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Another dark taxon comes to light: Semicentenialomycetes, a new class within the Pucciniomycotina (Basidiomycota), and its described living representative, Semicentenialea rex

Veera Tuovinen Nogerius — Wed, 28 Jan 2026 00:00:00 GMT

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.

Data for "New deep-branching environmental plastid genomes on the algal tree of life"

Mahwash Jamy — Tue, 28 Oct 2025 00:00:00 GMT

Data associated with the manuscript "New deep-branching environmental plastid genomes on the algal tree of life" (Jamy et al 2025). It includes the plastid MAGs (metagenome-assembled genomes), along with individual gene alignments, concatenated and trimmed alignments, and maximum-likelihood and Bayesian tree files for the phylogenomic dataset. General informationAuthor: Jamy et al, 2025 Contact email: mahwash.jamy@slu.se DOI: https://doi.org/10.17044/scilifelab.28212173 License: CC BY 4.0 Last updated: 2025-10-27 Please cite as: Jamy et al (2025). Data for "New deep-branching environmental plastid genomes on the algal tree of life". https://doi.org/10.17044/scilifelab.28212173 Corresponding manuscript: Jamy M, Huber T, Antoine T, Ruscheweyh HJ, Paoli L, Pelletier E, Delmont TO, Burki F. New deep-branching environmental plastid genomes on the algal tree of life. bioRxiv. 2025:2025-01. https://doi.org/10.1101/2025.01.16.633336

Phylogenomics of aquatic bacteria

Krzysztof Jurdzinski — Mon, 17 Feb 2025 00:00:00 GMT

Intermediate data files obtained during the work on the manuscript "Phylogenomics of aquatic bacteria reveal molecular mechanisms behind the limits of their adaptation to salinity". The files published here were used at various stages of the analysis (or sum-up the stages) and should allow reproduction of the results as well as expanded investigation of the dataset. These files are: ar_mags_info.txt - information table for collected archeal MAGs. It contains names of the MAGs in format {data source 2-letter code}_{name of the MAG as in ENA}, the biome of origin and taxonomic classification. For the brackish MAGs there is also annotation to the basin (Baltic/Caspian) of origin and additional metadata for the Baltic Sea MAGs. bac_mags_info.txt - information table for collected bacterial MAGs. It contains names of the MAGs in format {data source 2-letter code}_{name of the MAG as in ENA}, the biome of origin and taxonomic classification. For the brackish MAGs there is also annotation to the basin (Baltic/Caspian) of origin and additional metadata for the Baltic Sea MAGs. CheckM_all_MAGs.csv - CheckM results for all the investigated MAGs (completness, contamination, strain heterogeneity). ani_file.txt - average nucleotide indentity between all the pairs of investigated MAGs. MAG-cluster-stats-interbiome-clusters.xlsx - Excel file with a table annotating MAGs to >95% ANI clusters and the represtatives chosen for further analysis marked. Contains also sheets with just the representatives, clusters common between the brackish basins and between the biomes, as well as MSG_table.tsv imported into Excel spreadsheet. The first sheet also contains accession numbers for the bacterial MAGs used in this study. nozero.bifurc.bac.tree.nwk - phylogenetic tree of all the MAGs and GTDB reference genomes. Obtained using GTDB-tk. pruned95.nozero.bifurc.bac.tree.nwk - the phylogenetic tree (nozero.bifurc.bac.tree.nwk) pruned to contain only one represtative for a biome from each >95% ANI cluster. Does not contain GTDB reference genomes. subsampled.pruned95.nozero.bifurc.bac.tree.nwk - the phylogenetic tree with >95% ANI cluster respresntatives further randomly pruned the same number of freshwater and marine representatives. timetree_evo_rate_100.nwk - the full phylogenetic tree (nozero.bifurc.bac.tree.nwk) with branch length adjusted to correspond to estimated times since divergence in mya [million years ago]. time_calibration.txt - constraint file used for estimating time since divergence, input for RelTime (MEGA11). Minimal estimates of time since host species diverged [mya], based on the fossil record, were used to set the constraints MSG_table.tsv - a table (tab-separated) with all the MAGs within identified monobiomic sister groups (MSGs), annotated to appropriate transition_ID, biome and transition type. Taxonomic classification and transition times and directions are also included. make_MSG_table.R - R script used to make MSG_table.tsv. assess_datetree.R - R scirpt used to find the cross-biome transitions on the time-adjusted phylogenetic tree and obtained the information about the estimated time since they occured. transition_directions.R - R script used to estimate the ancestral biome-states of MRCAs (most recent common ancestors) of MSG pair and thus infer the most probable transition directions. all_MSG_ids.txt - a text file with names of all the representative MAGs within all the MSG pairs. filter_MSGs.py - a Python script to extract the MAGs from within the MSGs (given all_MSG_ids.txt) from a folder containing a larger set of sequences. Snakefile_proteins - Snakefile with a pipeline to go from nucleotide MAG sequences to pepstats statistics for inferred proteins. Includes proteome inference step using Prodigal (same procedure was used to infer amino-acid sequences for other purposes, including the taxonomic classification and reconstruction of the phylogenetic tree). MSGs_whole_proteomes.py - a Python script to concatanate inferred proteomes into continous amino acid sequences (for amino acid usage statistics). Snakefile_whole_proteome - Snakefile with a pipeline to obtain amino acid relative frequencies within proteomes. As an input takes proteomes in form of one continous sequence (MSGs_whole_proteomes.py output). MSGs_pI_rel_freq_table.tsv - a table (tab separated) with relative frequencies of proteins with pIs (isoelectric points) within 0.5 pH wide bins. aa_freqs_MSGs_list.json and assessed_aas.tsv - a json file with amino acid relative frequencies for each inferred proteome and a tab-separated list of IUPAC amino acid codes in order corresponding to values in the list. aa_cat_freqs_MSGs_list.json and assessed_aa_cats.tsv - a json file with relative frequencies of amino acid categories for each inferred proteome and a tab-separated list names of the categories ordered accoridngly as in the .json file. pI_aa_statistics.xlsx - statistics (p-values and differences sizes) for pairwise comparisons of inferred proteome properties and composition, i.e. i) relative frequencies of acidic, neutral and basic (isoelectric point (pI) categories) proteins ; ii) genome sizes as defined by number of inferred protein-coding genes; iii) amino acid relative frequencies; iv) relative frequencies of amino acids categories. {transition type}.annotation.gz and MSG_ids_{transition type}_pairs.txt - annotation files (zipped) of inferred genes for random pairs of MAGs from each MSG pair, together with text file with MSG represntatives. Seperate pair of files for each transition type. Used for investigating coannotation. ko_annot_full_everything.tsv - table with multilevel annotation of KEGG orthologs, adpoted from KEGG orthology website ko_anno.rar - compressed table with numbers of genes annotated to respective KEGG orthologs in representative genomes from all the >95% ANI bacterial clusters (used for gene gain/loss analysis). iterate_rarefying.R - R script used to indentify the differentially present genes. gain_loss_tables.xlsx - Sheets 1-3: results of MSG-based (phylogeny-aware) gene content analysis. Tables with all the significant (FDR < 0.1, shaded in orange) differentially present genes across pairs of MSGs. For FB and FM type transitions additional genes were added to the table to show at least the top 25 most significant genes regardless of the FDR values. Sheets 4-6: Biome(s) in which the differentially present KOs were found across the identified transitions (MSG pairs), i.e. the data presented in Fig. 6 in text form and annotated to more specific taxa and single transition events. Includes taxonomic annotation of the transitions and numbers of bacterial species in MSGs from respective biomes. Sheets 7-9: Fraction of cases in which gene A (row) was also annotated as gene B (column), based on {transition type}.annotation.gz files. Sheets 10-12: Results of phylogeny-unaware gene content analysis. Tables with all the significant (FDR < 0.1) differentially present genes from an unpaired comparison of all bacterial species from each biome.

Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis

Anna Rosling — Mon, 20 May 2024 00:00:00 GMT

- Suppl datafile 1 MCGC_Shadi_10_21-with analysis 2023 This file contains the analysis and results presence / absence for so called Missing Core Glomeromycota Genes (MCGC). - Suppl datafile 2 CAZyme_22_10-31 This file contains the gene family counts for CAZyme families, as well as an analysis of families previously identified as Plant Cell Wall Degrading Enzymes (PCWDE) and familes selected for Figure 2 in the manuscript. Files with summary statistics from comparative genomic analysis based on Funnanotate and used for the anlaysis in the paper: busco-complete-summary-Shadis-genomes; CAZyme.all.results; CAZyme.summar.results; MEROPS.all.results; MEROPS.summary.results; pfam.results; signalp Ancestral reconstruction trees for CAZyme families and Peptideases with significant changes are available in the files Cazyme_trees and plots_peptidases_pdf.

Growth analysis of Apilactobacillus kunkeei strains

Christian Seeger — Tue, 04 Oct 2022 00:00:00 GMT

Growth analysis of Apilactobacillus kunkeei strains used for manuscript "Dyrhage et al. Genome Evolution of a Symbiont Population for Pathogen Defence in Honeybees, Genome Biology and Evolution, 2022." The dataset contains the raw data from the Bioscreen C instrument, the column names and the RMarkdown scripts for analysis of the individual growth experiments. A summary file (EXP-20-BQ4058_growthanalysis.summary.Rmd) merges the results from the individual experiments to produce the final summary of growth kinetics for all the tested strains. *growthanalysis.csv: raw growthdata from Bioscreen C *growthanalysis.colnames.csv: sample IDs used in the corresponding *Akunkeei.Rmd scripts to associate plate position with the sample. *Akunkeei.Rmd: RMarkdown script to analyze the growthdata using the growthcurver package EXP-20-BQ4058_growthanalysis.summary.Rmd: RMarkdown script to combine the collected growthdata and to generate the results that are part of "Dyrhage et al. Genome Evolution of a Symbiont Population for Pathogen Defence in Honeybees, Genome Biology and Evolution, 2022."

Bayesian NrdA phylogeny

Daniel Lundin — Thu, 09 Jan 2020 00:00:00 GMT

Bayesian phylogeny of NrdA, class I ribonucleotide reductase catalytic component. Sequences from NCBI's RefSeq and Genbank databases (Haft et al. 2018; https://doi.org/10.1093/nar/gkx1068), downloaded March 2019, was searched with subclass specific HMMER (Eddy 2011; https://doi.org/10.1371/journal.pcbi.1002195) profiles for NrdA and NrdJ, class II RNR, serving as outgroup, (Lundin et al. in preparation). The resulting sequences were clustered at 60% identity with UCLUST (Edgar 2010; https://doi.org/10.1093/bioinformatics/btq461) to create a representative set of sequences. After manual inspection of sequences, 342 out of 27821 original NrdA sequences remained, plus 26 NrdJ sequences selected for aligning well to NrdA. The sequences were aligned with ProbCons (Do et al. 2005; https://doi.org/10.1101/gr.2821705) and 283 reliably aligned positions were selected with BMGE (Criscuolo & Gribaldo 2010; https://doi.org/10.1186/1471-2148-10-210) using the BLOSUM30 matrix. The alignment file is NrdA_uc0.60.NrdJ_uc0.30_outgroup.intr.correct.nolb.co.profile.BLOSUM30.bmge.mb.nxs. A bayesian phylogeny was estimated with MrBayes v. 3.2.6 (Ronquist & Huelsenbeck 2003; https://doi.org/10.1093/bioinformatics/btg180; https://github.com/NBISweden/MrBayes) using a gamma distribution for rate variation and rjMCMC to jump between amino acid models. MrBayes was run with four chains and five runs until average standard deviation of split frequencies reached 0.015. (See NrdA_uc0.60.NrdJ_uc0.30_outgroup.intr.correct.nolb.co.profile.BLOSUM30.bmge.mb.) The phylogeny, in Dendroscope (Huson et al. 2007; https://doi.org/10.1186/1471-2105-8-460) nexml format, isNrdA_uc0.60.NrdJ_uc0.30_outgroup.intr.correct.nolb.co.profile.BLOSUM30.bmge.mb.con.fullname.nexml .

NrdBik phylogeny

Daniel Lundin — Mon, 01 Jul 2019 00:00:00 GMT

Maximum likelihood phylogeny of NrdBk and NrdBi class I ribonucleotide reductase radical generating subunits. Sequences from NCBI's RefSeq database (Haft et al. 2018; https://doi.org/10.1093/nar/gkx1068), downloaded July 2018, was searched with subclass specific HMMER (Eddy 2011; https://doi.org/10.1371/journal.pcbi.1002195) profiles from RNRdb (http://rnrdb.pfitmap.org) representing the NrdBk and NrdBi subclasses plus an outgroup consisting of NrdBe and NrdBn. The choice of outgroup was made by analysis of the full NrdB phylogeny presented in Grinberg et al. 2018 (https://doi.org/10.7554/eLife.31529). The resulting sequences were clustered at 70% identity with UCLUST (Edgar 2010; https://doi.org/10.1093/bioinformatics/btq461) to create a representative set of sequences. After manual inspection of sequences, 144 out of 7725 original sequences remained. The sequences were aligned with ProbCons (Do et al. 2005; https://doi.org/10.1101/gr.2821705) and 158 reliably aligned positions were selected with BMGE (Criscuolo & Gribaldo 2010; https://doi.org/10.1186/1471-2148-10-210) using the BLOSUM30 matrix. The alignment file is NrdBik_with_NrdBen.uc0.70.c.pb.BLOSUM30.bmge.alnfaa. A maximum likelihood phylogeny was estimated using RAxML v. 8.2.4 (Stamatakis 2014; https://doi.org/10.1093/bioinformatics/btu033) with the PROTGAMMAAUTO model using the rapid bootstopping algorithm and subsequent maximum likelihood search. The phylogeny, in Dendroscope (Huson et al. 2007; https://doi.org/10.1186/1471-2105-8-460) nexml format, is NrdBik_with_NrdBen.uc0.70.c.pb.BLOSUM30.bmge.PROTGAMMAAUTO.raxml.bipartitions.nexml.

dN/dS calculation of Thermus virus NrdJm evolution

Daniel Lundin — Tue, 29 Jan 2019 00:00:00 GMT

A log ratio test of significant overrepresentation of non-synonymous to silent (dN/dS) was estimated with codonml from PAML (Yang 1997, https://doi.org/10.1093/bioinformatics/13.5.555 ; Yang 2007, https://doi.org/10.1093/molbev/msm088) by running the program with a fixed and free dN/dS respectively, and the branch leading to the two Thermus virus sequences (marked with “#1” in reftree.newick) designated as the “foreground” branch in the free dN/dS run. This analysis was performed on the Thermus virus/Firmicutes subtree in https://doi.org/10.17045/sthlmuni.7117430.v2, using the same alignment as for the full tree, reverse translated into nucleotides. We could not find correct gene sequences for seven taxa (RefSeq accession numbers: WP_102410887, WP_033167051, WP_054955013, WP_065068364, WP_088370373, WP_087372021, WP_093315575), so they were left out of the analysis. Scripts in files ending with .codeml; output in .codeml.out files.

LysM phylogeny including Datisca glomerata and Ceanothus thyrsiflorus

Daniel Lundin — Tue, 29 May 2018 00:00:00 GMT

Phylogeny of LysM paralogs with sequences harvested from newly sequenced transcriptomes from Datisca glomerata and Ceanothus thyrsiflorus plus the following species as references: Arabidopsis thaliana, Cicer arietinum, Cucurbita pepo, Fragaria vesca, Glycine max, Lotus japonicus, Manihot esculenta, Medicago trunculata, Morus notabilis, Oryza sativa, Prunus persica, Ricinus communis, Solanum lycopersicum, Sorghum bicolor, Theobroma cacao, Vigna radiata and Ziziphus jujuba. Sequences were collected with blastp searches against the RefSeq database subset by the above list of species, using presumed D. glomerata and C. thyrsiflorus orthologs. Sequences were aligned with Clustal Omega (http://www.clustal.org/omega/; Sievers et al. 2014) and reliable alignment positions were selected with the BMGE algorithm (Criscuolo and Gribaldo 2010) using the BLOSUM62 substitution matrix. Sequences that were identical after BMGE, were discarded. The tree was estimated with RAxML v. 8.2.4 (https://sco.h-its.org/exelixis/web/software/raxml/index.html; Stamatakis 2014) using the PROTGAMMAAUTO model and automatic bootstopping. Files provided are: 1. The full alignment after BMGE selection of positions and removal of identical sequences: lysm.refseq_harvest_plus_selected.co.BLOSUM62.bmge.rx.red.phylip 2. The maximum likelihood tree labelled with bootstrap values in:a. newick format: lysm.refseq_harvest_plus_selected.co.BLOSUM62.bmge.rx.red.PROTGAMMAAUTO.raxml.besttree.newickb. Dendroscope (http://dendroscope.org/; Huson et al. 2007): lysm.refseq_harvest_plus_selected.co.BLOSUM62.bmge.rx.red.PROTGAMMAAUTO.raxml.bipartitions.nexml

NrdJd/NrdJa+b + unclassified NrdJ phylogeny

Daniel Lundin — Thu, 06 Jul 2017 00:00:00 GMT

Maximum likelihood phylogeny (RAxML; Stamatakis 2014) of representatives of 75% identity clusters of the full diversity of class II ribonucleotide reductases except monomeric, subclass NrdJm. Reliable positions in Probcons (Do et al. 2005) alignment selected with the BMGE algorithm using the BLOSUM30 matrix (Criscuolo & Gribaldo 2010) PROTGAMMAAUTO model. File can be opened in Dendroscope (http://dendroscope.org/) and other tree viewers.