{"entity": "researcher", "timestamp": "2026-07-13T10:04:13.302Z", "family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M", "orcid": "0000-0002-0635-6281", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/5ccb3584fa144e178750ff2fc4666cfe.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/5ccb3584fa144e178750ff2fc4666cfe"}}, "publications": [{"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": "c6cb0a80038d48c69c3e38c25d0ed018", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6cb0a80038d48c69c3e38c25d0ed018.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6cb0a80038d48c69c3e38c25d0ed018"}}, "title": "Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum.", "authors": [{"family": "Sahraei", "given": "Shadi Eshghi", "initials": "SE", "orcid": "0000-0003-4741-5871", "researcher": {"href": "https://publications.scilifelab.se/researcher/98f7d11029704e33b61a8c27daa54378.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": "Montoliu-Nerin", "given": "Merce", "initials": "M", "orcid": "0000-0002-5200-0411", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f89e94a04c6429db7e706b4d8d6626a.json"}}, {"family": "Manyara", "given": "David", "initials": "D", "orcid": "0000-0002-8370-2651", "researcher": {"href": "https://publications.scilifelab.se/researcher/2132548af20445b2b0561fa38b8f8b89.json"}}, {"family": "Bergin", "given": "Claudia", "initials": "C", "orcid": "0000-0001-7960-1789", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdd58ab07d964bcfb865ce67f7826816.json"}}, {"family": "Rosendahl", "given": "S\u00f8ren", "initials": "S", "orcid": "0000-0001-5202-6585", "researcher": {"href": "https://publications.scilifelab.se/researcher/111116b3b09343f783385c30207fd9b3.json"}}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "Mycorrhiza", "issn": "1432-1890", "issn-l": "0940-6360", "volume": "32", "issue": "5-6", "pages": "361-371"}, "abstract": "Arbuscular mycorrhizal (AM) fungi are ubiquitous mutualistic symbionts of most terrestrial plants and many complete their lifecycles underground. Whole genome analysis of AM fungi has long been restricted to species and strains that can be maintained under controlled conditions that facilitate collection of biological samples. There is some evidence suggesting that AM fungi can adapt to culture resulting in phenotypic and possibly also genotypic changes in the fungi. In this study, we used field isolated spores of AM fungi and identified them as Funneliformis geosporum based on morphology and phylogenetic analyses. We separately assembled the genomes of two representative spores using DNA sequences of 19 and 22 individually amplified nuclei. The genomes were compared with previously published data from other members of Glomeraceae including two strains of F. mosseae. No significant differences were observed among the species in terms of gene content, while the single nucleotide polymorphism density was higher in the strains of F. geosporum than in the strains of F. mosseae. In this study, we demonstrate that it is possible to sequence and assemble genomes from AM fungal spores sampled in the field, which opens up the possibility to include uncultured AM fungi in phylogenomic and comparative genomic analysis and to study genomic variation in natural populations of these important plant symbionts.", "doi": "10.1007/s00572-022-01091-4", "pmid": "36161535", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Microbial Single Cell Genomics": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9560946"}, {"db": "pii", "key": "10.1007/s00572-022-01091-4"}], "notes": [], "created": "2022-11-29T12:15:19.004Z", "modified": "2024-01-16T13:48:34.535Z"}, {"entity": "publication", "iuid": "796149f9eb4f4e3980d73a2969461850", "links": {"self": {"href": "https://publications.scilifelab.se/publication/796149f9eb4f4e3980d73a2969461850.json"}, "display": {"href": "https://publications.scilifelab.se/publication/796149f9eb4f4e3980d73a2969461850"}}, "title": "Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei.", "authors": [{"family": "Montoliu-Nerin", "given": "Merce", "initials": "M", "orcid": "0000-0002-5200-0411", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f89e94a04c6429db7e706b4d8d6626a.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": "Bergin", "given": "Claudia", "initials": "C"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Ellis", "given": "Barbara", "initials": "B"}, {"family": "Kutschera", "given": "Verena Esther", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2020-01-28", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "1303"}, "abstract": "The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.", "doi": "10.1038/s41598-020-58025-3", "pmid": "31992756", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Microbial Single Cell Genomics": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-58025-3"}, {"db": "pmc", "key": "PMC6987183"}], "notes": [], "created": "2020-02-03T10:35:42.153Z", "modified": "2024-01-16T13:48:43.036Z"}]}