Computational protocol: Modification and functional adaptation of the MBF1 gene family in the lichenized fungus Endocarpon pusillum under environmental stress

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[…] Other five MBF1s from the genomes of the lichen-forming fungi, C. metacorallifera , C. macilenta , G. flavorubescens , U. muehlenbergii and L. pustulata (GenBank assembly accession: GCA_900169345.1), were annotated using a local BLASTP algorithm-based search tool. Based on the previous study, 48 MBF1 amino acid sequences were divided into three groups by using NJ tree. Among these sequences, 30 representative sequences were selected used in this study. Including the four Endocarpon MBF1 sequences from this study, a dataset of 39 MBF1 sequences were included. These sequences from representative species of other fungi, animals, plants and archaea, in addition to the above mentioned lichen species, were aligned using the MAFFT multiple alignment tool in BioEdit 7.2.5. The introns were excluded manually and the ambiguously aligned regions were removed by using Gblocks Server (http://molevol.cmima.csic.es/castresana/Gblocks_server.html). The alignment was used to perform NJ and Bayesian Markov chain Monte Carlo analyses with 1,000 pseudo replicates with Mega 5 and MrBayes 3.2.6,, respectively, on the CIPRES Science Gateway (http://www.phylo.org). The best model for constructing the Bayesian tree was determined using PhyML online (http://www.atgc-montpellier.fr/). Two parallel Markov chain Monte Carlo runs were performed each using 8,000,000 generations and sampling every 1,000 steps. A 50% majority rule consensus tree was generated from the sampled trees of both runs after discarding the first 25% as burn-in. The Bayesian results were visualised with FigTree 1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). […]

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