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Phylogenetic analyses used for the re-identification of Penicillium and Talaromyces catalogued in South African culture collections

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posted on 2024-05-14, 11:00 authored by Cobus VisagieCobus Visagie

DNA sequence datasets, alignments and phylogenetic trees used in a publication to describe eight Penicillium and three Talaromyces species. Datasets were aligned in MAFFT v. 7.490 (Katoh & Standley 2013) with the G-INS-I option selected, with alignments manually trimmed, adjusted and concatenated in Geneious where needed. The most appropriate partition schemes and substitution models were selected based on Bayesian information criterion using a greedy strategy implemented in PartitionFinder v. 2.1 (Lanfear et al. 2017), allowing gene regions, introns, exons and codon positions to be independent datasets. Phylogenies were calculated using both Maximum Likelihood (ML) and Bayesian tree Inference (BI). ML was performed in IQtree v. 2.2.0 (Minh et al. 2020) with support in nodes calculated using a bootstrap analysis of 1000 replicates. BI was performed in MrBayes v. 3.2.7 (Ronquist et al. 2012), with three sets of four chains (1 cold and three heated) and was stopped at an average standard deviation for split frequencies of 0.01 using the "stoprule". Trees were visualised in TreeViewer v. 2.0.1 (https://treeviewer.org/) and edited in Affinity Publisher 2.0.3 (Serif (Europe), Nottingham, UK) for publication. ML tree topologies were used to present the results, with both bootstrap and posterior probability values shown for the supported branches. Alignments, Partitionfinder results and phylogenetic trees were uploaded.


Funding

Foundational Biodiversity Information Programme (FBIP) of the National Research Foundation (NRF) of South Africa, Grant No: 110442

the European Union’s Horizon 2020 Research and Innovation Program (RISE) under the Marie Skłodowska-Curie, Grant No: 101008129

the University of Pretoria's University Capacity Development Programme (UCDP) Grant

History

Department/Unit

Forestry and Agricultural Biotechnology Institute

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