https://researchdata.se/sv/catalogue Search results sv Only a small fraction of the world’s fungi is described, and a large number of fungal sequences from environmental DNA (eDNA) currently lack relevant reference sequences for taxonomic identification in metabarcoding studies. Partially because there are several deeply divergent fungal lineages, including hypothesized class- and order-level lineages, currently known only by eDNA sequences. Here, we describe the first living representative of one such lineage (previously referred to as Clade GS25). We use a phylogenomic approach to test the placement and taxonomic rank hypothesized for this lineage, and present the formally described Semicentenialea rex, as the first known species in the novel class Semicentenialomycetes (Pucciniomycotina, Basidiomycota). Additionally, we provide the first phylogenomic resolution of Pucciniomycotina, using reference genomes from all described classes with the exception of Cryptomycocolacomycetes. We propose a set of practices that could be adopted by the research community to help facilitate more connections between living fungi and eDNA sequences. The use of such practices would in turn help to alleviate some of the complications associated with fungal DNA sequences in reference databases and contribute towards a more complete understanding of fungal diversity. Wed, 28 Jan 2026 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-26894242 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-26894242 Uppsala universitet Veera Tuovinen Nogerius Marisol Sanchez Garcia Kerri Kluting Jussi Heinonsalo Martin Ryberg Merje Toome Sajeet Haridas Stephen J. Mondo Kurt LaButti Matt Nolan Anna Lipzen Diane Bauer Igor V. Grigoriev Maxim Koriabine Mary Cathrine Aime Kerrie Barry Anna Rosling The data in this repository is the result of querying the PlutoF API (https://plutof.docs.apiary.io, Abarenkov et al 2010) with all sequence names in the UNITE general FASTA release (https://doi.org/10.15156/BIO/2959332; Abarenkov et al. 2024), in order to find the sequence hypothesis (SH) at level 1.5, version 10, for each sequence, resulting in a sequence-to-SH matching file (*.seq2SH.tsv). For each SH, the complete taxonomy is extracted from PlutoF by querying the PlutoF API, and stored in the *.SH.tax files. Files are available for UNITE version 10.0; sh_general_release_dynamic_04.04.2024.seq2sh.tsv.bz2 containing sequence to SH matchings, and sh_general_release_dynamic_04.04.2024.SHs.tax.bz2 containing SH taxonomies. Corresponding files are also available for the all eukaryotes version of the UNITE database (https://doi.org/10.15156/BIO/2959334; Abarenkov et al 2024b). All files are tab separated text files compressed with bzip2. Assignment of species hypothesis to ITS amplicons using this data and the UNITE general FASTA release is available as an optional argument to the nf-core/ampliseq Nextflow workflow from version 2.3.2: `--addsh` together with `--dada_ref_taxonomy unite-fungi` or `--dada_ref_taxonomy unite-alleuk` (https://nf-co.re/ampliseq; Straub et al. 2020). Generation of files After download and file extraction of the UNITE general FASTA release, each sequence name in the fasta file was used as query to PlutoF to find which SH at level 1.5 in release 10 the sequence belongs to, in order to generate the *.seq2sh.tsv files with sequence to SH matchings. Each SH was subsequently used as query to PlutoF to extract the complete taxonomy for the SH, stored in the *.SHs.tax files. Two python scripts for automatic querying and generation of the files can be found in the `scripts` folder in the GitHub repo: https://github.com/biodiversitydata-se/unite-shinfo. See the accompanying README file for usage information. Tue, 19 Nov 2024 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-19411403 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-19411403 Uppsala universitet Jeanette Tångrot