Phylogenetic analysis

Preliminary identification of genes obtained from fresh strains by GenBank database. The LSU, ITS, SSU, TEF1-α, and RPB2 used for phylogenetic analysis are selected based on the preliminary identification results and the related publications (Yang et al. 2018; Monkai et al. 2020). The sequences were aligned using MAFFT online service: Multiple alignment program for amino acid or nucleotide sequences MAFFT version 7 (Katoh and Standley 2013: http://mafft.cbrc.jp/alignment/server/index.html), and edited manually in BioEdit v. 7.0 (Hall 1999). The sequence dataset was combined using SquenceMatrix v.1.7.8 (Vaidya et al. 2011). The alignment formats were change to PHYLIP and NEXUS formats by ALigment Transformation EnviRonment (ALTER) website (http://sing.ei.uvigo.es/ALTER/).

Maximum likelihood (ML) analysis was carried out using the RAxML-HPC2 on XSEDE (8.2.12) (Stamatakis 2006; Stamatakis et al. 2008) of CIPRES Science Gateway website (Miller et al. 2010: http://www.phylo.org/portal2) and the estimated proportion of invariant sites is (GTRGAMMA+I) model.

Bayesian analyses were performed in MrBayes 3.2.6 (Ronquist et al. 2012) and the best-fit model (LSU, ITS, SSU, TEF1-α, and RPB2 are all GTR+I+G) of sequences evolution was estimated via MrModeltest 2.2 (Guindon and Gascuel 2003; Nylander 2004; Darriba et al. 2012). The Markov Chain Monte Carlo (MCMC) sampling approach was used to calculate posterior probabilities (PP) (Rannala and Yang 1996). Bayesian analyses of six simultaneous Markov chains were run for 10000000 generations with trees sampled every 1000 generations.

Phylogenetic trees were visualized using FigTree v1.4.0 (Rambaut 2012: http://tree.bio.ed.ac.uk/software/figtree/), editing and typesetting using Adobe Illustrator (AI) (Adobe Systems Inc., the United States). The new sequences were submitted in GenBank and the strain information used in this paper is provided in Table ​Table1.1. The alignments and phylogenetic trees were deposited in TreeBASE (http://www.treebase.org/, accession number: 28758).

Strains used for phylogenetic analysis and their corresponding GenBank numbers. The type strain are in bold font.

*¹ Ex-type strain of Distoseptisporasubmersa.