{"entity": "researcher", "timestamp": "2026-08-08T16:33:43.122Z", "family": "Mank", "given": "Judith E", "initials": "JE", "orcid": "0000-0002-2450-513X", "affiliations": ["Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.", "Centre for Ecology and Conservation, University of Exeter, Penryn Campus, UK."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/42f3e1ac3beb4d9cb0c6687ec7d94c68.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/42f3e1ac3beb4d9cb0c6687ec7d94c68"}}, "publications": [{"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": "959380267d6149ad8c41e56a069865c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/959380267d6149ad8c41e56a069865c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/959380267d6149ad8c41e56a069865c6"}}, "title": "Comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia.", "authors": [{"family": "Darolti", "given": "Iulia", "initials": "I"}, {"family": "Almeida", "given": "Pedro", "initials": "P"}, {"family": "Wright", "given": "Alison E", "initials": "AE"}, {"family": "Mank", "given": "Judith E", "initials": "JE", "orcid": "0000-0002-2450-513X", "researcher": {"href": "https://publications.scilifelab.se/researcher/42f3e1ac3beb4d9cb0c6687ec7d94c68.json"}}], "type": "journal article", "published": "2022-05-04", "journal": {"title": "J. Evol. Biol.", "issn": "1420-9101", "issn-l": "1010-061X", "volume": "35", "issue": "12", "pages": "1646-1658"}, "abstract": "Studies of sex chromosome systems at early stages of divergence are key to understanding the initial process and underlying causes of recombination suppression. However, identifying signatures of divergence in homomorphic sex chromosomes can be challenging due to high levels of sequence similarity between the X and the Y. Variations in methodological precision and underlying data can make all the difference between detecting subtle divergence patterns or missing them entirely. Recent efforts to test for X-Y sequence differentiation in the guppy have led to contradictory results. Here, we apply different analytical methodologies to the same data set to test for the accuracy of different approaches in identifying patterns of sex chromosome divergence in the guppy. Our comparative analysis reveals that the most substantial source of variation in the results of the different analyses lies in the reference genome used. Analyses using custom-made genome assemblies for the focal population or species successfully recover a signal of divergence across different methodological approaches. By contrast, using the distantly related Xiphophorus reference genome results in variable patterns, due to both sequence evolution and structural variations on the sex chromosomes between the guppy and Xiphophorus. Changes in mapping and filtering parameters can additionally introduce noise and obscure the signal. Our results illustrate how analytical differences can alter perceived results and we highlight best practices for the study of nascent sex chromosomes.", "doi": "10.1111/jeb.14013", "pmid": "35506576", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2022-11-29T11:58:52.373Z", "modified": "2022-12-07T08:53:17.615Z"}]}