Computational protocol: A new species of Gymnoascus with verruculose ascospores

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Protocol publication

[…] DNA sequences obtained from the sequencer were manually edited for inconsistencies using ChromasLite v. 2.01 (http:/ The sequences of the ITS, LSU and SSU regions of the new isolate were submitted to BLASTn sequence homology searches. On the basis of the results, phylogenetically related species were chosen for the construction of the phylogenetic trees, including 18 Gymnoascus spp. and 11 species belonging to the genera Amauroascus, Arthroderma, Byssoonygena, Ctenomyces, Kraurogymnocarpa, Onygena, Pectinotrichum, and Uncinocarpus. Additionally, related sequences of authentic or ex-type strains of all genera compared were retrieved from GenBank, derived from , and . Alignment was performed using CLUSTAL W ( and tree construction with MEGA v.5 software (). The alignments have been submitted in TreeBASE ( Neighbourjoining (NJ) analysis () was conducted with aligned sequences using Kimura-2 parameter distance model (the ) and complete deletion of gaps option. The robustness of the branches was assessed by bootstrap analysis () of 1000 replicates. Besides NJ, Maximum Likelihood (ML) and Maximum Parsimony (MP) analyses was also conducted with aligned sequences. […]

Pipeline specifications

Software tools BLASTN, Clustal W, MEGA-V, PhyloWS
Databases TreeBASE
Applications Phylogenetics, GWAS