gene responsible for spore killing in Sk-1 by generating both long- and short-read genomic data and by using these data to perform a genome-wide association test. We name this gene Spk-1 Through molecular dissection, we show that a single 405-nt-long open reading frame generates a product that both acts as a poison capable of killing sibling spores and as an antidote that rescues spores that produce it. By phylogenetic analysis, we demonstrate that the gene has likely been introgressed from the closely related species Neurospora hispaniola, and we identify three subclades of N. sitophila, one where Sk-1 is fixed, another where Sk-1 is absent, and a third where both killer and sensitive strain are found. Finally, we show that spore killing can be suppressed through an RNA interference-based genome defense pathway known as meiotic silencing by unpaired DNA. Spk-1 is not related to other known meiotic drive genes, and similar sequences are only found within Neurospora These results shed light on the diversity of genes capable of causing meiotic drive, their origin and evolution, and their interaction with the host genome.", "doi": "10.1073/pnas.2026605118", "pmid": "33875604", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2026605118"}, {"db": "pmc", "key": "PMC8092558"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5093585.v1"}], "notes": [], "created": "2021-06-01T20:57:22.667Z", "modified": "2024-01-16T13:48:39.983Z"}, {"entity": "publication", "iuid": "befd645e5e764eac97f5d53eb795294d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/befd645e5e764eac97f5d53eb795294d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/befd645e5e764eac97f5d53eb795294d"}}, "title": "Comparative analysis of genome-wide DNA methylation in Neurospora.", "authors": [{"family": "Hosseini", "given": "Sara", "initials": "S"}, {"family": "Meunier", "given": "C\u00e9cile", "initials": "C"}, {"family": "Nguyen", "given": "Diem", "initials": "D"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Epigenetics", "issn": "1559-2308", "volume": "15", "issue": "9", "pages": "972-987", "issn-l": "1559-2294"}, "abstract": "DNA methylation is an epigenetic mark that plays an important role in genetic regulation in eukaryotes. Major progress has been made in dissecting the molecular pathways that regulate DNA methylation. Yet, little is known about DNA methylation variation over evolutionary time. Here we present an investigation of the variation of DNA methylation and transposable element (TE) content in species of the filamentous ascomycetes Neurospora. We generated genome-wide DNA methylation data at single-base resolution, together with genomic TE content and gene expression data, of 10 individuals representing five closely related Neurospora species. We found that the methylation levels were low (ranging from 1.3% to 2.5%) and varied among the genomes in a species-specific way. Furthermore, we found that the TEs over 400 bp long were targeted by DNA methylation, and in all genomes, high methylation correlated with low GC, confirming a conserved link between DNA methylation and Repeat Induced Point (RIP) mutations in this group of fungi. Both TE content and DNA methylation pattern showed phylogenetic signal, and the species with the highest TE load (N. crassa) also exhibited the highest methylation level per TE. Our results suggest that DNA methylation is an evolvable trait and indicate that the genomes of Neurospora are shaped by an evolutionary arms race between TEs and host defence.", "doi": "10.1080/15592294.2020.1741758", "pmid": "32228351", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7518705"}], "notes": [], "created": "2020-04-23T08:47:49.215Z", "modified": "2024-01-16T13:48:41.837Z"}, {"entity": "publication", "iuid": "6d28ace9457d4629bb9f751492ef60e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d28ace9457d4629bb9f751492ef60e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d28ace9457d4629bb9f751492ef60e0"}}, "title": "Asexual reproduction and growth rate: independent and plastic life history traits in Neurospora crassa.", "authors": [{"family": "Anderson", "given": "Jennifer L", "initials": "JL", "orcid": "0000-0002-0713-6897", "researcher": {"href": "https://publications.scilifelab.se/researcher/925e9736bd84401ca54158c320ed0b55.json"}}, {"family": "Nieuwenhuis", "given": "Bart P S", "initials": "BPS", "orcid": "0000-0001-8159-4784", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e3278c557ff403aa061ee99a8631d6e.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2019-03-00", "journal": {"volume": "13", "issn": "1751-7370", "issue": "3", "pages": "780-788", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Trade-offs among traits influencing fitness are predicted by life history theory because resources allocated to one function are unavailable to another. Here we examine the relationship between two such traits, asexual reproduction and growth rate, in the filamentous fungus Neurospora crassa, where shared genetic and physiological factors and a source-sink energetic relationship between growth and reproduction may constrain the evolution of these traits. To test growth-reproduction relationships in this species, we independently selected on mycelial growth rate or asexual spore production in a heterogeneous lab-derived population and evaluated the response of the non-selected traits. Combined with phenotypes for the 20 wild strains used to produce the heterogeneous population and the genome-wide genotypes of 468 strains, these data show that growth and reproduction are highly plastic in N. crassa and do not trade off either among wild strains or after laboratory selection in two environments. Rather, we find no predictable growth-reproduction relationship in the environments tested, indicating an effective absence of genetic constraint between these traits. Our results suggest that growth rate and asexual reproduction may not respond predictably to environmental change and suggest that reliance on a single trait as a proxy for fitness in fungal studies may be inadvisable.", "doi": "10.1038/s41396-018-0294-7", "pmid": "30413765", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41396-018-0294-7"}, {"db": "pmc", "key": "PMC6462030"}], "notes": [], "created": "2019-01-07T22:49:26.024Z", "modified": "2021-06-21T14:01:01.937Z"}]}