Data from: ITS and LSU sequences of Tricholyophyllum rubrum sp. nov. and associated taxa
Data files
Jul 20, 2024 version files 34.81 KB
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README.md
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Tricholyophyllum_Dryad_deposition.fas
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Abstract
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.
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
DNA Extraction
DNA from exsiccata was extracted using the CTAB method of Gardes and Briuns (1993).
Polymerase Chain Reactions
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.
Phylogenetic analysis
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.
References
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. Phytotaxa, 312(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. Molecular biology and evolution, 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.