{"entity": "researcher", "timestamp": "2026-08-20T21:36:09.694Z", "family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274"}}, "publications": [{"entity": "publication", "iuid": "add2b8ce98554b33b638371a55661e85", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/add2b8ce98554b33b638371a55661e85.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/add2b8ce98554b33b638371a55661e85"}}, "title": "Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation.", "authors": [{"family": "Buzan", "given": "Elena", "initials": "E"}, {"family": "de Guttry", "given": "Christian", "initials": "C"}, {"family": "Bortoluzzi", "given": "Chiara", "initials": "C"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274.json"}}, {"family": "Lucek", "given": "Kay", "initials": "K", "orcid": "0000-0002-2253-2556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/34f501f8758e4bf491c1d6537167f952.json"}}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0664c029a14140b09f9f9f74440e8008.json"}}, {"family": "Ometto", "given": "Lino", "initials": "L", "orcid": "0000-0002-2679-625X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d1929464e274502afc6f33686ba5efe.json"}}, {"family": "Mouton", "given": "Alice", "initials": "A"}, {"family": "Marins", "given": "Lu\u00edsa S", "initials": "LS"}, {"family": "Ruiz-L\u00f3pez", "given": "Mar\u00eda Jos\u00e9", "initials": "MJ"}, {"family": "Melo-Ferreira", "given": "Jos\u00e9", "initials": "J", "orcid": "0000-0003-4473-1908", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0e8294f10334ab2a152fb70a3ef8698.json"}}, {"family": "Ottosson", "given": "Elisabet", "initials": "E"}, {"family": "Mazzoni", "given": "Camila J", "initials": "CJ", "orcid": "0000-0001-6758-5427", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eac18d3385e64bdd8d7799e6c1e2065e.json"}}, {"family": "Waterhouse", "given": "Robert M", "initials": "RM", "orcid": "0000-0003-4199-9052", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92337cf65e03479fb7d1a0d34c709dbe.json"}}], "type": "journal article", "published": "2025-12-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "34", "issue": "23", "pages": "e70001", "issn-l": "0962-1083"}, "abstract": "Biodiversity resilience relies on genetic diversity, which sustains the evolutionary potential of organisms in dynamic ecosystems. Genomics is a powerful tool for accurately estimating genetic diversity across genomes of species and populations. However, integration of genomic data into conservation efforts faces challenges due to the heterogeneity of approaches employed. Establishing common sets of standards for genomic data production and analysis is essential to consistently interpret results and clearly communicate outcomes to stakeholders. While the European Reference Genome Atlas (ERGA) community has contributed significantly to the standardisation of reference genome methodologies in synergy with other initiatives, there is now an urgent need to extend these principles to downstream analyses. ERGA aims to build on its experience to help establish harmonised approaches in applied biodiversity genomics research, aligned with ongoing efforts to define standardised metrics for measuring and reporting genetic diversity. Establishing consensus on best practices for genome-wide data generation methods and applications will substantially increase accuracy, interpretability, and comparability, together with enhanced stakeholder capacities. By identifying key opportunities and challenges, as well as conducting preliminary stakeholder mapping and examining case studies, the goal is to build an inclusive framework that ensures the relevance and widespread adoption of these best practices: fostering trust and confidence in genomics research practices to meet stakeholder needs in biodiversity conservation. We call upon the broader research community to join efforts in establishing these approaches, recognising the importance of participation of end-users, to foster the integration of genomic data into the toolkit for measuring and reporting genetic diversity.", "doi": "10.1111/mec.70001", "pmid": "40574266", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12684358"}], "notes": [], "created": "2026-08-20T11:19:01.976Z", "modified": "2026-08-20T11:19:02.141Z"}, {"entity": "publication", "iuid": "a7f307369cff411bb2b61f62432345f5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a7f307369cff411bb2b61f62432345f5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a7f307369cff411bb2b61f62432345f5"}}, "title": "An evo-devo resource for wood: Comparative regulomics across dicot and conifer trees", "authors": [{"family": "Hvidsten", "given": "Torgeir", "initials": "T", "orcid": "0000-0001-6097-2539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f385ace6dda41249296c3ca55adaaf6.json"}}, {"family": "Rodriguez", "given": "Eduardo", "initials": "E"}, {"family": "Birkeland", "given": "Siri", "initials": "S", "orcid": "0000-0002-8104-8537", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75849a804b7549d3b0a1b21707439f3e.json"}}, {"family": "Chapple", "given": "Ellen", "initials": "E"}, {"family": "Fredriksson", "given": "Samuel", "initials": "S"}, {"family": "Lorenzo", "given": "Zulema", "initials": "Z"}, {"family": "Kalman", "given": "Teitur", "initials": "T"}, {"family": "Kumar", "given": "Vikash", "initials": "V", "orcid": "0000-0003-1670-3491", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cab758e482a843c0b0d7ff7e64717413.json"}}, {"family": "Mccann", "given": "Jamie", "initials": "J"}, {"family": "Hill", "given": "Jason", "initials": "J", "orcid": "0000-0002-0151-8931", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a24b7bc510949189e95f46c3bb64135.json"}}, {"family": "Kjendseth", "given": "\u00c5smund", "initials": "\u00c5"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}, {"family": "Mellerowicz", "given": "Ewa", "initials": "E", "orcid": "0000-0001-6817-1031", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4c1dc447b23416196a7068026015506.json"}}, {"family": "Street", "given": "Nathaniel", "initials": "N", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274.json"}}], "type": "posted-content", "published": "2025-10-30", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-7656402/v1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:00:07.635Z", "modified": "2026-08-20T13:00:07.783Z"}, {"entity": "publication", "iuid": "0370b4ea41f14da9846a9c43cfa9fcf4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0370b4ea41f14da9846a9c43cfa9fcf4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0370b4ea41f14da9846a9c43cfa9fcf4"}}, "title": "A Metabolomics and Transcriptomics Resource for Identifying Candidate Genes in the Biosynthesis of Specialised Metabolites in Populus tremula.", "authors": [{"family": "Rydman", "given": "Sara M", "initials": "SM"}, {"family": "Lihavainen", "given": "Jenna", "initials": "J", "orcid": "0000-0001-7979-8876", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/243306dc35c54c02b15933e323f27137.json"}}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM", "orcid": "0000-0002-5249-604X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ade70e2e96145dc87e8dd758ffddae5.json"}}, {"family": "Jansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7906-6891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da3b149834d54e1684d45ca5cb775af5.json"}}, {"family": "Albrectsen", "given": "Benedicte R", "initials": "BR", "orcid": "0000-0002-9337-4540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0339baea628a462495b5b9556b875fbc.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274.json"}}], "type": "journal article", "published": "2025-10-09", "journal": {"title": "Physiol Plant", "issn": "1399-3054", "volume": "177", "issue": "5", "pages": "e70567", "issn-l": "0031-9317"}, "abstract": "This study aims to identify candidate genes involved in the biosynthesis of salicinoid phenolic glycosides (SPGs), a group of specialised metabolites characteristic of the Salicaceae family. While the integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis, suitable multi-omics data resources are scarce. We present a comprehensive dataset comprising untargeted liquid chromatography-mass spectrometry (LC-MS) and mRNA-sequencing data from various organs of European aspen (Populus tremula L.) and from genotypes that produce contrasting sets of SPGs. We present a reproducible pipeline for the analysis of the LC-MS data, including predicted annotation of potential novel SPGs. We demonstrate the utility of the resource by identifying candidate genes involved in the biosynthesis of SPGs with a cinnamoyl moiety. By integrating gene and metabolite differential analyses with a gene co-expression network, we identified two HXXXD-type acyltransferase genes and one UDP-glucosyltransferase gene as candidates for future downstream characterisation. The combined gene expression and metabolomics resource is integrated into PlantGenIE.org to facilitate easy access and data mining. All raw data are available in public databases, and all data and results files are available at an associated Figshare repository.", "doi": "10.1111/ppl.70567", "pmid": "41063380", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12508522"}], "notes": [], "created": "2026-08-20T11:19:21.768Z", "modified": "2026-08-20T11:19:21.959Z"}, {"entity": "publication", "iuid": "4b2bd02c88e246a39e79bf13c9bafb55", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4b2bd02c88e246a39e79bf13c9bafb55.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4b2bd02c88e246a39e79bf13c9bafb55"}}, "title": "1000 conifer genomes: Genome innovation, organisation and diversity", "authors": [{"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Kalman", "given": "Teitur Ahlgren", "initials": "TA"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Eriksson", "given": "Mimmi", "initials": "M", "orcid": "0000-0002-9548-8226", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8736c6470734a65a6b4bb81efd4ce84.json"}}, {"family": "Hill", "given": "Jason", "initials": "J"}, {"family": "Kumar", "given": "Vikash", "initials": "V"}, {"family": "Larsson", "given": "Tomas", "initials": "T"}, {"family": "M\u00e4hler", "given": "Niklas", "initials": "N"}, {"family": "Nandi", "given": "Soumyadeep", "initials": "S"}, {"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47dae455224d4af4a35865907088f0b1.json"}}, {"family": "Valk", "given": "Tom van der", "initials": "Tvd"}, {"family": "Zuccolo", "given": "Andrea", "initials": "A"}, {"family": "Chen", "given": "Zhi Qiang", "initials": "ZQ"}, {"family": "Barcala", "given": "Maximiliano Estravis", "initials": "ME"}, {"family": "Rodriguez", "given": "Eduardo", "initials": "E"}, {"family": "Funda", "given": "Tom\u00e1\u0161", "initials": "T"}, {"family": "Chaudhary", "given": "Rajiv", "initials": "R"}, {"family": "Birkeland", "given": "Siri", "initials": "S"}, {"family": "Olsen", "given": "Remi Andre", "initials": "RA"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Mccann", "given": "Jamie", "initials": "J"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}, {"family": "Canovi", "given": "Camilla", "initials": "C"}, {"family": "Piombo", "given": "Edoardo", "initials": "E"}, {"family": "Lorenzo", "given": "Zulema Carracedo", "initials": "ZC"}, {"family": "Zalen", "given": "Elena van", "initials": "Ev"}, {"family": "Suontama", "given": "Mari", "initials": "M"}, {"family": "Hallingb\u00e4ck", "given": "Henrik", "initials": "H"}, {"family": "Mosbech", "given": "Mai Britt", "initials": "MB"}, {"family": "Vassilieff", "given": "Helena", "initials": "H"}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Bakker", "given": "Linda", "initials": "L"}, {"family": "Schijlen", "given": "Elio", "initials": "E"}, {"family": "Benstein", "given": "Ruben", "initials": "R", "orcid": "0000-0002-5799-7572", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c22a29452d1548d9939ba592587c322c.json"}}, {"family": "Sundstr\u00f6m", "given": "Jens", "initials": "J", "orcid": "0000-0003-2848-5284", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3f874bf5d22d447293d5fa7f774baa5d.json"}}, {"family": "Westrin", "given": "Karl Johan", "initials": "KJ"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Pettersson", "given": "Olga", "initials": "O"}, {"family": "Hvidsten", "given": "Torgeir", "initials": "T", "orcid": "0000-0001-6097-2539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f385ace6dda41249296c3ca55adaaf6.json"}}, {"family": "Sherwood", "given": "Ellen", "initials": "E"}, {"family": "Ingvarsson", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0001-9225-7521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb09a6889bc64651ac6eb90b67edca3d.json"}}, {"family": "Wu", "given": "Harry", "initials": "H", "orcid": "0000-0002-7072-4704", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d09d9cea430d4bf7907374fd9fc44b18.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eacfdf2095e947e99ac45fe994261b72.json"}}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33ba67b99d2b477d9588d40e8cc0fed2.json"}}, {"family": "Street", "given": "Nathaniel", "initials": "N", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274.json"}}], "type": "posted-content", "published": "2025-05-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-6502828/v1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:59:45.001Z", "modified": "2026-08-20T12:59:45.202Z"}, {"entity": "publication", "iuid": "e76b8f1df8744c0d9d05c9ae95c82b8f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e76b8f1df8744c0d9d05c9ae95c82b8f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e76b8f1df8744c0d9d05c9ae95c82b8f"}}, "title": "Data-driven resources and computational tools in non-model plant species.", "authors": [{"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274.json"}}], "type": "editorial", "published": "2025-02-20", "journal": {"title": "Physiol Plant", "issn": "1399-3054", "volume": "177", "issue": "1", "pages": "e70133", "issn-l": "0031-9317"}, "abstract": null, "doi": "10.1111/ppl.70133", "pmid": "39972994", "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:19:19.963Z", "modified": "2026-08-20T11:19:20.023Z"}, {"entity": "publication", "iuid": "c86387afec0548ab9e7e1efdc06956fd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c86387afec0548ab9e7e1efdc06956fd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c86387afec0548ab9e7e1efdc06956fd"}}, "title": "A resource of identified and annotated lincRNAs expressed during somatic embryogenesis development in Norway spruce.", "authors": [{"family": "Canovi", "given": "Camilla", "initials": "C"}, {"family": "Stojkovi\u010d", "given": "Katja", "initials": "K"}, {"family": "Ben\u00edtez", "given": "Aar\u00f3n Ayll\u00f3n", "initials": "AA"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Egertsdotter", "given": "Ulrika", "initials": "U"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274.json"}}], "type": "journal article", "published": "2024-09-25", "journal": {"title": "Physiol Plant", "issn": "1399-3054", "volume": "176", "issue": "5", "pages": "e14537", "issn-l": "0031-9317"}, "abstract": "Long non-coding RNAs (lncRNAs) have emerged as important regulators of many biological processes, although their regulatory roles remain poorly characterized in woody plants, especially in gymnosperms. A major challenge of working with lncRNAs is to assign functional annotations, since they have a low coding potential and low cross-species conservation. We utilised an existing RNA-Sequencing resource and performed short RNA sequencing of somatic embryogenesis developmental stages in Norway spruce (Picea abies L. Karst). We implemented a pipeline to identify lncRNAs located within the intergenic space (lincRNAs) and generated a co-expression network including protein coding, lincRNA and miRNA genes. To assign putative functional annotation, we employed a guilt-by-association approach using the co-expression network and integrated these results with annotation assigned using semantic similarity and co-expression. Moreover, we evaluated the relationship between lincRNAs and miRNAs, and identified which lincRNAs are conserved in other species. We identified lincRNAs with clear evidence of differential expression during somatic embryogenesis and used network connectivity to identify those with the greatest regulatory potential. This work provides the most comprehensive view of lincRNAs in Norway spruce and is the first study to perform global identification of lincRNAs during somatic embryogenesis in conifers. The data have been integrated into the expression visualisation tools at the PlantGenIE.org web resource to enable easy access to the community. This will facilitate the use of the data to address novel questions about the role of lincRNAs in the regulation of embryogenesis and facilitate future comparative genomics studies.", "doi": "10.1111/ppl.14537", "pmid": "39319989", "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:19:17.983Z", "modified": "2026-08-20T11:19:18.044Z"}, {"entity": "publication", "iuid": "7a6e3f3f8ec745eb8e1b8e3c2e5d43c7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7a6e3f3f8ec745eb8e1b8e3c2e5d43c7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7a6e3f3f8ec745eb8e1b8e3c2e5d43c7"}}, "title": "Genomic basis of the distinct biosynthesis of \u03b2-glucogallin, a biochemical marker for hydrolyzable tannin production, in three oak species.", "authors": [{"family": "Yang", "given": "Qinsong", "initials": "Q", "orcid": "0000-0002-9895-1917", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4841be2bec064e57ba36cd09dffbe2c6.json"}}, {"family": "Li", "given": "Jinjin", "initials": "J"}, {"family": "Wang", "given": "Yan", "initials": "Y", "orcid": "0009-0007-4804-6736", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7cce421866c47e994212de99e5d38c5.json"}}, {"family": "Wang", "given": "Zefu", "initials": "Z", "orcid": "0000-0002-5440-4188", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6b75a1fa8cf49db8db7adb6d053e9f2.json"}}, {"family": "Pei", "given": "Ziqi", "initials": "Z"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274.json"}}, {"family": "Bhalerao", "given": "Rishikesh P", "initials": "RP", "orcid": "0000-0003-4384-7036", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ddd69add89849b7bdeac3959ab9cfa6.json"}}, {"family": "Yu", "given": "Zhaowei", "initials": "Z"}, {"family": "Gao", "given": "Yuhao", "initials": "Y"}, {"family": "Ni", "given": "Junbei", "initials": "J"}, {"family": "Jiao", "given": "Yang", "initials": "Y"}, {"family": "Sun", "given": "Minghui", "initials": "M"}, {"family": "Yang", "given": "Xiong", "initials": "X"}, {"family": "Chen", "given": "Yixin", "initials": "Y"}, {"family": "Liu", "given": "Puyuan", "initials": "P"}, {"family": "Wang", "given": "Jiaxi", "initials": "J"}, {"family": "Liu", "given": "Yong", "initials": "Y"}, {"family": "Li", "given": "Guolei", "initials": "G", "orcid": "0000-0002-2244-4716", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/822709e7c15f4714a6e682f5df09e609.json"}}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "242", "issue": "6", "pages": "2702-2718", "issn-l": "0028-646X"}, "abstract": "Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used in grape wine aging, feed additives, and human healthcare. However, the limited availability of a high-quality reference genome of oaks greatly hampered the recognition of the mechanism of HT biosynthesis. Here, high-quality reference genomes of three Asian oak species (Quercus variabilis, Quercus aliena, and Quercus dentata) that have different HT contents were generated. Multi-omics studies were carried out to identify key genes regulating HT biosynthesis. In vitro enzyme activity assay was also conducted. Dual-luciferase and yeast one-hybrid assays were used to reveal the transcriptional regulation. Our results revealed that \u03b2-glucogallin was a biochemical marker for HT production in the cupules of the three Asian oaks. UGT84A13 was confirmed as the key enzyme for \u03b2-glucogallin biosynthesis. The differential expression of UGT84A13, rather than enzyme activity, was the main reason for different \u03b2-glucogallin and HT accumulation. Notably, sequence variations in UGT84A13 promoters led to different trans-activating activities of WRKY32/59, explaining the different expression patterns of UGT84A13 among the three species. Our findings provide three high-quality new reference genomes for oak trees and give new insights into different transcriptional regulation for understanding \u03b2-glucogallin and HT biosynthesis in closely related oak species.", "doi": "10.1111/nph.19711", "pmid": "38515244", "labels": [], "xrefs": [{"db": "figshare", "key": "10.6084/m9.figshare.23910282"}, {"db": "figshare", "key": "10.6084/m9.figshare.23911602"}, {"db": "figshare", "key": "10.6084/m9.figshare.23911776"}], "notes": [], "created": "2026-08-20T11:19:05.670Z", "modified": "2026-08-20T11:19:05.925Z"}, {"entity": "publication", "iuid": "a3655c24f81d4a16b7a1e5d2be6c48ea", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a3655c24f81d4a16b7a1e5d2be6c48ea.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a3655c24f81d4a16b7a1e5d2be6c48ea"}}, "title": "Effects of small-scale outplanting fertilization on conifer seedling growth and fungal community establishment", "authors": [{"family": "Schneider", "given": "Andreas N", "initials": "AN", "orcid": "0000-0001-5431-955X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48114cc89d3a4f559ea05c66d9e61025.json"}}, {"family": "Castro", "given": "David", "initials": "D", "orcid": "0000-0003-0836-6624", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56acf316faae4537a714d89b304c7b05.json"}}, {"family": "Holmlund", "given": "Mattias", "initials": "M"}, {"family": "N\u00e4sholm", "given": "Torgny", "initials": "T", "orcid": "0000-0002-2275-2030", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6c2139fefb42f6b3db3d24107e2d36.json"}}, {"family": "Hurry", "given": "Vaughan", "initials": "V", "orcid": "0000-0001-5151-5184", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd3bcd1b0bf9486a94c3db5e63d2629e.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274.json"}}], "type": "journal-article", "published": "2024-06-00", "journal": {"title": "Trees, Forests and People", "issn": "2666-7193", "volume": "16", "pages": "100568", "issn-l": null}, "abstract": null, "doi": "10.1016/j.tfp.2024.100568", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T08:05:09.584Z", "modified": "2026-08-20T08:05:09.864Z"}, {"entity": "publication", "iuid": "f356e1fd1654402bb52f82930872a056", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f356e1fd1654402bb52f82930872a056.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f356e1fd1654402bb52f82930872a056"}}, "title": "Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce.", "authors": [{"family": "Schneider", "given": "Andreas N", "initials": "AN", "orcid": "0000-0001-5431-955X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48114cc89d3a4f559ea05c66d9e61025.json"}}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Sundstr\u00f6m", "given": "G\u00f6rel", "initials": "G"}, {"family": "Richau", "given": "Kerstin", "initials": "K"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Hurry", "given": "Vaughan", "initials": "V"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274.json"}}], "type": "journal article", "published": "2021-02-16", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "6", "issue": "1", "issn-l": "2379-5077"}, "abstract": "The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.", "doi": "10.1128/mSystems.00884-20", "pmid": "33594001", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8573963"}, {"db": "pii", "key": "6/1/e00884-20"}], "notes": [], "created": "2026-08-20T12:01:03.176Z", "modified": "2026-08-20T12:01:03.198Z"}, {"entity": "publication", "iuid": "2b1afda1cd5845418c79f50889ce3074", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2b1afda1cd5845418c79f50889ce3074.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2b1afda1cd5845418c79f50889ce3074"}}, "title": "A major locus controls local adaptation and adaptive life history variation in a perennial plant", "authors": [{"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Ding", "given": "Jihua", "initials": "J"}, {"family": "Tan", "given": "Biyue", "initials": "B"}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM"}, {"family": "Michelson", "given": "Ingrid H", "initials": "IH"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33ba67b99d2b477d9588d40e8cc0fed2.json"}}, {"family": "Scofield", "given": "Douglas G", "initials": "DG", "orcid": "0000-0001-5235-6461", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a2cc7a4bad04f5ab664027a374f5698.json"}}, {"family": "Nilsson", "given": "Ove", "initials": "O", "orcid": "0000-0002-1033-1909", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec49ae91b4e54d749850771265c69812.json"}}, {"family": "Jansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7906-6891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da3b149834d54e1684d45ca5cb775af5.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274.json"}}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK", "orcid": "0000-0001-9225-7521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb09a6889bc64651ac6eb90b67edca3d.json"}}], "type": "posted-content", "published": "2017-08-21", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/178921", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:54:50.220Z", "modified": "2026-08-20T09:54:50.358Z"}]}