Computational protocol: Expression of fatty-acid-modifying enzymes in the halotolerant black yeast Aureobasidium pullulans (de Bary) G. Arnaud under salt stress

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Protocol publication

[…] Homologues of the Δ9-desaturase and Δ12-desaturase and the elongase were identified by BLAST searches () against a GenBank non-redundant protein database. In addition to fungal homologues, sequences from other species were added. Protein sequences were aligned using ClustalX () and edited in BioEdit software (). Gene trees were generated with MrBayes software applying Bayesian inference (, ). Runs were performed for two million generations with mixed amino-acid models, default temperature and numbers of chains. The trees were sampled every 100 generations. Trees sampled before the analysis reached stationarity of likelihood values and those sampled before the average standard deviation of the split frequencies lowered under 0.5 % were excluded from the final analysis. The stationarity of likelihood values was checked using the Tracer software (). Enzymes from non-fungal organisms were used as outgroups: Vibrio fischeri (Δ9-desaturases) and Arabidopsis thaliana (Δ12-desaturases and elongases). Fig. 1. […]

Pipeline specifications

Software tools Clustal W, BioEdit, MrBayes
Application Phylogenetics
Organisms Saccharomyces cerevisiae
Chemicals Fatty Acids