Computational protocol: The Epichloë festucae antifungal protein has activity against the plant pathogen Sclerotinia homoeocarpa, the causal agent of dollar spot disease

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Protocol publication

[…] The MCM7 (gene model EfM3.060700) and antifungal protein (gene model EfM3.063660) gene sequences were obtained from the Genome Project at the University of Kentucky website, (http://www.endophyte.uky.edu/). The Clustal-X program was used to align the sequences. The alignments generated by Clustal-X were modified manually to minimize gaps. The phylogenetic analysis was performed with the PAUP* program, version 4.0b10 for Macintosh. The MCM7 phylogenetic analysis was done by using the maximum parsimony full heuristic search option set to random sequence addition, tree-bisection-reconnection (TBR) branch swapping, and Multrees on, with 1000 bootstrap replications. Gaps were treated as missing data. The antifungal protein gene and protein phylogenetic trees were done by using an exhaustive maximum parsimony analysis, which returned a single most parsimonious tree in both cases. […]

Pipeline specifications

Software tools Clustal W, PAUP*
Application Phylogenetics