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

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.

本数据集包含用于描述八种青霉菌属和三种肉座菌属物种的DNA序列数据集、比对结果和系统发育树。数据集在MAFFT v. 7.490（Katoh & Standley 2013）软件中进行比对，并选择G-INS-I选项，比对结果在必要时通过Geneious软件手动修剪、调整和拼接。根据贝叶斯信息准则（Bayesian information criterion）和采用PartitionFinder v. 2.1（Lanfear et al. 2017）中实现的贪婪策略，选定了最合适的分区方案和替换模型，从而使得基因区段、内含子、外显子和密码子位置能够成为独立的独立数据集。系统发育树的构建采用最大似然法（Maximum Likelihood, ML）和贝叶斯树推断（Bayesian tree Inference, BI）两种方法。ML分析在IQtree v. 2.2.0（Minh et al. 2020）软件中完成，并通过1000次重复的bootstrap分析计算节点支持度。BI分析在MrBayes v. 3.2.7（Ronquist et al. 2012）软件中执行，使用三组四个链（1个冷链和3个热链），并停止于分裂频率平均标准差为0.01时，使用“stoprule”。树形图通过TreeViewer v. 2.0.1（https://treeviewer.org/）软件进行可视化，并在Affinity Publisher 2.0.3（Serif (Europe), Nottingham, UK）软件中进行编辑，以供发表。结果展示采用ML树拓扑结构，同时显示支持分支的bootstrap和后验概率值。比对、Partitionfinder结果和系统发育树已上传。