PCR amplification was conducted using Phusion® High-Fidelity DNA

PCR amplification was conducted using Phusion® High-Fidelity DNA Polymerase (Thermo scientific/Finnzymes)

according to the manufacturer’s specifications using a 1:4 dilution of template DNA. PCR products were purified with GeneJET™ PCR Purification Kit (Fermentas). Amplicons were sequenced by Macrogen Inc. (South Korea) in the forward and reverse directions using the same primers as during amplification. Sequences for each sample were assembled into contigs using Geneious v5.4 (Drummond et al. 2011) and the consensus sequences used for further analyses. For samples that failed BGB324 manufacturer to amplify using the Phusion PCR method, amplification was conducted using PuReTaq Ready-To-Go PCR Beads (GE Healthcare, Piscataway NJ, USA) according to the manufacturer’s instructions with the primers LROR & LR7 (Vilgalys and Hester 1990) or ITS1F & ITS4, and 3 μL of template DNA in a total PCR reaction volume of 25 μL. These amplicons were then sequenced using an ABI 3100 automated sequencer (Applied Biosystems Inc., Foster Selleckchem PLX3397 City, CA, USA) with the

primers ITS1F & ITS4, and LROR, LR3, LR5, and LR7. Phylogenetic analyses A concatenated dataset was composed of both the ITS and LSU sequences that were generated, and previous accessions from NCBI GenBank. The GenBank sequences were selected following two criteria: both ITS and LSU sequences were from the same voucher material (with the exception of Mycocalicium sequoiae from which only the LSU sequence was available), and sequences were from species with unequivocal taxonomic status. Pyruvate dehydrogenase The dataset was aligned with MAFFT version 6 (Katoh and Toh 2008) and adjusted manually in PhyDE® 0.9971 (Müller et al. 2010). Unequivocal short (1–3 nucleotides) uninformative insertions were first removed from the alignment, and the program Gblocks 0.91 (Castresana 2000) was then used to remove ambiguously aligned regions. Phylogenetic relationships and confidence statistics were inferred using a partitioned Bayesian approach

in which models of evolution were generated independently with jModeltest 1.1 (Posada 2008) for each of the gene regions (LSU, ITS1, 5.8S, ITS2). The suggested evolutionary models (TIM2ef + G, HKY + G, TIM2ef + G, TIM3ef + G, respectively) were implied for the partitioned dataset. Bayesian analyses were carried out with MrBayes 3.1.2 (Ronquist and Huelsenbeck 2003) on the freely available computational resource Bioportal at the University of Oslo (http://​www.​bioportal.​uio.​no; Kumar et al. 2009). Two independent runs, each with four chains, were conducted simultaneously for 10 million generations with trees sampled every 100th generation. Average standard deviations of split frequency (ASDSF) values lower than 0.01 were taken as an indication that convergence had been achieved. Five percent of the sampled trees were discarded as burnin and the remaining trees were used to estimate branch lengths and posterior probabilities.

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