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Pipeline publication

[…] //www.ncbi.nlm.nih.gov/nuccore/) using the accession numbers provided in . The rDNA sequence for isolate FD01 (complete 18S, ITS1-5.8S-ITS2, and partial 28S [GenBank accession number JX967274]) was added to the sampling. For placement of isolate FD01 relative to environmental samples, 18S sequences were downloaded from NCBI using accession numbers provided in , . The 18S rDNA sequences for isolate FD01 and strain X-5 were added to the sampling., For the primary multi-gene analysis, rDNA sequences were trimmed to remove spacer regions (ITS) and flanking genes. The 18S and 28S sequences were aligned using SINA 1.2.11 with reference databases version 111, and 5.8S sequences were aligned using Muscle 3.8.31 with default parameters , . The alignments were manually refined using Jalview and then concatenated. The resulting alignment was subjected to Bayesian phylogenetic analysis. For this, we used MrBayes with four runs (nruns = 4), each with four Markov chains (nchains = 4) for 1 000 000 generations (ngen = 1000000) with a sampling frequency of 250 generations (samplefreg = 250), six substitution categories (nst = 6) and an eight-category gamma model with spatial autocorrelation between rates at adjacent sites (rates = adgamma) and a covarion-like model (covarion = yes). The Metropolis-coupled Markov chain Monte Carlo log likelihood results were compared and the first 25 000 generations were discarded as the burn in. The resulting samples of trees were then used to construct the majority-rule consensus tree. In addition, support for nodes was assessed with maximum likelihood bootstr […]

Pipeline specifications

Software tools MUSCLE, Jalview, MrBayes
Diseases Parasitic Diseases, Ectoparasitic Infestations