DOI: 10.5061/dryad.8w9ghx3w5
title: Data from: ITS and LSU sequences of Tricholyophyllum rubrum sp. nov. and associated taxa

description: Phylogenetic analysis of ITS and LSU sequence data and morphological
 characters support the recognition of Tricholyophyllum rubrum as a new
 species. The new species differs from the type species of the genus by its
 reddish brown pileus surface, the presence of pleurocystidia, and
 comparatively broader basidiospores. This is the first report of a
 Tricholyophyllum species from Pakistan and the second in the world.
description: <strong>DNA Extraction</strong>
 DNA from exsiccata was extracted using the CTAB method of Gardes
 and Briuns (1993). <strong>Polymerase Chain
 Reactions</strong> The internal transcribed
 spacer regions (ITS) and parts of LSU were amplified using the primer
 pairs of ITS1F (Gardes and Bruns 1993) and ITS4 (White et al. 1990)
 LR0R/LR5 (Vilgalys and Hester 1990) respectively. The PCR protocols for
 ITS and LSU followed those mentioned in Khan et al., (2018). The generated
 sequences were assembled in BioEdit software and searched for homology
 using BLAST tool at NCBI website. The closely matching sequences from the
 BLAST search and those mentioned in Cai et al., (2022) were downloaded and
 aligned using the online MAFFT software. A concatenated dataset of ITS-LSU
 was used to make the maximum likelihood tree. 
 <strong>Phylogenetic analysis</strong>
 Maximum Likelihood (ML) analyses were performed through the
 online IQ-TREE webserver at http://iqtree.cibiv.univie.ac.at/ (Nguyen et
 al. 2015). The tree was constructed using the ultrafast bootstrap method
 with 1000 bootstrap replicates. According to the Bayesian information
 criterion (BIC), the best-fit model was TIM2+F+G4 with a log-likelihood of
 −5587.28.
 <strong>References </strong>
 Gardes, M. and Bruns, T. D. 1993. ITS primers with enhanced
 specificity for basidiomycetes-application to the identification of
 mycorrhizae and rusts. – Mol. Ecol. 2: 113–118. Khan,
 J., Kiran, M., Jabeen, S., Sher, H., & Khalid, A. N. (2017).
 Gymnopilus penetrans and G. swaticus sp. nov.(Agaricomycota:
 Hymenogastraceae); a new record and a new species from northwest Pakistan.
 <em>Phytotaxa</em>, <em>312</em>(1),
 60-70. Nguyen, L. T., Schmidt, H. A., Von Haeseler, A.,
 & Minh, B. Q. (2015) IQ-TREE: a fast and effective stochastic
 algorithm for estimating maximum-likelihood phylogenies.
 <em>Molecular biology and evolution</em>, 32(1):
 268−274. Vilgalys, R. and Hester, M. 1990. Rapid
 genetic identification and mapping of enzymatically amplified DNA from
 several Cryptococcus species. – J. Bacteriol. 172: 4238–4246.
 White, T. J. et al. 1990. Amplification and direct sequencing of
 fungal ribosomal RNA genes for phylogenetics. – In: Innis, M. A. et al.
 (eds), PCR protocols: a guide to methods and applications. Academic Press,
 pp. 315–322.
description: # Data from: ITS and LSU sequences of Tricholyophyllum rubrum sp. nov. and
 associated taxa
 [https://doi.org/10.5061/dryad.8w9ghx3w5](https://doi.org/10.5061/dryad.8w9ghx3w5) The combined ITS-LSU dataset of Tricholyophyllumrubrum and associated taxa after trimming the motifs and ambiguous sites contained 1489 sites of which 1059 sites were constant, 457 distinct, and 278 parsimony informative. Upon ML analysis, the sequences of Pakistani collections (SH18 and SH20) clustered with *T. brunnneum *(HKAS 107494) from China forming a sister branch with a strong bootstrap value of 100%. A GenBank sequence of *Tephrocybe *sp. (PAM04112801) also clustered within the *Tricholoyophyllum* clade with a strong bootstrap support. The two separate clades, one with *Lyophyllum konradianum *(Maire) Kühner & Romagn.* *and the other containing *Tephrocybe mephetica *(Fr.) M.M. Moser were sister to the *Tricholyophyllum *clade. ## Description of the data and file structure This is the aligned dataset containing concatenated and aligned sequences (ITS and LSU) of Tricholyophyllum rubrum and associated taxa. ## Sharing/Access information Data was derived from the following sources: * SWAT001370 (Holotype) and SWAT001371 ## Code/Software BioEdit, MAFFT, MEGA11