{"entity": "researcher", "timestamp": "2026-08-15T13:31:26.899Z", "family": "Bass", "given": "David", "initials": "D", "orcid": "0000-0002-9883-7823", "affiliations": ["Department of Life Sciences Natural History Museum London UK", "Centre for Environment Fisheries and Aquaculture Science (Cefas) Weymouth UK"], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5b8a1f98bf6430c8a04b7c8d74a2c58.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5b8a1f98bf6430c8a04b7c8d74a2c58"}}, "publications": [{"entity": "publication", "iuid": "cc3f8abcb67b4ff2863f9c71ba7b2d04", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cc3f8abcb67b4ff2863f9c71ba7b2d04.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cc3f8abcb67b4ff2863f9c71ba7b2d04"}}, "title": "Long-read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity.", "authors": [{"family": "Jamy", "given": "Mahwash", "initials": "M", "orcid": "0000-0002-2930-9226", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/24e76a7ec6fe4bb29f02ad43f701fdea.json"}}, {"family": "Foster", "given": "Rachel", "initials": "R"}, {"family": "Barbera", "given": "Pierre", "initials": "P"}, {"family": "Czech", "given": "Lucas", "initials": "L"}, {"family": "Kozlov", "given": "Alexey", "initials": "A"}, {"family": "Stamatakis", "given": "Alexandros", "initials": "A"}, {"family": "Bending", "given": "Gary", "initials": "G"}, {"family": "Hilton", "given": "Sally", "initials": "S"}, {"family": "Bass", "given": "David", "initials": "D", "orcid": "0000-0002-9883-7823", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5b8a1f98bf6430c8a04b7c8d74a2c58.json"}}, {"family": "Burki", "given": "Fabien", "initials": "F"}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "issn-l": "1755-098X", "volume": "20", "issue": "2", "pages": "429-443"}, "abstract": "High-throughput DNA metabarcoding of amplicon sizes below 500 bp has revolutionized the analysis of environmental microbial diversity. However, these short regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. This lesser phylogenetic resolution of short amplicons may be overcome by new long-read sequencing technologies. To test this idea, we amplified soil DNA and used PacBio Circular Consensus Sequencing (CCS) to obtain an ~4500-bp region spanning most of the eukaryotic small subunit (18S) and large subunit (28S) ribosomal DNA genes. We first treated the CCS reads with a novel curation workflow, generating 650 high-quality operational taxonomic units (OTUs) containing the physically linked 18S and 28S regions. To assign taxonomy to these OTUs, we developed a phylogeny-aware approach based on the 18S region that showed greater accuracy and sensitivity than similarity-based methods. The taxonomically annotated OTUs were then combined with available 18S and 28S reference sequences to infer a well-resolved phylogeny spanning all major groups of eukaryotes, allowing us to accurately derive the evolutionary origin of environmental diversity. A total of 1,019 sequences were included, of which a majority (58%) corresponded to the new long environmental OTUs. The long reads also allowed us to directly investigate the relationships among environmental sequences themselves, which represents a key advantage over the placement of short reads on a reference phylogeny. Together, our results show that long amplicons can be treated in a full phylogenetic framework to provide greater taxonomic resolution and a robust evolutionary perspective to environmental DNA.", "doi": "10.1111/1755-0998.13117", "pmid": "31705734", "labels": {"Fabien Burki": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-09-28T11:56:20.550Z", "modified": "2022-11-04T11:32:15.260Z"}, {"entity": "publication", "iuid": "fc25db5ffd584d6289271119cfd64e89", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fc25db5ffd584d6289271119cfd64e89.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fc25db5ffd584d6289271119cfd64e89"}}, "title": "Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes.", "authors": [{"family": "Adl", "given": "Sina M", "initials": "SM", "orcid": "0000-0001-6324-6065", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e67d791e3f8d488b941e1b27d4689ca2.json"}}, {"family": "Bass", "given": "David", "initials": "D", "orcid": "0000-0002-9883-7823", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5b8a1f98bf6430c8a04b7c8d74a2c58.json"}}, {"family": "Lane", "given": "Christopher E", "initials": "CE"}, {"family": "Luke\u0161", "given": "Julius", "initials": "J", "orcid": "0000-0002-8679-8812", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/079b734d7dd14f3b9e3477563090fa0e.json"}}, {"family": "Schoch", "given": "Conrad L", "initials": "CL"}, {"family": "Smirnov", "given": "Alexey", "initials": "A"}, {"family": "Agatha", "given": "Sabine", "initials": "S"}, {"family": "Berney", "given": "Cedric", "initials": "C", "orcid": "0000-0001-8689-9907", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a08993669b14d389d0891eea58e0a70.json"}}, {"family": "Brown", "given": "Matthew W", "initials": "MW"}, {"family": "Burki", "given": "Fabien", "initials": "F"}, {"family": "C\u00e1rdenas", "given": "Paco", "initials": "P", "orcid": "0000-0003-4045-6718", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b70b2fbc150465d868ad2d833d5db47.json"}}, {"family": "\u010cepi\u010dka", "given": "Ivan", "initials": "I"}, {"family": "Chistyakova", "given": "Lyudmila", "initials": "L"}, {"family": "Del Campo", "given": "Javier", "initials": "J"}, {"family": "Dunthorn", "given": "Micah", "initials": "M", "orcid": "0000-0003-1376-4109", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66aa11c34b0b473a90bf51cd288351fc.json"}}, {"family": "Edvardsen", "given": "Bente", "initials": "B", "orcid": "0000-0002-6806-4807", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b1db56f2d8043ef98a2577e1fa97800.json"}}, {"family": "Eglit", "given": "Yana", "initials": "Y"}, {"family": "Guillou", "given": "Laure", "initials": "L"}, {"family": "Hampl", "given": "Vladim\u00edr", "initials": "V"}, {"family": "Heiss", "given": "Aaron A", "initials": "AA"}, {"family": "Hoppenrath", "given": "Mona", "initials": "M"}, {"family": "James", "given": "Timothy Y", "initials": "TY"}, {"family": "Karnkowska", "given": "Anna", "initials": "A"}, {"family": "Karpov", "given": "Sergey", "initials": "S"}, {"family": "Kim", "given": "Eunsoo", "initials": "E"}, {"family": "Kolisko", "given": "Martin", "initials": "M"}, {"family": "Kudryavtsev", "given": "Alexander", "initials": "A"}, {"family": "Lahr", "given": "Daniel J G", "initials": "DJG"}, {"family": "Lara", "given": "Enrique", "initials": "E", "orcid": "0000-0001-8500-522X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d59c662dc47d46e7975f519c6d709708.json"}}, {"family": "Le Gall", "given": "Line", "initials": "L", "orcid": "0000-0001-7807-4569", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e74fdb3407e47c68485b3e316d358e1.json"}}, {"family": "Lynn", "given": "Denis H", "initials": "DH", "orcid": "0000-0002-1554-7792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01e191f7465b4fa4af1556552a2e482c.json"}}, {"family": "Mann", "given": "David G", "initials": "DG"}, {"family": "Massana", "given": "Ramon", "initials": "R"}, {"family": "Mitchell", "given": "Edward A D", "initials": "EAD", "orcid": "0000-0003-0358-506X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9378a3ec8584f0f9da42b1000522f62.json"}}, {"family": "Morrow", "given": "Christine", "initials": "C"}, {"family": "Park", "given": "Jong Soo", "initials": "JS", "orcid": "0000-0001-6253-5199", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47e15e3c522e4c50b7d432119f76e0f8.json"}}, {"family": "Pawlowski", "given": "Jan W", "initials": "JW"}, {"family": "Powell", "given": "Martha J", "initials": "MJ"}, {"family": "Richter", "given": "Daniel J", "initials": "DJ"}, {"family": "Rueckert", "given": "Sonja", "initials": "S"}, {"family": "Shadwick", "given": "Lora", "initials": "L"}, {"family": "Shimano", "given": "Satoshi", "initials": "S"}, {"family": "Spiegel", "given": "Frederick W", "initials": "FW"}, {"family": "Torruella", "given": "Guifr\u00e9", "initials": "G", "orcid": "0000-0002-6534-4758", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77f8f948cf6e478c8716d2f136ed3a2d.json"}}, {"family": "Youssef", "given": "Noha", "initials": "N"}, {"family": "Zlatogursky", "given": "Vasily", "initials": "V", "orcid": "0000-0002-2688-3900", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21c74059cedc4132be6c8121406448bc.json"}}, {"family": "Zhang", "given": "Qianqian", "initials": "Q"}], "type": "journal article", "published": "2019-01-00", "journal": {"title": "J. Eukaryot. Microbiol.", "issn": "1550-7408", "issn-l": "1066-5234", "volume": "66", "issue": "1", "pages": "4-119"}, "abstract": "This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.", "doi": "10.1111/jeu.12691", "pmid": "30257078", "labels": {"Fabien Burki": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6492006"}], "notes": [], "created": "2020-09-28T12:01:42.279Z", "modified": "2022-11-04T11:32:16.932Z"}]}