{"entity": "researcher", "timestamp": "2026-07-11T14:21:47.869Z", "family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "affiliations": ["Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyv\u00e4gen 18D, 752 36, Uppsala, Sweden. Anna.Rosling@ebc.uu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2"}}, "publications": [{"entity": "publication", "iuid": "3a1a5b9ee3754ffbb4b6a74c5b1396cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a1a5b9ee3754ffbb4b6a74c5b1396cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a1a5b9ee3754ffbb4b6a74c5b1396cd"}}, "title": "Forest Fire Influence on Tomicus piniperda-Associated Fungal Communities and Phloem Nutrient Availability of Colonized Pinus sylvestris.", "authors": [{"family": "Kluting", "given": "Kerri", "initials": "K"}, {"family": "Strid", "given": "Ylva", "initials": "Y"}, {"family": "Six", "given": "Diana", "initials": "D"}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "issn-l": "0095-3628", "volume": "86", "issue": "1", "pages": "224-239"}, "abstract": "Forest fire is known to positively affect bark beetle populations by providing fire-damaged trees with impaired defenses for infestation. Tomicus piniperda, the common pine shoot beetle, breeds and lays eggs under the bark of stressed pine trees and is considered a serious forest pest within its native range. Wood-colonizing fungi have been hypothesized to improve substrate quality and detoxify tree defensive chemistry to indirectly facilitate tree colonization by beetles. While some bark beetle species form symbiotic associations with fungi and actively vector their partners when colonizing new trees, T. piniperda does not have mycangia or body hairs for specific vectoring of fungi. To explore the T. piniperda-associated fungal community for signs of specific association, we used ITS metabarcoding to separately characterize fungal communities associated with surface and gut of male and female beetles. We also characterized the temporal changes in fungal community and nutrient status of pine phloem with and without beetle galleries. Sampling was performed 2 years after a natural forest fire and included both burnt and unburnt sites. In our study system, we find that forest fire significantly impacts the fungal community composition associated with T. piniperda and that fire may also indirectly change nutrient availability in phloem to beetle galleries. We conclude that T. piniperda can vector fungi to newly colonized trees but the absence of positive effects on substrate quality and minimal effects of sex indicate that vectoring of associated fungal communities is not a strategy associated with the T. piniperda life cycle.", "doi": "10.1007/s00248-022-02066-w", "pmid": "35831642", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10293462"}, {"db": "pii", "key": "10.1007/s00248-022-02066-w"}], "notes": [], "created": "2023-09-04T12:09:36.897Z", "modified": "2024-01-16T13:48:33.043Z"}, {"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": "436dafbcf3644397a7fb3f855f9e961a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/436dafbcf3644397a7fb3f855f9e961a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/436dafbcf3644397a7fb3f855f9e961a"}}, "title": "Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long-read metabarcoding.", "authors": [{"family": "Eshghi Sahraei", "given": "Shadi", "initials": "S", "orcid": "0000-0003-4741-5871", "researcher": {"href": "https://publications.scilifelab.se/researcher/98f7d11029704e33b61a8c27daa54378.json"}}, {"family": "Furneaux", "given": "Brendan", "initials": "B", "orcid": "0000-0003-3522-7363", "researcher": {"href": "https://publications.scilifelab.se/researcher/df196c994b3c4086b4f94eacf4e57239.json"}}, {"family": "Kluting", "given": "Kerri", "initials": "K", "orcid": "0000-0002-2328-8081", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc941190363e475e818618f5ede34218.json"}}, {"family": "Zakieh", "given": "Mustafa", "initials": "M"}, {"family": "Rydin", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-7582-3998", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee9ea3f8490b43128a5710c693855584.json"}}, {"family": "Hytteborn", "given": "H\u00e5kan", "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": "2022-03-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "12", "issue": "3", "pages": "e8676", "issn-l": "2045-7758"}, "abstract": "Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communities of microeukaryotes in soil. Here, we amplified and sequenced the ITS and LSU regions of the rDNA operon (around 1500 bp) from grassland soils using PacBio SMRT sequencing. We tested how three different methods for generation of operational taxonomic units (OTUs) effected estimated richness and identified taxa, and how well large-scale ecological patterns associated with shifting environmental conditions were recovered in data from the three methods. The field site at Kungs\u00e4ngen Nature Reserve has drawn frequent visitors since Linnaeus's time, and its species rich vegetation includes the largest population of Fritillaria meleagris in Sweden. To test the effect of different OTU generation methods, we sampled soils across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic-dry part that has a species rich grass-dominated plant community including a high frequency of F. meleagris. We used the moisture and plant community transition as a framework to investigate how detected belowground microeukaryotic community composition was influenced by OTU generation methods. Soil communities in both moisture regimes were dominated by protists, a large fraction of which were taxonomically assigned to Ciliophora (Alveolata) while 30%-40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of OTU generation method used. However, different methods strongly affect richness estimates and the taxonomic and phylogenetic resolution of the characterized community with implications for how well members of the microeukaryotic communities can be recognized in the data.", "doi": "10.1002/ece3.8676", "pmid": "35342585", "labels": {"NGI Long read": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8928899"}, {"db": "pii", "key": "ECE38676"}], "notes": [], "created": "2022-03-29T04:46:34.688Z", "modified": "2024-01-16T13:48:37.364Z"}, {"entity": "publication", "iuid": "c627962c4fb849df853d4ce183c38491", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c627962c4fb849df853d4ce183c38491.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c627962c4fb849df853d4ce183c38491"}}, "title": "Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities.", "authors": [{"family": "Furneaux", "given": "Brendan", "initials": "B", "orcid": "0000-0003-3522-7363", "researcher": {"href": "https://publications.scilifelab.se/researcher/df196c994b3c4086b4f94eacf4e57239.json"}}, {"family": "Bahram", "given": "Mohammad", "initials": "M", "orcid": "0000-0002-9539-3307", "researcher": {"href": "https://publications.scilifelab.se/researcher/26b5310cd872405aa2716c09a3f9d4bf.json"}}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}, {"family": "Yorou", "given": "Nourou S", "initials": "NS", "orcid": "0000-0001-6997-811X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a56781052962486cb78d1b4462a52fcb.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": "2021-08-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "issn-l": "1755-098X", "volume": "21", "issue": "6", "pages": "1833-1849"}, "abstract": "Fungi form diverse communities and play essential roles in many terrestrial ecosystems, yet there are methodological challenges in taxonomic and phylogenetic placement of fungi from environmental sequences. To address such challenges, we investigated spatiotemporal structure of a fungal community using soil metabarcoding with four different sequencing strategies: short-amplicon sequencing of the ITS2 region (300-400 bp) with Illumina MiSeq, Ion Torrent Ion S5 and PacBio RS II, all from the same PCR library, as well as long-amplicon sequencing of the full ITS and partial LSU regions (1200-1600 bp) with PacBio RS II. Resulting community structure and diversity depended more on statistical method than sequencing technology. The use of long-amplicon sequencing enables construction of a phylogenetic tree from metabarcoding reads, which facilitates taxonomic identification of sequences. However, long reads present issues for denoising algorithms in diverse communities. We present a solution that splits the reads into shorter homologous regions prior to denoising, and then reconstructs the full denoised reads. In the choice between short and long amplicons, we suggest a hybrid approach using short amplicons for sampling breadth and depth, and long amplicons to characterize the local species pool for improved identification and phylogenetic analyses.", "doi": "10.1111/1755-0998.13387", "pmid": "33811446", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-08-23T06:33:39.481Z", "modified": "2024-01-16T13:48:38.968Z"}, {"entity": "publication", "iuid": "f470c71971e84209bc3eef845edc1f9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f470c71971e84209bc3eef845edc1f9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f470c71971e84209bc3eef845edc1f9f"}}, "title": "Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa.", "authors": [{"family": "Meidl", "given": "Peter", "initials": "P"}, {"family": "Furneaux", "given": "Brendan", "initials": "B", "orcid": "0000-0003-3522-7363", "researcher": {"href": "https://publications.scilifelab.se/researcher/df196c994b3c4086b4f94eacf4e57239.json"}}, {"family": "Tchan", "given": "Kassim I", "initials": "KI"}, {"family": "Kluting", "given": "Kerri", "initials": "K"}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}, {"family": "Guissou", "given": "Marie-Laure", "initials": "ML"}, {"family": "Soro", "given": "Bakary", "initials": "B"}, {"family": "Traor\u00e9", "given": "A\u00efssata", "initials": "A"}, {"family": "Konomou", "given": "Gbamon", "initials": "G"}, {"family": "Yorou", "given": "Nourou S", "initials": "NS", "orcid": "0000-0001-6997-811X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a56781052962486cb78d1b4462a52fcb.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": "2021-06-11", "journal": {"title": "MycoKeys", "issn": "1314-4049", "volume": "81", "pages": "45-68", "issn-l": null}, "abstract": "Forests and woodlands in the West African Guineo-Sudanian transition zone contain many tree species that form symbiotic interactions with ectomycorrhizal (ECM) fungi. These fungi facilitate plant growth by increasing nutrient and water uptake and include many fruiting body-forming fungi, including some edible mushrooms. Despite their importance for ecosystem functioning and anthropogenic use, diversity and distribution of ECM fungi is severely under-documented in West Africa. We conducted a broad regional sampling across five West African countries using soil eDNA to characterize the ECM as well as the total soil fungal community in gallery forests and savanna woodlands dominated by ECM host tree species. We subsequently sequenced the entire ITS region and much of the LSU region to infer a phylogeny for all detected soil fungal species. Utilizing a long read sequencing approach allows for higher taxonomic resolution by using the full ITS region, while the highly conserved LSU gene allows for a more accurate higher-level assignment of species hypotheses, including species without ITS-based taxonomy assignments. We detect no overall difference in species richness between gallery forests and woodlands. However, additional gallery forest plots and more samples per plot would have been needed to firmly conclude this pattern. Based on both abundance and richness, species from the families Russulaceae and Inocybaceae dominate the ECM fungal soil communities across both vegetation types. The community structure of both total soil fungi and ECM fungi was significantly influenced by vegetation types and showed strong correlation within plots. However, we found no significant difference in fungal community structure between samples collected adjacent to different host tree species within each plot. We conclude that within plots, the fungal community is structured more by the overall ECM host plant community than by the species of the individual host tree that each sample was collected from.", "doi": "10.3897/mycokeys.81.66249", "pmid": "34475800", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8390883"}, {"db": "pii", "key": "66249"}], "notes": [], "created": "2022-11-24T15:07:20.969Z", "modified": "2022-11-24T15:07:21.002Z"}, {"entity": "publication", "iuid": "a2b1311ee277443ca4d6f14652b535cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2b1311ee277443ca4d6f14652b535cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2b1311ee277443ca4d6f14652b535cb"}}, "title": "Naming the untouchable - environmental sequences and niche partitioning as taxonomical evidence in fungi.", "authors": [{"family": "Kalsoom Khan", "given": "Faheema", "initials": "F"}, {"family": "Kluting", "given": "Kerri", "initials": "K"}, {"family": "T\u00e5ngrot", "given": "Jeanette", "initials": "J"}, {"family": "Urbina", "given": "Hector", "initials": "H"}, {"family": "Ammunet", "given": "Tea", "initials": "T"}, {"family": "Eshghi Sahraei", "given": "Shadi", "initials": "S"}, {"family": "Ryd\u00e9n", "given": "Martin", "initials": "M"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2020-11-03", "journal": {"title": "IMA Fungus", "issn": "2210-6340", "volume": "11", "issue": "1", "pages": "23", "issn-l": null}, "abstract": "Due to their submerged and cryptic lifestyle, the vast majority of fungal species are difficult to observe and describe morphologically, and many remain known to science only from sequences detected in environmental samples. The lack of practices to delimit and name most fungal species is a staggering limitation to communication and interpretation of ecology and evolution in kingdom Fungi. Here, we use environmental sequence data as taxonomical evidence and combine phylogenetic and ecological data to generate and test species hypotheses in the class Archaeorhizomycetes (Taphrinomycotina, Ascomycota). Based on environmental amplicon sequencing from a well-studied Swedish pine forest podzol soil, we generate 68 distinct species hypotheses of Archaeorhizomycetes, of which two correspond to the only described species in the class. Nine of the species hypotheses represent 78% of the sequenced Archaeorhizomycetes community, and are supported by long read data that form the backbone for delimiting species hypothesis based on phylogenetic branch lengths.Soil fungal communities are shaped by environmental filtering and competitive exclusion so that closely related species are less likely to co-occur in a niche if adaptive traits are evolutionarily conserved. In soil profiles, distinct vertical horizons represent a testable niche dimension, and we found significantly differential distribution across samples for a well-supported pair of sister species hypotheses. Based on the combination of phylogenetic and ecological evidence, we identify two novel species for which we provide molecular diagnostics and propose names. While environmental sequences cannot be automatically translated to species, they can be used to generate phylogenetically distinct species hypotheses that can be further tested using sequences as ecological evidence. We conclude that in the case of abundantly and frequently observed species, environmental sequences can support species recognition in the absences of physical specimens, while rare taxa remain uncaptured at our sampling and sequencing intensity.", "doi": "10.1186/s43008-020-00045-9", "pmid": "33292867", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s43008-020-00045-9"}, {"db": "pmc", "key": "PMC7607712"}], "notes": [], "created": "2020-11-11T15:11:33.579Z", "modified": "2024-01-16T13:48:41.430Z"}, {"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"}]}