Background data for "Combined short- and long-read metabarcoding of the soil fungi Archaeorhizomycetes reveals high phylogenetic diversity structured by vegetation and climate"

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Thoen, Ella, 2025, "Background data for "Combined short- and long-read metabarcoding of the soil fungi Archaeorhizomycetes reveals high phylogenetic diversity structured by vegetation and climate"", https://doi.org/10.18710/NCKZD7, DataverseNO, V1
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Description
Archaeorhizomycetes is a class of globally widespread soil-dwelling fungi, originally proposed to be associated with plant roots, but their ecology and nutritional mode are not clearly defined. Here, we have sequenced and aligned approximately 2500 bp of the ribosomal DNA from 18S (covering the V4 region), ITS and well into 28S. Sequences have been aligned using the 'linsi' algorithm in MAFFT v7.505 (Katoh & Standley, 2013). The alignment was trimmed for ambiguously aligned positions with trimAl using the –gappyout option (Capella_Gutiérrez et al., 2009).The phylogenetic tree was constructed with IQ-TREE v2.2.2.3 (Nguyen et al., 2015). The best fitting model was determined to be GTR+F+I+R5 by ModelFinder (Kalyaanamoorthy et al., 2017), and support values for the tree were calculated with the SH-like approximate likelihood ratio test (aLRT) and ultrafast bootstrap approximation UFBoot (Hoang et al., 2018), both with 1000 replicates. (2025-09-05)
Subject Earth and Environmental Sciences
Keyword ribosomal operon alignment, sequence alignment, Archaeorhizomycetes
Related Publication "Combined short- and long-read metabarcoding of the soil fungi Archaeorhizomycetes reveals high phylogenetic diversity structured by vegetation and climate" under review in New Phytologist.
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00_README.txt
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Published Sep 24, 2025
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MD5: 33785d08b1ac333e2c8d6522dda1c6cf
Read me file describing the dataset Archaeorhizomycetes alignment and tree 2500 bp long read sequences
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Archies_tree.newick
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Published Sep 24, 2025
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MD5: e93a18bd1b2638986d16cf601fbd5dc9
Tree file in .newick format of 120 Archaeorhizomycetes OTUs from Norway
Archies_trimmed_alignment.fasta
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Published Sep 24, 2025
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MD5: 823418450f706701b969d3aee49bb36b
Alignment file in .fasta format of 120 Archaeorhizomycetes OTUs from Norway
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